diff --git a/jasmine/spec/collapse_tool_test.js b/jasmine/spec/collapse_tool_test.js
index 6ab136e5..6f6d4cf8 100644
--- a/jasmine/spec/collapse_tool_test.js
+++ b/jasmine/spec/collapse_tool_test.js
@@ -1,4 +1,58 @@
 describe('collapse_tool_test', function () {
+  it('maxmeanprobe',
+    function () {
+      var heatmap = new morpheus.HeatMap({
+        dataset: new morpheus.Dataset({
+          array: [[1, 3], [4, 6], [7, 9], [10, 12]],
+          rows: 4,
+          columns: 2
+        })
+      });
+      heatmap.getProject().getFullDataset().getRowMetadata()
+        .add('id').array = ['a', 'b', 'a', 'a'];
+      var newHeatMap = new morpheus.CollapseDatasetTool().execute({
+        heatMap: heatmap,
+        project: heatmap.getProject(),
+        input: {
+          collapse_method: 'Maximum Mean Probe',
+          collapse: 'Rows',
+          collapse_to_fields: ['id']
+        }
+      });
+      expect(newHeatMap.getProject().getFullDataset())
+        .toBeDatasetValues(new morpheus.Dataset({
+          array: [[10, 12], [4, 6]],
+          rows: 2,
+          columns: 2
+        }), 0.00001);
+    });
+  it('maxmedianprobe',
+    function () {
+      var heatmap = new morpheus.HeatMap({
+        dataset: new morpheus.Dataset({
+          array: [[1, 3], [4, 6], [7, 9], [10, 12]],
+          rows: 4,
+          columns: 2
+        })
+      });
+      heatmap.getProject().getFullDataset().getRowMetadata()
+        .add('id').array = ['a', 'b', 'a', 'a'];
+      var newHeatMap = new morpheus.CollapseDatasetTool().execute({
+        heatMap: heatmap,
+        project: heatmap.getProject(),
+        input: {
+          collapse_method: 'Maximum Median Probe',
+          collapse: 'Rows',
+          collapse_to_fields: ['id']
+        }
+      });
+      expect(newHeatMap.getProject().getFullDataset())
+        .toBeDatasetValues(new morpheus.Dataset({
+          array: [[10, 12], [4, 6]],
+          rows: 2,
+          columns: 2
+        }), 0.00001);
+    });
   it('mean',
     function () {
       var heatmap = new morpheus.HeatMap({
diff --git a/js/morpheus-latest.min.js b/js/morpheus-latest.min.js
index f4ae3418..10501cd3 100644
--- a/js/morpheus-latest.min.js
+++ b/js/morpheus-latest.min.js
@@ -1 +1 @@
-(function(global){"use strict";var morpheus=typeof morpheus!=="undefined"?morpheus:{};if(typeof module!=="undefined"&&module.exports){module.exports=morpheus}else if(typeof define==="function"&&define.amd){define(function(){return morpheus})}else{global.morpheus=morpheus}morpheus.Util=function(){};morpheus.Util.RIGHT_ARROW=String.fromCharCode(8594);morpheus.Util.extend=function(c1,c2){for(var key in c2.prototype){if(!(key in c1.prototype)){c1.prototype[key]=c2.prototype[key]}}};morpheus.Util.isFetchStreamingSupported=function(){return typeof navigator!=="undefined"&&navigator.userAgent.indexOf("Chrome")!==-1};morpheus.Util.viewPortSize=function(){return window.getComputedStyle(document.body,":before").content.replace(/"/g,"")};morpheus.Util.TRACKING_ENABLED=true;morpheus.Util.TRACKING_CODE_LOADED=false;morpheus.Util.loadTrackingCode=function(){if(morpheus.Util.TRACKING_ENABLED&&typeof window!=="undefined"&&typeof navigator!=="undefined"&&navigator.onLine){if(morpheus.Util.TRACKING_CODE_LOADED){return}else if(typeof ga==="undefined"){morpheus.Util.TRACKING_CODE_LOADED=true;(function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date;a=s.createElement(o),m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)})(window,document,"script","https://www.google-analytics.com/analytics.js","ga")}if(typeof ga!=="undefined"){ga("create","UA-53973555-1","auto","morpheus");ga("morpheus.send","pageview")}morpheus.Util.TRACKING_CODE_LOADED=true}};morpheus.Util.measureScrollbar=function(){var $c=$("<div style='position:absolute; top:-10000px; left:-10000px; width:100px; height:100px; overflow:scroll;'></div>").appendTo("body");var dim={width:Math.max(0,$c.width()-$c[0].clientWidth),height:$c.height()-$c[0].clientHeight};$c.remove();return dim};morpheus.Util.trackEvent=function(options){if(typeof window!=="undefined"){if(!morpheus.Util.TRACKING_CODE_LOADED){morpheus.Util.loadTrackingCode()}if(morpheus.Util.TRACKING_CODE_LOADED&&typeof ga!=="undefined"){ga("morpheus.send",{hitType:"event",eventCategory:options.eventCategory,eventAction:options.eventAction,eventLabel:options.eventLabel})}}};morpheus.Util.isString=function(value){return typeof value==="string"||value instanceof String};morpheus.Util.getDataType=function(val){var dataType;var isArray=morpheus.Util.isArray(val);if(isArray&&val.length>0){val=val[0]}if(morpheus.Util.isString(val)){dataType="string"}else if(_.isNumber(val)){dataType="number"}else{dataType="object"}if(isArray){dataType="["+dataType+"]"}return dataType};morpheus.Util.isArray=function(array){var types=[Array,Int8Array,Uint8Array,Uint8ClampedArray,Int16Array,Uint16Array,Int32Array,Uint32Array,Float32Array,Float64Array];for(var i=0,length=types.length;i<length;i++){if(array instanceof types[i]){return true}}return false};morpheus.Util.getWindowSearchObject=function(){var searchObject={};var hashObject={};if(window.location.search.length>0){searchObject=morpheus.Util.getQueryParams(window.location.search.substring(1))}if(window.location.hash.length>0){hashObject=morpheus.Util.getQueryParams(window.location.hash.substring(1))}return _.extend(hashObject,searchObject)};morpheus.Util.copyString=function(s){return(" "+s).substr(1)};morpheus.Util.getQueryParams=function(s){var params={};if(!s){return params}var search=decodeURIComponent(s);var keyValuePairs=search.split("&");for(var i=0;i<keyValuePairs.length;i++){var pair=keyValuePairs[i].split("=");if(pair[1]!=null&&pair[1]!==""){var array=params[pair[0]];if(array===undefined){array=[];params[pair[0]]=array}array.push(pair[1])}}return params};morpheus.Util.getScriptPath=function(name){if(!name){name="morpheus-latest.min.js"}var scripts=document.getElementsByTagName("script");for(var i=scripts.length-1;i>=0;i--){var src=scripts[i].src;var index=src.lastIndexOf("/");if(index!==-1){src=src.substring(index+1)}if(src===name){return scripts[i].src}}if(name==="morpheus-latest.min.js"){return morpheus.Util.getScriptPath("morpheus.js")}return scripts.length>0?scripts[0].src:""};morpheus.Util.forceDelete=function(obj){try{var _garbageCollector=function(){var ef=URL.createObjectURL(new Blob([""],{type:"text/javascript"})),w=new Worker(ef);URL.revokeObjectURL(ef);return w}();_garbageCollector.postMessage(obj,[obj])}catch(x){console.log("Unable to delete")}};morpheus.Util.getFileName=function(fileOrUrl){if(morpheus.Util.isFile(fileOrUrl)){return fileOrUrl.name}if(fileOrUrl.name!==undefined){return fileOrUrl.name}var name=""+fileOrUrl;var question=name.indexOf("?");if(question!==-1){var params=name.substring(question+1);var keyValuePairs=decodeURIComponent(params).split("&");for(var i=0;i<keyValuePairs.length;i++){var pair=keyValuePairs[i].split("=");if(pair[0]==="file"||pair[0]==="name"){name=pair[1];break}}}else{var slash=name.lastIndexOf("/");if(slash===name.length-1){name=name.substring(0,name.length-1);slash=name.lastIndexOf("/")}if(slash!==-1){name=name.substring(slash+1)}}return name};morpheus.Util.prefixWithZero=function(value){return value<10?"0"+value:value};morpheus.Util.getExtension=function(name){name=""+name;var dotIndex=name.lastIndexOf(".");if(dotIndex>0){var suffix=name.substring(dotIndex+1).toLowerCase();if(suffix==="txt"||suffix==="gz"||suffix==="tsv"){var newPath=name.substring(0,dotIndex);var secondDotIndex=newPath.lastIndexOf(".");if(secondDotIndex>0){var secondSuffix=newPath.substring(secondDotIndex+1,newPath.length).toLowerCase();if(secondSuffix==="segtab"||secondSuffix==="seg"||secondSuffix==="maf"||secondSuffix==="gct"||secondSuffix==="txt"||secondSuffix==="gmt"){return secondSuffix}}}return suffix}return""};morpheus.Util.getBaseFileName=function(name){var dotIndex=name.lastIndexOf(".");if(dotIndex>0){var suffix=name.substring(dotIndex+1,name.length);if(suffix==="gz"||suffix==="zip"||suffix==="bz2"){return morpheus.Util.getBaseFileName(name.substring(0,dotIndex))}return name.substring(0,dotIndex)}return name};morpheus.Util.seq=function(length){var array=[];for(var i=0;i<length;i++){array.push(i)}return array};morpheus.Util.sequ32=function(length){var array=new Uint32Array(length);for(var i=0;i<length;i++){array[i]=i}return array};morpheus.Util.paramsToObject=function(hash){var search=hash?window.location.hash:window.location.search;if(search.length<=1){return{}}search=decodeURIComponent(search);var keyValuePairs=search.substring(1).split("&");var result={};for(var i=0,length=keyValuePairs.length;i<length;i++){var pair=keyValuePairs[i].split("=");var values=result[pair[0]];if(values===undefined){values=[];result[pair[0]]=values}values.push(pair[1])}return result};morpheus.Util.isHeadless=function(){return typeof $.ui==="undefined"};morpheus.Util.isFile=function(f){return typeof File!=="undefined"&&f instanceof File};morpheus.Util.endsWith=function(string,suffix){return string.length>=suffix.length&&string.substr(string.length-suffix.length)===suffix};morpheus.Util.measureSvgText=function(text,classname){if(!text||text.length===0){return{height:0,width:0}}var container=d3.select("body").append("svg");if(classname){container.attr("class",classname)}container.append("text").attr({x:-1e3,y:-1e3}).text(text);var bbox=container.node().getBBox();container.remove();return{height:bbox.height,width:bbox.width}};morpheus.Util.IS_MAC=false;if(typeof navigator!=="undefined"){morpheus.Util.IS_MAC=navigator.platform.match(/(Mac|iPhone|iPod|iPad)/i)?true:false}morpheus.Util.COMMAND_KEY=morpheus.Util.IS_MAC?"&#8984;":"Ctrl+";morpheus.Util.hammer=function(el,recognizers){if(typeof Hammer!=="undefined"){var hammer=new Hammer(el,{recognizers:[]});if(_.indexOf(recognizers,"pan")!==-1){hammer.add(new Hammer.Pan({threshold:1,direction:Hammer.DIRECTION_ALL}))}else if(_.indexOf(recognizers,"panh")!==-1){hammer.add(new Hammer.Pan({threshold:1,direction:Hammer.DIRECTION_HORIZONTAL}))}else if(_.indexOf(recognizers,"panv")!==-1){hammer.add(new Hammer.Pan({threshold:1,direction:Hammer.DIRECTION_VERTICAL}))}if(_.indexOf(recognizers,"tap")!==-1){hammer.add(new Hammer.Tap)}if(_.indexOf(recognizers,"pinch")!==-1){hammer.add(new Hammer.Pinch)}if(_.indexOf(recognizers,"longpress")!==-1){hammer.add(new Hammer.Press({event:"longpress",time:1e3}))}if(_.indexOf(recognizers,"press")!==-1){hammer.add(new Hammer.Press)}if(_.indexOf(recognizers,"swipe")!==-1){hammer.add(new Hammer.Swipe)}return hammer}else{return $()}};morpheus.Util.createTextDecoder=function(){if(typeof TextDecoder!=="undefined"){var textDecoder=new TextDecoder;return function(buf,start,end){return textDecoder.decode(buf.subarray(start,end))}}else{return function(buf,start,end){var s=[];for(var i=start;i<end;i++){s.push(String.fromCharCode(buf[i]))}return s.join("")}}};morpheus.Util.autocompleteArrayMatcher=function(token,cb,array,fields,max){var filteredSet=new morpheus.Set;var regex=new RegExp(morpheus.Util.escapeRegex(token),"i");var regexMatch=new RegExp("("+morpheus.Util.escapeRegex(token)+")","i");if(fields){var nfields=fields.length;for(var i=0,n=array.length;i<n;i++){var item=array[i];for(var j=0;j<nfields;j++){var field=fields[j];var value=item[field];if(regex.test(value)){filteredSet.add(value);break}}if(filteredSet.size()===max){break}}}else{for(var i=0,n=array.length;i<n;i++){var value=array[i];if(regex.test(value)){filteredSet.add(value);if(filteredSet.size()===max){break}}}}var matches=[];filteredSet.forEach(function(value){var quotedValue=value;if(quotedValue.indexOf(" ")!==-1){quotedValue='"'+quotedValue+'"'}matches.push({value:quotedValue,label:"<span>"+value.replace(regexMatch,"<b>$1</b>")+"</span>"})});cb(matches)};morpheus.Util.setClipboardData=function(clipboardData,delay){var isRTL=document.documentElement.getAttribute("dir")=="rtl";var fakeElem=document.createElement("div");fakeElem.contentEditable=true;fakeElem.style.fontSize="12pt";fakeElem.style.border="0";fakeElem.style.padding="0";fakeElem.style.margin="0";fakeElem.style.position="absolute";fakeElem.style[isRTL?"right":"left"]="-999999px";fakeElem.style.top=(window.pageYOffset||document.documentElement.scrollTop)+"px";fakeElem.setAttribute("readonly","");var f=function(e){clipboardData.forEach(function(elem){e.clipboardData.setData(elem.format,elem.data)});e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();fakeElem.removeEventListener("copy",f)};fakeElem.addEventListener("copy",f);document.body.appendChild(fakeElem);fakeElem.focus();var selection=window.getSelection();var range=document.createRange();range.selectNodeContents(fakeElem);selection.removeAllRanges();selection.addRange(range);if(delay){setTimeout(function(){if(!document.execCommand("copy")){console.log("copy failed")}document.body.removeChild(fakeElem)},20)}else{if(!document.execCommand("copy")){console.log("copy failed")}document.body.removeChild(fakeElem)}};morpheus.Util.autosuggest=function(options){options=$.extend({},{multi:true,delay:500,minLength:0,suggestWhenEmpty:true},options);var searching=false;function _select(event,ui,isKey){if(ui.item.skip){return false}if(options.multi){var terms=morpheus.Util.getAutocompleteTokens(options.$el[0].value,{trim:false,selectionStart:options.$el[0].selectionStart});var field=event.toElement&&event.toElement.dataset?event.toElement.dataset.autocomplete:null;var value=field?ui.item[field]:ui.item.value;var show=ui.item.show;if(terms.length===0){terms.push(value)}else if(ui.item.clear){terms=[value]}else{terms[terms.selectionStartIndex===-1||terms.selectionStartIndex===undefined?terms.length-1:terms.selectionStartIndex]=value}options.$el[0].value=terms.join(" ");if(show&&!isKey||isKey&&event.which===13){searching=true;setTimeout(function(){options.$el.autocomplete("search",options.$el.val())},20);setTimeout(function(){searching=false},100)}if(!isKey&&options.select){options.select()}return false}if(!isKey&&options.select){options.select()}if(!isKey&&event.which===13){event.stopImmediatePropagation()}}options.$el.on("keydown",function(event){if(event.keyCode===$.ui.keyCode.TAB&&$(this).data("ui-autocomplete").menu.active){event.preventDefault()}}).autocomplete({minLength:options.minLength,delay:options.delay,source:function(request,response){if(request.term.history&&options.history){return options.history(response)}var terms=morpheus.Util.getAutocompleteTokens(request.term,{trim:false,selectionStart:options.$el[0].selectionStart});if(terms.selectionStartIndex===undefined||terms.selectionStartIndex===-1){terms.selectionStartIndex=terms.length-1}if(options.suggestWhenEmpty||terms.length>0){options.filter(terms,response)}},focus:function(event,ui){var original=event.originalEvent;while(original.originalEvent!=null){original=original.originalEvent}if(original&&/^key/.test(original.type)){return _select(original,ui,true)}return false},select:function(event,ui){return _select(event,ui,false)}});var instance=options.$el.autocomplete("instance");if(instance!=null){instance._renderItem=function(ul,item){if(item.value==null){return $('<li class="'+(item.class?" "+item.class:"")+' search-category">').append($("<div>").html(item.label)).appendTo(ul)}return $('<li class="'+(item.class?" "+item.class:"")+' search-item">').append($("<div>").html(item.label)).appendTo(ul)};instance._normalize=function(items){return items};instance._resizeMenu=function(){var ul=this.menu.element;ul.outerWidth(instance.element.outerWidth())}}var menu=options.$el.autocomplete("widget");menu.menu("option","items","> :not(.search-category)");if(menu){menu.addClass("search-menu")}if(options.suggestWhenEmpty){options.$el.on("focus",function(){options.$el.autocomplete("search",options.$el.val())})}options.$el.on("keyup",function(e){if(e.which===13&&!searching){options.$el.autocomplete("close")}else if(e.which===38&&options.history){options.$el.autocomplete("search",{history:true})}else if(options.suggestWhenEmpty&&options.$el.val()===""){options.$el.autocomplete("search","")}})};morpheus.Util.getAutocompleteTokens=function(text,options){options=$.extend({},{trim:true},options);if(options.trim){text=$.trim(text)}if(text===""){return[]}var inQuote=false;var inParen=false;var tokens=[];var currentToken=[];for(var i=0,n=text.length;i<n;i++){var c=text[i];if(c==='"'){inQuote=!inQuote;currentToken.push(c)}else if(c==="("||c===")"){inParen=c==="(";currentToken.push(c)}else{if((c===" "||c==="\t")&&!inQuote&&!inParen){tokens.push({s:currentToken.join(""),inSelectionStart:currentToken.inSelectionStart});currentToken=[]}else{currentToken.push(c)}}if(i===options.selectionStart-1){currentToken.inSelectionStart=true}}tokens.push({s:currentToken.join(""),inSelectionStart:currentToken.inSelectionStart});if(!options.trim&&!inQuote&&text[text.length-1]===" "){tokens.push({s:" ",inSelectionStart:false})}var filteredTokens=[];var selectionStartIndex=-1;for(var i=0,ntokens=tokens.length;i<ntokens;i++){var token=tokens[i];var s=token.s;if(options.trim||i<ntokens-1){s=$.trim(s)}if(s!==""){if(token.inSelectionStart){selectionStartIndex=filteredTokens.length}filteredTokens.push(s)}}filteredTokens.selectionStartIndex=selectionStartIndex;return filteredTokens};morpheus.Util.showDialog=function($el,title,options){var $dialog=$("<div></div>");$el.appendTo($dialog);$dialog.appendTo($(document.body));if(!options){options={}}$dialog.dialog({width:670,height:590,title:title,close:function(event,ui){$dialog.remove();if(options.close){options.close()}}})};morpheus.Util.sheetToArray=function(sheet,delim){var r=XLSX.utils.decode_range(sheet["!ref"]);var rows=[];var colors=[];var header=[];for(var C=r.s.c;C<=r.e.c;++C){var val=sheet[XLSX.utils.encode_cell({c:C,r:r.s.r})];var txt=String(XLSX.utils.format_cell(val));header.push(txt)}for(var R=r.s.r;R<=r.e.r;++R){var row=[];var isRowEmpty=true;for(var C=r.s.c;C<=r.e.c;++C){var val=sheet[XLSX.utils.encode_cell({c:C,r:R})];if(!val){row.push("");continue}isRowEmpty=false;var txt=String(XLSX.utils.format_cell(val));if(val.s!=null&&val.s.fgColor!=null){var color="#"+val.s.fgColor.rgb;colors.push({header:header[row.length],color:color,value:txt})}row.push(txt)}if(!isRowEmpty){rows.push(delim?row.join(delim):row)}}rows.colors=colors;return rows};morpheus.Util.linesToObjects=function(lines){var header=lines[0];var array=[];var nfields=header.length;for(var i=1,length=lines.length;i<length;i++){var line=lines[i];var obj={};for(var f=0;f<nfields;f++){var value=line[f];var field=header[f];obj[field]=value}array.push(obj)}return array};morpheus.Util.xlsxTo2dArray=function(options,callback){var workbook=XLSX.read(options.data,{type:"binary",cellFormula:false,cellHTML:false,cellStyles:true});var sheetNames=workbook.SheetNames;if(options.prompt&&sheetNames.length>1){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"sheet",type:"bootstrap-select",options:sheetNames,required:true,style:"max-width:100px;"});morpheus.FormBuilder.showInModal({title:"Choose Sheet",html:formBuilder.$form,focus:document.activeElement,onClose:function(){var worksheet=workbook.Sheets[formBuilder.getValue("sheet")];var lines=morpheus.Util.sheetToArray(worksheet);callback(null,lines)}})}else{var worksheet=workbook.Sheets[sheetNames[0]];var lines=morpheus.Util.sheetToArray(worksheet);callback(null,lines)}};morpheus.Util.xlsxTo1dArray=function(options,callback){var workbook=XLSX.read(options.data,{type:"binary",cellFormula:false,cellHTML:false,cellStyles:true});var sheetNames=workbook.SheetNames;if(options.prompt&&sheetNames.length>1){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"sheet",type:"bootstrap-select",options:sheetNames,required:true,style:"max-width:100px;"});morpheus.FormBuilder.showOkCancel({title:"Choose Sheet",cancel:false,focus:document.activeElement,content:formBuilder.$form,okCallback:function(){var worksheet=workbook.Sheets[formBuilder.getValue("sheet")];callback(null,morpheus.Util.sheetToArray(worksheet,"\t"))}})}else{var worksheet=workbook.Sheets[sheetNames[0]];callback(null,morpheus.Util.sheetToArray(worksheet,"\t"))}};morpheus.Util.getText=function(fileOrUrl){var deferred=$.Deferred();if(morpheus.Util.isString(fileOrUrl)){fetch(fileOrUrl).then(function(response){if(response.ok){return response.text()}else{deferred.reject(response.status+" "+response.statusText)}}).then(function(text){deferred.resolve(text)}).catch(function(err){deferred.reject(err)})}else if(morpheus.Util.isFile(fileOrUrl)){var reader=new FileReader;reader.onload=function(event){deferred.resolve(event.target.result)};reader.readAsText(fileOrUrl)}else{deferred.resolve(fileOrUrl)}return deferred.promise()};morpheus.Util.createOptions=function(values,none){var html=[];if(none){html.push('<option value="">(None)</option>')}_.each(values,function(val){html.push('<option value="');html.push(val);html.push('">');html.push(val);html.push("</option>")});return html.join("")};morpheus.Util.rankIndexArray=function(index){var rank=[];var n=index.length;for(var j=0;j<n;j++){rank[index[j]]=j+1}return rank};morpheus.Util.indexSort=function(array,ascending){var pairs=[];for(var i=0,length=array.length;i<length;i++){pairs.push({value:array[i],index:i})}return morpheus.Util.indexSortPairs(pairs,ascending)};morpheus.Util.indexSortPairs=function(array,ascending){if(ascending){array.sort(function(a,b){return a.value<b.value?-1:a.value===b.value?a.index<b.index?-1:1:1})}else{array.sort(function(a,b){return a.value<b.value?1:a.value===b.value?a.index<b.index?1:-1:-1})}var indices=[];array.forEach(function(item){indices.push(item.index)});return indices};morpheus.Util.arrayEquals=function(array1,array2,comparator){if(array1==array2){return true}if(array1==null||array2==null){return false}if(!comparator){comparator=function(a,b){return a===b}}var length=array1.length;if(array2.length!==length){return false}for(var i=0;i<length;i++){if(!comparator(array1[i],array2[i])){return false}}return true};morpheus.Util._intFormat=typeof d3!=="undefined"?d3.format(",i"):function(d){return""+Math.round(d)};morpheus.Util.intFormat=function(n){return morpheus.Util._intFormat(n)};morpheus.Util._nf=typeof d3!=="undefined"?d3.format(".2f"):function(d){return""+d};morpheus.Util.getNumberFormatPatternFractionDigits=function(pattern){return parseInt(pattern.substring(1,pattern.length-1))||0};morpheus.Util.nf=function(n){return morpheus.Util._nf(n)};morpheus.Util.createNumberFormat=function(pattern){var f=d3.format(pattern);f.toJSON=function(){return{pattern:pattern}};return f};morpheus.Util.wrapNumber=function(value,object){var n=new Number(value);n.toObject=function(){return object};return n};morpheus.Util.toString=function(value){if(value==null){return""}else if(_.isNumber(value)){return morpheus.Util.nf(value)}else if(morpheus.Util.isArray(value)){return morpheus.Util.arrayToString(value,", ")}return""+value};morpheus.Util.arrayToString=function(value,sep){var s=[];for(var i=0,length=value.length;i<length;i++){var val_i=value[i];if(_.isNumber(val_i)){s.push(morpheus.Util.nf(val_i))}else{s.push(""+val_i)}}return s.join(sep)};morpheus.Util.removeTrailingZerosInFraction=function(str){var index=str.lastIndexOf(".");if(index!==-1){var len=str.length;var zeros=len;for(var i=len-1;i>index;i--,zeros--){if(str[i]!="0"){break}}if(zeros===index+1){return str.substring(0,index)}if(zeros<len){return str.substring(0,index)+str.substring(index,zeros)}}return str};morpheus.Util.s=function(n){return n===1?"":"s"};morpheus.Util.create2dArray=function(rows,columns){var array2d=[];for(var i=0;i<rows;i++){var array=[];for(var j=0;j<columns;j++){array[j]=NaN}array2d.push(array)}return array2d};morpheus.Util.escapeRegex=function(value){return value.replace(/[*]/g,".*").replace(/[-[\]{}()+?,\\^$|#\s]/g,"\\$&")};morpheus.Util.createSearchPredicates=function(options){options=$.extend({},{validateFieldNames:true,caseSensitive:true},options);var tokens=options.tokens;if(tokens==null){return[]}var availableFields=options.fields;if(!options.caseSensitive&&availableFields!=null){for(var i=0;i<availableFields.length;i++){availableFields[i]=availableFields[i].toLowerCase()}}var validateFieldNames=options.validateFieldNames;var fieldSearchEnabled=!validateFieldNames||availableFields!=null&&availableFields.length>0;var fieldRegExp=/\\:/g;var predicates=[];var defaultIsExactMatch=options.defaultMatchMode==="exact";tokens.forEach(function(token){var isNot=false;if(token[0]==="-"){token=token.substring(1);isNot=true}var field=null;var semi=token.indexOf(":");if(semi>0){if(!fieldSearchEnabled||token.charCodeAt(semi-1)===92){token=token.replace(fieldRegExp,":")}else{var possibleToken=$.trim(token.substring(semi+1));var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[possibleField.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}else if(possibleField.length>0&&possibleField[0]==='"'&&possibleToken[possibleToken.length-1]==='"'&&possibleToken[0]!=='"'){possibleField=possibleField.substring(1,possibleField.length);possibleToken='"'+possibleToken}if(!validateFieldNames||availableFields.indexOf(options.caseSensitive?possibleField:possibleField.toLowerCase())!==-1){token=possibleToken;field=possibleField}}}var predicate;var rangeIndex=-1;var rangeToken=null;var rangeIndicators=["..",">=",">","<=","<","="];for(var i=0;i<rangeIndicators.length;i++){rangeIndex=token.indexOf(rangeIndicators[i]);if(rangeIndex!==-1){rangeToken=rangeIndicators[i];break}}if(rangeIndex!==-1){if(rangeToken===".."){var start=parseFloat(token.substring(0,rangeIndex));var end=parseFloat(token.substring(rangeIndex+2));if(!isNaN(start)&&!isNaN(end)){predicate=new morpheus.Util.NumberRangePredicate(field,start,end)}}else if(rangeToken===">"){var val=parseFloat(token.substring(rangeIndex+1));if(!isNaN(val)){predicate=new morpheus.Util.GreaterThanPredicate(field,val)}}else if(rangeToken===">="){var val=parseFloat(token.substring(rangeIndex+2));if(!isNaN(val)){predicate=new morpheus.Util.GreaterThanOrEqualPredicate(field,val)}}else if(rangeToken==="<"){var val=parseFloat(token.substring(rangeIndex+1));if(!isNaN(val)){predicate=new morpheus.Util.LessThanPredicate(field,val)}}else if(rangeToken==="<="){var val=parseFloat(token.substring(rangeIndex+2));if(!isNaN(val)){predicate=new morpheus.Util.LessThanOrEqualPredicate(field,val)}}else if(rangeToken==="="){var val=parseFloat(token.substring(rangeIndex+1));predicate=new morpheus.Util.EqualsPredicate(field,val)}else{console.log("Unknown range token:"+rangeToken)}}else if(token[0]==='"'&&token[token.length-1]==='"'){token=token.substring(1,token.length-1);predicate=new morpheus.Util.ExactTermPredicate(field,token)}else if(token[0]==="("&&token[token.length-1]===")"){token=token.substring(1,token.length-1);var values=morpheus.Util.getAutocompleteTokens(token);if(values.length>0){predicate=new morpheus.Util.ExactTermsPredicate(field,values.map(function(val){if(val[0]==='"'&&val[val.length-1]==='"'){val=val.substring(1,val.length-1)}return val.toLowerCase()}))}}else if(token.indexOf("*")!==-1){predicate=new morpheus.Util.RegexPredicate(field,token)}else{predicate=defaultIsExactMatch?new morpheus.Util.ExactTermPredicate(field,token):new morpheus.Util.RegexPredicate(field,token)}if(predicate!=null){predicates.push(isNot?new morpheus.Util.NotPredicate(predicate):predicate)}});return predicates};morpheus.Util.createRegExpStringToMatchText=function(text){var tokens=morpheus.Util.getAutocompleteTokens(text);if(tokens.length===0){return null}var regex=[];_.each(tokens,function(token){if(token[0]==='"'&&token[token.length-1]==='"'){token=token.substring(1,token.length-1);regex.push("^"+morpheus.Util.escapeRegex(token)+"$")}else{regex.push(morpheus.Util.escapeRegex(token))}});return"("+regex.join("|")+")"};morpheus.Util.createRegExpToMatchText=function(text){var s=morpheus.Util.createRegExpStringToMatchText(text);return s==null?null:new RegExp(s,"i")};morpheus.Util.reorderArray=function(array,index){var newArray=[];for(var i=0;i<index.length;i++){newArray.push(array[index[i]])}return newArray};morpheus.Util.getSearchString=function(){var s=window.location.search;return s.length>1?s.substring(1):""};morpheus.Util.splitLines=function(lines){var tab=/\t/;var tokens=[];for(var i=0,nlines=lines.length;i<nlines;i++){var line=lines[i];if(line===""){continue}tokens.push(line.split(tab))}return tokens};morpheus.Util.readLines=function(fileOrUrl,interactive){var isFile=morpheus.Util.isFile(fileOrUrl);var isString=morpheus.Util.isString(fileOrUrl);var name=morpheus.Util.getFileName(fileOrUrl);var ext=morpheus.Util.getExtension(name);var deferred=$.Deferred();if(isString){if(ext==="xlsx"){var fetchOptions={};if(fileOrUrl.headers){fetchOptions.headers=new Headers;for(var header in fileOrUrl.headers){fetchOptions.headers.append(header,fileOrUrl.headers[header])}}fetch(fileOrUrl,fetchOptions).then(function(response){if(response.ok){return response.arrayBuffer()}else{deferred.reject(response)}}).then(function(arrayBuffer){if(arrayBuffer){var data=new Uint8Array(arrayBuffer);var arr=[];for(var i=0;i!=data.length;++i){arr[i]=String.fromCharCode(data[i])}var bstr=arr.join("");morpheus.Util.xlsxTo1dArray({data:bstr,prompt:interactive},function(err,lines){deferred.resolve(lines)})}else{deferred.reject()}})}else{fetch(fileOrUrl,fetchOptions).then(function(response){if(response.ok){return response.text()}else{deferred.reject()}}).then(function(text){deferred.resolve(morpheus.Util.splitOnNewLine(text))}).catch(function(err){deferred.reject(err)})}}else if(isFile){var reader=new FileReader;reader.onerror=function(){console.log("Unable to read file");deferred.reject("Unable to read file")};reader.onload=function(event){if(ext==="xlsx"||ext==="xls"){var data=new Uint8Array(event.target.result);var arr=[];for(var i=0;i!=data.length;++i){arr[i]=String.fromCharCode(data[i])}var bstr=arr.join("");morpheus.Util.xlsxTo1dArray({data:bstr,prompt:interactive},function(err,lines){deferred.resolve(lines)})}else{deferred.resolve(morpheus.Util.splitOnNewLine(event.target.result))}};if(ext==="xlsx"||ext==="xls"){reader.readAsArrayBuffer(fileOrUrl)}else{reader.readAsText(fileOrUrl)}}else{deferred.resolve(fileOrUrl)}return deferred};morpheus.Util.createValueToIndices=function(array,field){var map=new morpheus.Map;_.each(array,function(item){var key=item[field];var values=map.get(key);if(values===undefined){values=[];map.set(key,values)}values.push(item)});return map};morpheus.Util.createMorpheusHeader=function(){var html=[];html.push('<div style="display:inline-block;'+' vertical-align:top;font-size:24px;font-family:sans-serif;">');html.push("<span>M</span>");html.push("<span>O</span>");html.push("<span>R</span>");html.push("<span>P</span>");html.push("<span>H</span>");html.push("<span>E</span>");html.push("<span>U</span>");html.push("<span>S</span>");html.push("</span>");html.push("</div>");var $div=$(html.join(""));var colorScale=d3.scale.linear().domain([0,4,7]).range(["#ca0020","#999999","#0571b0"]).clamp(true);var brands=$div.find("span");var index=0;var step=function(){brands[index].style.color=colorScale(index);index++;if(index<brands.length){setTimeout(step,200)}};setTimeout(step,500);return $div};morpheus.Util.createLoadingEl=function(){return $('<div style="overflow:hidden;text-align:center;"><i class="fa fa-spinner fa-spin fa-3x"></i><span style="padding-left:4px;vertical-align:middle;font-weight:bold;">Loading...</span></div>')};morpheus.Util.splitOnNewLine=function(text,commentChar){var commentCharCode=commentChar!==undefined?commentChar.charCodeAt(0):undefined;var lines=text.split(/\n/);if(lines.length===1){var tmp=text.split(/\r/);if(tmp.length>1){lines=tmp}}var rows=[];var rtrim=/\s+$/;for(var i=0,nlines=lines.length;i<nlines;i++){var line=lines[i].replace(rtrim,"");if(line!==""){if(commentCharCode!==undefined){if(line.charCodeAt(0)!==commentCharCode){rows.push(line)}}else{rows.push(line)}}}return rows};morpheus.Util.ContainsPredicate=function(field,text){this.field=field;text=text.toLowerCase();this.text=text};morpheus.Util.ContainsPredicate.prototype={accept:function(value){if(value==null){return false}value=(""+value).toLowerCase();return value.indexOf(this.text)!==-1},getField:function(){return this.field},getText:function(){return this.text},isNumber:function(){return false},toString:function(){return"ContainsPredicate "+this.field+":"+this.text}};morpheus.Util.ExactTermsPredicate=function(field,values){this.field=field;this.values=new morpheus.Set;for(var i=0,nvalues=values.length;i<nvalues;i++){this.values.add(values[i])}};morpheus.Util.ExactTermsPredicate.prototype={accept:function(value){if(value==null){return false}value=(""+value).toLowerCase();return this.values.has(value)},getField:function(){return this.field},getValues:function(){return this.values},isNumber:function(){return false},toString:function(){return"ExactTermsPredicate "+this.field+":"+this.text}};morpheus.Util.ExactTermPredicate=function(field,term){this.field=field;term=term.toLowerCase();this.text=term};morpheus.Util.ExactTermPredicate.prototype={accept:function(value){if(value==null){return false}value=(""+value).toLowerCase();return value===this.text},getField:function(){return this.field},getText:function(){return this.text},isNumber:function(){return false},toString:function(){return"ExactTermPredicate "+this.field+":"+this.text}};morpheus.Util.RegexPredicate=function(field,text){this.field=field;this.text=text;this.regex=new RegExp(morpheus.Util.escapeRegex(text),"i")};morpheus.Util.RegexPredicate.prototype={accept:function(value){return this.regex.test(""+value)},getField:function(){return this.field},getText:function(){return this.text},isNumber:function(){return false},toString:function(){return"RegexPredicate "+this.field+":"+this.regex}};morpheus.Util.NumberRangePredicate=function(field,min,max){this.field=field;this.min=min;this.max=max};morpheus.Util.NumberRangePredicate.prototype={accept:function(value){return value>=this.min&&value<=this.max},getField:function(){return this.field},isNumber:function(){return true},toString:function(){return"NumberRangePredicate "+this.field+":"+this.min+"..."+this.max}};morpheus.Util.GreaterThanPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.GreaterThanPredicate.prototype={accept:function(value){return value>this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.GreaterThanOrEqualPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.GreaterThanOrEqualPredicate.prototype={accept:function(value){return value>=this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.LessThanPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.LessThanPredicate.prototype={accept:function(value){return value<this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.LessThanOrEqualPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.LessThanOrEqualPredicate.prototype={accept:function(value){return value<=this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.EqualsPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.EqualsPredicate.prototype={accept:function(value){return value===this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.NotPredicate=function(p){this.p=p};morpheus.Util.NotPredicate.prototype={accept:function(value){return!this.p.accept(value)},getField:function(){return this.p.getField()},isNumber:function(){return this.p.isNumber()},toString:function(){return"NotPredicate "+this.p}};morpheus.Events=function(){};morpheus.Events.prototype={on:function(evtStr,handler){if(!handler){throw Error("Handler not specified")}if(!this.eventListeners){this.eventListeners={}}var events=evtStr.split(" "),len=events.length,n,event,parts,baseEvent,name;for(n=0;n<len;n++){event=events[n];parts=event.split(".");baseEvent=parts[0];name=parts[1]||"";if(!this.eventListeners[baseEvent]){this.eventListeners[baseEvent]=[]}this.eventListeners[baseEvent].push({name:name,handler:handler})}return this},getListeners:function(){if(!this.eventListeners){this.eventListeners={}}return this.eventListeners},setListeners:function(eventListeners){this.eventListeners=eventListeners},trigger:function(eventType,evt){if(!this.eventListeners){this.eventListeners={}}if(!evt){evt={}}evt.type=eventType;if(!evt.source){evt.source=this}var events=this.eventListeners[eventType];if(events){var len=events.length;for(var i=0;i<len;i++){events[i].handler.apply(this,[evt])}}return this},off:function(evtStr,handler){if(!this.eventListeners){this.eventListeners={}}var events=(evtStr||"").split(" "),len=events.length,n,t,event,parts,baseEvent,name;if(!evtStr){for(t in this.eventListeners){this._off(t,null,handler)}}for(n=0;n<len;n++){event=events[n];parts=event.split(".");baseEvent=parts[0];name=parts[1];if(baseEvent){if(this.eventListeners[baseEvent]){this._off(baseEvent,name,handler)}}else{for(t in this.eventListeners){this._off(t,name,handler)}}}return this},_off:function(type,name,handler){var evtListeners=this.eventListeners[type],i,evtName;for(i=0;i<evtListeners.length;i++){evtName=evtListeners[i].name;if((!name||evtName===name)&&(handler==null||handler==evtListeners[i].handler)){evtListeners.splice(i,1);if(evtListeners.length===0){delete this.eventListeners[type];break}i--}}}};morpheus.Identifier=function(array){this.array=array};morpheus.Identifier.prototype={toString:function(){return this.array.join(",")},equals:function(otherId){var other=otherId.getArray();var length=this.array.length;if(other.length!==length){return false}for(var i=0;i<length;i++){if(this.array[i]!==other[i]){return false}}return true},getArray:function(){return this.array}};morpheus.Map=function(){this.map={};this.n=0};morpheus.Map.prototype={toJSON:function(){var json={};this.forEach(function(value,key){json[key]=value});return json},toString:function(){var s=[];this.forEach(function(value,key){if(s.length>0){s.push(", ")}s.push(key);s.push("=");s.push(value)});return s.join("")},keys:function(){var keys=[];for(var key in this.map){var pair=this.map[key];keys.push(pair.key)}return keys},size:function(){return this.n},equals:function(m){if(m.size()!==this.size()){return false}var ret=true;try{this.forEach(function(value,key){if(value!==m.get(key)){ret=false;throw"break"}})}catch(e){}return ret},setAll:function(map){var _this=this;map.forEach(function(value,key){_this.set(key,value)})},set:function(key,value){var skey="\0"+key;var previous=this.map[skey];if(previous===undefined){this.n++}this.map[skey]={key:key,value:value}},forEach:function(callback){for(var key in this.map){var pair=this.map[key];callback(pair.value,pair.key)}},entries:function(){var array=[];this.forEach(function(value,key){array.push({value:value,key:key})});return array},values:function(){var values=[];for(var key in this.map){var pair=this.map[key];values.push(pair.value)}return values},get:function(key){var skey="\0"+key;var pair=this.map[skey];return pair!==undefined?pair.value:undefined},clear:function(){this.map={};this.n=0},remove:function(key){var skey="\0"+key;var pair=this.map[skey];if(pair!==undefined){delete this.map[skey];this.n--;return pair.value}},has:function(key){var skey="\0"+key;return this.map[skey]!==undefined}};morpheus.Map.fromJSON=function(json){var map=new morpheus.Map;for(var key in json){map.set(key,json[key])}return map};morpheus.Set=function(){this._map=new morpheus.Map};morpheus.Set.prototype={toJSON:function(){var json=[];this.forEach(function(value){json.push(value)});return json},toString:function(){var s=[];this.forEach(function(key){if(s.length>0){s.push(", ")}s.push(key)});return s.join("")},size:function(){return this._map.size()},equals:function(m){return this._map.equals(m)},forEach:function(callback){this._map.forEach(function(value,key){callback(key)})},add:function(value){this._map.set(value,true)},values:function(){var values=[];this._map.forEach(function(value,key){values.push(key)});return values},clear:function(){this._map.clear()},remove:function(key){this._map.remove(key)},has:function(key){return this._map.has(key)}};morpheus.Set.fromJSON=function(json){var set=new morpheus.Set;for(var i=0,length=json.length;i<length;i++){set.add(json[i])}return set};morpheus.ArrayBufferReader=function(buffer){this.buffer=buffer;this.bufferLength=buffer.length;this.index=0;this.decoder=morpheus.Util.createTextDecoder()};morpheus.ArrayBufferReader.prototype={readLine:function(){var index=this.index;var bufferLength=this.bufferLength;if(index>=bufferLength){return null}var buffer=this.buffer;var start=index;var end=start;for(;index<bufferLength;index++){var c=buffer[index];if(c===10||c===13){end=index;if(index!==bufferLength-1&&buffer[index+1]===10){index++}index++;break}}this.index=index;if(start===end&&index===bufferLength){return this.decoder(this.buffer,start,bufferLength)}return this.decoder(this.buffer,start,end)}};morpheus.ArrayBufferReader.getArrayBuffer=function(fileOrUrl,callback){var isString=typeof fileOrUrl==="string"||fileOrUrl instanceof String;if(isString){var fetchOptions={};if(fileOrUrl.headers){fetchOptions.headers=new Headers;for(var header in fileOrUrl.headers){fetchOptions.headers.append(header,fileOrUrl.headers[header])}}fetch(fileOrUrl,fetchOptions).then(function(response){if(response.ok){return response.arrayBuffer()}else{callback(new Error(fileOrUrl+" status: "+response.status))}}).then(function(buf){callback(null,buf)}).catch(function(error){console.log("Fetch error",error);callback(error)})}else{var reader=new FileReader;reader.onload=function(event){callback(null,event.target.result)};reader.onerror=function(event){callback(event)};reader.readAsArrayBuffer(fileOrUrl)}};morpheus.Array2dReaderInteractive=function(){};morpheus.Array2dReaderInteractive.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));var html=[];html.push("<div>");html.push("<label>Click the table cell containing the first data row and column.</label>");html.push('<div class="checkbox"> <label> <input name="transpose" type="checkbox">'+" Tranpose </label>"+" </div>");html.push("<div"+' style="display:inline-block;width:10px;height:10px;background-color:#b3cde3;"></div><span> Data Matrix</span>');html.push("<br /><div"+' style="display:inline-block;width:10px;height:10px;background-color:#fbb4ae;"></div><span> Column'+" Annotations</span>");html.push("<br /><div"+' style="display:inline-block;'+' width:10px;height:10px;background-color:#ccebc5;"></div><span> Row'+" Annotations</span>");html.push('<div class="slick-bordered-table" style="width:550px;height:300px;"></div>');html.push("</div>");var $el=$(html.join(""));morpheus.Util.readLines(fileOrUrl,true).done(function(lines){var tab=/\t/;for(var i=0,nrows=lines.length;i<nrows;i++){lines[i]=lines[i].split(tab)}var grid;var columns=[];for(var j=0,ncols=lines[0].length;j<ncols;j++){columns.push({id:j,field:j})}var dataRowStart=1;var dataColumnStart=1;var _lines=lines;var grid=new Slick.Grid($el.find(".slick-bordered-table")[0],lines,columns,{enableCellNavigation:true,headerRowHeight:0,showHeaderRow:false,multiColumnSort:false,multiSelect:false,topPanelHeight:0,enableColumnReorder:false,enableTextSelectionOnCells:true,forceFitColumns:false,defaultFormatter:function(row,cell,value,columnDef,dataContext){var color="white";if(cell>=dataColumnStart&&row>=dataRowStart){color="#b3cde3"}else if(row<=dataRowStart-1&&cell>=dataColumnStart){color="#fbb4ae"}else if(cell<dataColumnStart&&row>=dataRowStart){color="#ccebc5"}var html=['<div style="width:100%;height:100%;background-color:'+color+'">'];if(_.isNumber(value)){html.push(morpheus.Util.nf(value))}else if(morpheus.Util.isArray(value)){var s=[];for(var i=0,length=value.length;i<length;i++){if(i>0){s.push(", ")}var val=value[i];s.push(value[i])}html.push(s.join(""))}else{html.push(value)}html.push("</div>");return html.join("")}});var transposedLines;var transposedColumns;$el.find("[name=transpose]").on("click",function(e){if($(this).prop("checked")){if(transposedLines==null){transposedLines=[];for(var j=0,ncols=lines[0].length;j<ncols;j++){var row=[];transposedLines.push(row);for(var i=0,nrows=lines.length;i<nrows;i++){row.push(lines[i][j])}}transposedColumns=[];for(var j=0,ncols=transposedLines[0].length;j<ncols;j++){transposedColumns.push({id:j,field:j})}}lines=transposedLines;grid.setData(transposedLines);grid.setColumns(transposedColumns);grid.resizeCanvas();grid.invalidate()}else{grid.setData(_lines);grid.setColumns(columns);grid.resizeCanvas();grid.invalidate();lines=_lines}});grid.onClick.subscribe(function(e,args){dataRowStart=args.row;dataColumnStart=args.cell;grid.invalidate()});$el.find(".slick-header").remove();var footer=[];footer.push('<button name="ok" type="button" class="btn btn-default">OK</button>');footer.push('<button name="cancel" type="button" data-dismiss="modal" class="btn btn-default">Cancel</button>');var $footer=$(footer.join(""));morpheus.FormBuilder.showOkCancel({title:"Open",content:$el,close:false,focus:document.activeElement,cancelCallback:function(){callback(null)},okCallback:function(){_this._read(name,lines,dataColumnStart,dataRowStart,callback)}});grid.resizeCanvas()}).fail(function(err){callback(err)})},_read:function(datasetName,lines,dataColumnStart,dataRowStart,cb){var columnCount=lines[0].length;var columns=columnCount-dataColumnStart;var rows=lines.length-dataRowStart;var dataset=new morpheus.Dataset({name:datasetName,rows:rows,columns:columns,dataType:"Float32"});if(dataColumnStart>0){for(var i=0;i<dataRowStart;i++){var name=lines[i][0];if(name==null||name===""||name==="na"){name="id"}var unique=1;while(dataset.getColumnMetadata().getByName(name)!=null){name=name+"-"+unique;unique++}var v=dataset.getColumnMetadata().add(name);var nonEmpty=false;for(var j=0;j<columns;j++){var s=lines[i][j+dataColumnStart];if(s!=null&&s!==""){nonEmpty=true;v.setValue(j,s)}}if(!nonEmpty){dataset.getColumnMetadata().remove(morpheus.MetadataUtil.indexOf(dataset.getColumnMetadata(),v.getName()))}}}if(dataRowStart>0){for(var j=0;j<dataColumnStart;j++){var name=lines[0][j];if(name==null||name===""){name="id"}var unique=1;while(dataset.getRowMetadata().get(name)!=null){name=name+"-"+unique;unique++}dataset.getRowMetadata().add(name)}}for(var i=0;i<rows;i++){for(var j=0,k=0;k<dataset.getRowMetadata().getMetadataCount();j++,k++){var metaDataValue=lines[i+dataRowStart][j];dataset.getRowMetadata().get(j).setValue(i,metaDataValue)}}for(var i=0;i<rows;i++){for(var j=0;j<columns;j++){var s=lines[i+dataRowStart][j+dataColumnStart];dataset.setValue(i,j,parseFloat(s))}}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);cb(null,dataset)}};morpheus.BufferedReader=function(reader,callback,doneCallback){var textDecoder=morpheus.Util.createTextDecoder();var skipLF=false;var text="";reader.read().then(function processResult(result){text+=result.done?"":textDecoder(result.value,0,result.value.length);var start=0;for(var i=0,length=text.length;i<length;i++){var c=text[i];if(skipLF&&c==="\n"){start++;skipLF=false}else if(c==="\n"||c==="\r"){skipLF=c==="\r";var s=morpheus.Util.copyString(text.substring(start,i));callback(s);start=i+1}else{skipLF=false}}text=start<text.length?text.substring(start):"";if(!result.done){return reader.read().then(processResult)}else{if(text!==""&&text!=="\r"){callback(text)}doneCallback()}})};morpheus.BufferedReader.parse=function(url,options){var delim=options.delimiter;var regex=new RegExp(delim);var handleTokens=options.handleTokens;var complete=options.complete;var fetchOptions={};if(url.headers){fetchOptions.headers=new Headers;for(var header in url.headers){fetchOptions.headers.append(header,url.headers[header])}}fetch(url,fetchOptions).then(function(response){if(response.ok){var reader=response.body.getReader();new morpheus.BufferedReader(reader,function(line){handleTokens(line.split(regex))},function(){complete()})}else{options.error("Network error")}}).catch(function(error){options.error(error)})};morpheus.ClsReader=function(){};morpheus.ClsReader.prototype={read:function(lines){var regex=/[ ,]+/;var header=lines[0].split(regex);if(header.length<3){throw new Error("Header line needs three numbers")}var headerNumbers=[];try{for(var i=0;i<3;i++){headerNumbers[i]=parseInt($.trim(header[i]))}}catch(e){throw new Error("Header line element "+i+" is not a number")}if(headerNumbers[0]<=0){throw new Error("Header line missing first number, number of data points")}if(headerNumbers[1]<=0){throw new Error("Header line missing second number, number of classes")}var numClasses=headerNumbers[1];var numItems=headerNumbers[0];var classDefinitionLine=lines[1];classDefinitionLine=classDefinitionLine.substring(classDefinitionLine.indexOf("#")+1);var classNames=$.trim(classDefinitionLine).split(regex);if(classNames.length<numClasses){throw new Error("First line specifies "+numClasses+" classes, but found "+classNames.length+".")}var dataLine=lines[2];var assignments=dataLine.split(regex);for(var i=0;i<assignments.length;i++){var assignment=$.trim(assignments[i]);var index=parseInt(assignment);var tmp=classNames[index];if(tmp!==undefined){assignments[i]=tmp}}return assignments}};morpheus.ClsWriter=function(){};morpheus.ClsWriter.prototype={write:function(vector){var pw=[];var size=vector.size();pw.push(size);pw.push(" ");var set=morpheus.VectorUtil.getSet(vector);pw.push(set.size());pw.push(" ");pw.push("1\n");pw.push("#");var valueToIndex=new morpheus.Map;var index=0;set.forEach(function(name){pw.push(" ");pw.push(name);valueToIndex.set(name,index++)});pw.push("\n");for(var i=0;i<size;i++){if(i>0){pw.push(" ")}pw.push(valueToIndex.get(vector.getValue(i)))}pw.push("\n");return pw.join("")}};morpheus.GctReader=function(){};morpheus.GctReader.prototype={getFormatName:function(){return"gct"},read:function(fileOrUrl,callback){var _this=this;if(morpheus.Util.isFile(fileOrUrl)){this._readChunking(fileOrUrl,callback,false)}else{if(morpheus.Util.isFetchStreamingSupported()){this._readChunking(fileOrUrl,callback,true)}else{this._readNoChunking(fileOrUrl,callback)}}},_readChunking:function(fileOrUrl,callback,useFetch){var _this=this;var lineNumber=0;var version;var numRowAnnotations=1;var numColumnAnnotations=0;var nrows=-1;var ncols=-1;var version=2;var rowMetadataNames=[];var columnMetadataNames=[];var rowMetadata=[[]];var columnMetadata=[[]];var dataColumnStart;var matrix=[];var dataMatrixLineNumberStart;var columnIdFieldName="id";var rowIdFieldName="id";var columnNamesArray;var handleTokens=function(tokens){if(lineNumber===0){var text=tokens[0].trim();if("#1.2"===text){version=2}else if("#1.3"===text){version=3}else{console.log("Unknown version: assuming version 2")}}else if(lineNumber===1){var dimensions=tokens;if(version===3){if(dimensions.length>=4){nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);numRowAnnotations=parseInt(dimensions[2]);numColumnAnnotations=parseInt(dimensions[3])}else{numRowAnnotations=parseInt(dimensions[0]);numColumnAnnotations=parseInt(dimensions[1])}}else{nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);if(nrows<=0||ncols<=0){callback("Number of rows and columns must be greater than 0.")}}dataColumnStart=numRowAnnotations+1}else if(lineNumber===2){columnNamesArray=tokens;for(var i=0;i<columnNamesArray.length;i++){columnNamesArray[i]=morpheus.Util.copyString(columnNamesArray[i])}if(ncols===-1){ncols=columnNamesArray.length-numRowAnnotations-1}if(version==2){var expectedColumns=ncols+2;if(columnNamesArray.length!==expectedColumns){if(columnNamesArray.length>expectedColumns){var skip=columnNamesArray.length-1;for(var i=columnNamesArray.length-1;i>=0;i--,skip--){if(columnNamesArray[i]!==""){break}}if(skip!==columnNamesArray.length-1){columnNamesArray=columnNamesArray.slice(0,skip+1)}}if(columnNamesArray.length!==expectedColumns){return callback("Expected "+(expectedColumns-2)+" column names, but read "+(columnNamesArray.length-2)+" column names.")}}}var name=columnNamesArray[0];var slashIndex=name.lastIndexOf("/");if(slashIndex!=-1&&slashIndex<name.length-1){rowIdFieldName=name.substring(0,slashIndex);columnIdFieldName=name.substring(slashIndex+1)}rowMetadataNames.push(rowIdFieldName);columnMetadataNames.push(columnIdFieldName);for(var j=0;j<ncols;j++){var index=j+numRowAnnotations+1;var columnName=index<columnNamesArray.length?columnNamesArray[index]:null;columnMetadata[0].push(morpheus.Util.copyString(columnName))}for(var j=0;j<numRowAnnotations;j++){var rowMetadataName=""===columnNamesArray[1]?"description":columnNamesArray[j+1];rowMetadataNames.push(rowMetadataName);rowMetadata.push([])}dataMatrixLineNumberStart=3+numColumnAnnotations}else{if(lineNumber<dataMatrixLineNumberStart){var metadataName=morpheus.Util.copyString(tokens[0]);var v=[];columnMetadata.push(v);columnMetadataNames.push(metadataName);for(var j=0;j<ncols;j++){v.push(morpheus.Util.copyString(tokens[j+dataColumnStart]))}}else{if(tokens[0]!==""){var array=new Float32Array(ncols);matrix.push(array);for(var rowAnnotationIndex=0;rowAnnotationIndex<=numRowAnnotations;rowAnnotationIndex++){var rowMetadataValue=tokens[rowAnnotationIndex];rowMetadata[rowAnnotationIndex].push(morpheus.Util.copyString(rowMetadataValue))}for(var columnIndex=0;columnIndex<ncols;columnIndex++){var token=tokens[columnIndex+dataColumnStart];array[columnIndex]=parseFloat(token)}}}}lineNumber++};(useFetch?morpheus.BufferedReader:Papa).parse(fileOrUrl,{delimiter:"\t",newline:"",header:false,dynamicTyping:false,preview:0,encoding:"",worker:false,comments:false,handleTokens:handleTokens,step:function(result){handleTokens(result.data[0])},complete:function(){var dataset=new morpheus.Dataset({name:morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl)),rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});for(var i=0;i<rowMetadataNames.length;i++){dataset.getRowMetadata().add(rowMetadataNames[i]).array=rowMetadata[i]}for(var i=0;i<columnMetadataNames.length;i++){dataset.getColumnMetadata().add(columnMetadataNames[i]).array=columnMetadata[i]}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);callback(null,dataset)},error:function(err){callback(err)},download:!morpheus.Util.isFile(fileOrUrl),skipEmptyLines:false,chunk:undefined,fastMode:true,beforeFirstChunk:undefined,withCredentials:undefined})},_read:function(datasetName,reader){var tab=/\t/;var versionLine=morpheus.Util.copyString(reader.readLine().trim());if(versionLine===""){throw new Error("Missing version line")}var version=2;if("#1.2"===versionLine){version=2}else if("#1.3"===versionLine){version=3}else{console.log("Unknown version: assuming version 2")}var dimensionsLine=morpheus.Util.copyString(reader.readLine());if(dimensionsLine==null){throw new Error("No dimensions specified")}var dimensions=dimensionsLine.split(/[ \t]/);var numRowAnnotations=1;var numColumnAnnotations=0;var nrows=-1;var ncols=-1;if(version===3){if(dimensions.length>=4){nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);numRowAnnotations=parseInt(dimensions[2]);numColumnAnnotations=parseInt(dimensions[3])}else{numRowAnnotations=parseInt(dimensions[0]);numColumnAnnotations=parseInt(dimensions[1])}}else{nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);if(nrows<=0||ncols<=0){throw new Error("Number of rows and columns must be greater than 0.")}}var columnNamesLine=morpheus.Util.copyString(reader.readLine());if(columnNamesLine==null){throw new Error("No column annotations")}var columnNamesArray=columnNamesLine.split(tab);if(ncols===-1){ncols=columnNamesArray.length-numRowAnnotations-1}if(version==2){var expectedColumns=ncols+2;if(columnNamesArray.length!==expectedColumns){throw new Error("Expected "+(expectedColumns-2)+" column names, but read "+(columnNamesArray.length-2)+" column names.")}}var name=columnNamesArray[0];var slashIndex=name.lastIndexOf("/");var columnIdFieldName="id";var rowIdFieldName="id";if(slashIndex!=-1&&slashIndex<name.length-1){rowIdFieldName=name.substring(0,slashIndex);columnIdFieldName=name.substring(slashIndex+1)}if(nrows===-1){var matrix=[];var rowMetadataNames=[rowIdFieldName];var columnMetadataNames=[columnIdFieldName];var rowMetadata=[[]];var columnMetadata=[[]];for(var j=0;j<ncols;j++){var index=j+numRowAnnotations+1;var columnName=index<columnNamesArray.length?columnNamesArray[index]:null;columnMetadata[0].push(morpheus.Util.copyString(columnName))}for(var j=0;j<numRowAnnotations;j++){var rowMetadataName=""===columnNamesArray[1]?"description":columnNamesArray[j+1];rowMetadataNames.push(rowMetadataName);rowMetadata.push([])}var dataColumnStart=numRowAnnotations+1;var ntokens=ncols+numRowAnnotations+1;var linen=3;if(numColumnAnnotations>0){for(var columnAnnotationIndex=0;columnAnnotationIndex<numColumnAnnotations;columnAnnotationIndex++){var tokens=reader.readLine().split(tab);var metadataName=tokens[0];var v=[];columnMetadata.push(v);columnMetadataNames.push(metadataName);for(var j=0;j<ncols;j++){v.push(morpheus.Util.copyString(tokens[j+dataColumnStart]))}}}var nonEmptyDescriptionFound=false;var numRowAnnotationsPlusOne=numRowAnnotations+1;var s;while((s=reader.readLine())!==null){if(s!==""){var array=new Float32Array(ncols);matrix.push(array);var tokens=s.split(tab);for(var rowAnnotationIndex=0;rowAnnotationIndex<numRowAnnotationsPlusOne;rowAnnotationIndex++){var rowMetadataValue=tokens[rowAnnotationIndex];rowMetadata[rowAnnotationIndex].push(morpheus.Util.copyString(rowMetadataValue))}for(var columnIndex=0;columnIndex<ncols;columnIndex++){var token=tokens[columnIndex+dataColumnStart];array[columnIndex]=parseFloat(token)}}}var dataset=new morpheus.Dataset({name:datasetName,rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});for(var i=0;i<rowMetadataNames.length;i++){dataset.getRowMetadata().add(rowMetadataNames[i]).array=rowMetadata[i]}for(var i=0;i<columnMetadataNames.length;i++){dataset.getColumnMetadata().add(columnMetadataNames[i]).array=columnMetadata[i]}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);return dataset}else{var dataset=new morpheus.Dataset({dataType:"Float32",name:datasetName,rows:nrows,columns:ncols});var columnIds=dataset.getColumnMetadata().add(columnIdFieldName);if(version==3){for(var j=0;j<ncols;j++){var index=j+numRowAnnotations+1;var columnName=index<columnNamesArray.length?columnNamesArray[index]:null;columnIds.setValue(j,morpheus.Util.copyString(columnName))}}else{for(var j=0;j<ncols;j++){var columnName=columnNamesArray[j+numRowAnnotations+1];columnIds.setValue(j,morpheus.Util.copyString(columnName))}}var rowAnnotationVectors=[dataset.getRowMetadata().add(rowIdFieldName)];if(version===3){for(var j=0;j<numRowAnnotations;j++){var rowMetadataName=""===columnNamesArray[1]?"description":columnNamesArray[j+1];rowAnnotationVectors.push(dataset.getRowMetadata().add(rowMetadataName))}}else{rowAnnotationVectors.push(dataset.getRowMetadata().add(columnNamesArray[1]))}var dataColumnStart=numRowAnnotations+1;var ntokens=ncols+numRowAnnotations+1;var linen=3;if(numColumnAnnotations>0){for(var columnAnnotationIndex=0;columnAnnotationIndex<numColumnAnnotations;columnAnnotationIndex++){var tokens=reader.readLine().split(tab);var metadataName=tokens[0];var v=dataset.getColumnMetadata().add(metadataName);for(var j=0;j<ncols;j++){v.setValue(j,morpheus.Util.copyString(tokens[j+dataColumnStart]))}}}var nonEmptyDescriptionFound=false;var numRowAnnotationsPlusOne=numRowAnnotations+1;for(var rowIndex=0,nrows=dataset.getRowCount();rowIndex<nrows;rowIndex++){var s=reader.readLine();if(s===null){throw new Error("Missing data rows.")}var tokens=s.split(tab);if(version===2){rowAnnotationVectors[0].setValue(rowIndex,morpheus.Util.copyString(tokens[0]));var desc=tokens[1];if(!nonEmptyDescriptionFound){nonEmptyDescriptionFound=desc!==""}rowAnnotationVectors[1].setValue(rowIndex,morpheus.Util.copyString(desc))}else{for(var rowAnnotationIndex=0;rowAnnotationIndex<numRowAnnotationsPlusOne;rowAnnotationIndex++){var rowMetadataValue=tokens[rowAnnotationIndex];rowAnnotationVectors[rowAnnotationIndex].setValue(rowIndex,morpheus.Util.copyString(rowMetadataValue))}}for(var columnIndex=0;columnIndex<ncols;columnIndex++){var token=tokens[columnIndex+dataColumnStart];dataset.setValue(rowIndex,columnIndex,parseFloat(token))}}if(version===2&&!nonEmptyDescriptionFound){dataset.getRowMetadata().remove(1)}if(rowIndex!==nrows){throw new Error("Missing data rows")}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);return dataset}},_readNoChunking:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}})}};morpheus.GctWriter=function(){this.nf=morpheus.Util.createNumberFormat(".2f")};morpheus.GctWriter.idFirst=function(model){var fields=["id","Id","pr_id"];var idIndex=-1;for(var i=0;i<fields.length;i++){idIndex=morpheus.MetadataUtil.indexOf(model,fields[i]);if(idIndex!==-1){break}}if(idIndex!==-1){var order=[];order[0]=idIndex;for(var i=0,j=1,count=model.getMetadataCount();i<count;i++){if(i!==idIndex){order[j++]=i}}return new morpheus.MetadataModelColumnView(model,order)}return model};morpheus.GctWriter.prototype={setNumberFormat:function(nf){this.nf=nf},getExtension:function(){return"gct"},write:function(dataset,pw){if(pw==null){pw=[]}var rowMetadata=morpheus.GctWriter.idFirst(dataset.getRowMetadata());var columnMetadata=morpheus.GctWriter.idFirst(dataset.getColumnMetadata());this.writeHeader(rowMetadata,columnMetadata,pw);this.writeData(dataset,rowMetadata,pw);return pw.join("")},writeData:function(dataset,rowMetadata,pw){var ncols=dataset.getColumnCount();var rowMetadataCount=rowMetadata.getMetadataCount();var nf=this.nf;for(var i=0,rows=dataset.getRowCount();i<rows;i++){for(var rowMetadataIndex=0;rowMetadataIndex<rowMetadataCount;rowMetadataIndex++){if(rowMetadataIndex>0){pw.push("\t")}var vector=rowMetadata.get(rowMetadataIndex);var value=vector.getValue(i);if(value!==null){var toString=morpheus.VectorTrack.vectorToString(vector);pw.push(toString(value))}}for(var j=0;j<ncols;j++){pw.push("\t");var value=dataset.getValue(i,j);pw.push(nf(value))}pw.push("\n")}},writeHeader:function(rowMetadata,columnMetadata,pw){var rows=rowMetadata.getItemCount();var ncols=columnMetadata.getItemCount();pw.push("#1.3\n");var rowMetadataCount=rowMetadata.getMetadataCount();pw.push(rows+"\t"+ncols+"\t"+(rowMetadataCount-1)+"\t"+(columnMetadata.getMetadataCount()-1));pw.push("\n");for(var i=0;i<rowMetadataCount;i++){if(i>0){pw.push("\t")}var name=rowMetadata.get(i).getName();if(i===0&&name!==columnMetadata.get(0).getName()){name=name+"/"+columnMetadata.get(0).getName()}pw.push(name)}var toString=morpheus.VectorTrack.vectorToString(columnMetadata.get(0));for(var j=0;j<ncols;j++){pw.push("\t");pw.push(toString(columnMetadata.get(0).getValue(j)))}pw.push("\n");for(var columnMetadataIndex=1,metadataSize=columnMetadata.getMetadataCount();columnMetadataIndex<metadataSize;columnMetadataIndex++){pw.push(columnMetadata.get(columnMetadataIndex).getName());for(var i=1;i<rowMetadataCount;i++){pw.push("\t");pw.push("na")}for(var j=0;j<ncols;j++){pw.push("\t");var vector=columnMetadata.get(columnMetadataIndex);var value=vector.getValue(j);if(value!=null){toString=morpheus.VectorTrack.vectorToString(columnMetadata.get(0));pw.push(toString(value))}}pw.push("\n")}}};morpheus.GctWriter12=function(){this.options={rowDescription:"Description",rowId:"id",columnId:"id"};this.nf=morpheus.Util.createNumberFormat(".2f")};morpheus.GctWriter12.prototype={setNumberFormat:function(nf){this.nf=nf},getExtension:function(){return"gct"},write:function(dataset,pw){if(pw==null){pw=[]}var rows=dataset.getRowCount();var columns=dataset.getColumnCount();var version="#1.2";pw.push(version);pw.push("\n");pw.push(rows+"\t"+columns);pw.push("\n");var rowMetadata=morpheus.GctWriter.idFirst(dataset.getRowMetadata());var columnMetadata=morpheus.GctWriter.idFirst(dataset.getColumnMetadata());pw.push("Name");pw.push("\t");pw.push("Description");var columnIds=columnMetadata.getByName(this.options.columnId);if(!columnIds){columnIds=columnMetadata.get(0)}var columnIdToString=morpheus.VectorTrack.vectorToString(columnIds);for(var j=0;j<columns;j++){pw.push("\t");pw.push(columnIdToString(columnIds.getValue(j)))}var rowIds=rowMetadata.get(this.options.rowId);if(!rowIds){rowIds=rowMetadata.get(0)}var rowDescriptions=rowMetadata.getByName(this.options.rowDescription);if(rowDescriptions==null&&rowMetadata.getMetadataCount()>1){rowDescriptions=rowMetadata.get(1)}var rowIdToString=morpheus.VectorTrack.vectorToString(rowIds);var rowDescriptionToString=rowDescriptions!=null?morpheus.VectorTrack.vectorToString(rowDescriptions):null;var nf=this.nf;for(var i=0;i<rows;i++){pw.push("\n");pw.push(rowIdToString(rowIds.getValue(i)));pw.push("\t");var rowDescription=rowDescriptions!=null?rowDescriptions.getValue(i):null;if(rowDescription!=null){pw.push(rowDescriptionToString(rowDescription))}for(var j=0;j<columns;j++){pw.push("\t");pw.push(nf(dataset.getValue(i,j)))}}pw.push("\n");return pw.join("")}};morpheus.GisticReader=function(){};morpheus.GisticReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}catch(x){if(x.stack){console.log(x.stack)}callback(x)}}})},_read:function(datasetName,reader){var tab=/\t/;var header=reader.readLine().trim().split(tab);var ncols=header.length-9;var matrix=[];var s;var rowIds=[];var qValues=[];while((s=reader.readLine())!==null){s=s.trim();if(s!==""){var tokens=s.split(tab);if(tokens[8]==="Actual Copy Change Given"){var array=new Float32Array(ncols);matrix.push(array);rowIds.push(String($.trim(tokens[1])));qValues.push(parseFloat(tokens[5]));for(var j=9;j<=ncols;j++){var token=tokens[j];array[j-9]=parseFloat(token)}}}}var dataset=new morpheus.Dataset({name:datasetName,rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});var columnIds=dataset.getColumnMetadata().add("id");for(var j=0;j<ncols;j++){columnIds.setValue(j,String(header[j+9]))}dataset.getRowMetadata().add("id").array=rowIds;dataset.getRowMetadata().add("q_value").array=qValues;return dataset}};morpheus.GmtDatasetReader=function(){};morpheus.GmtDatasetReader.prototype={getFormatName:function(){return"gmt"},read:function(fileOrUrl,callback){var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,morpheus.DatasetUtil.geneSetsToDataset(name,(new morpheus.GmtReader).read(new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer)))))}catch(x){callback(x)}}})}};morpheus.GmtReader=function(){};morpheus.GmtReader.prototype={read:function(reader){var sets=[];var tab=/\t/;var s;while((s=reader.readLine())!=null){if(s===""||s[0]==="#"){continue}var tokens=s.split(tab);var name=tokens[0].trim();var description=tokens.length>1?tokens[1].trim():"";if("BLANK"===description){description=""}var ids=[];for(var i=2;i<tokens.length;i++){var geneName=tokens[i].trim();if(geneName!==""){ids.push(geneName)}}var set={name:name,description:description,ids:ids};set.toString=function(){return this.name};sets.push(set)}return sets}};morpheus.JsonDatasetReader=function(){};morpheus.JsonDatasetReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));var isString=typeof fileOrUrl==="string"||fileOrUrl instanceof String;if(isString){fetch(fileOrUrl).then(function(response){if(response.ok){return response.text()}else{callback(response.status+" "+response.statusText)}}).then(function(text){callback(null,morpheus.Dataset.fromJSON(JSON.parse(text.trim())))}).catch(function(err){callback(err)})}else{var reader=new FileReader;reader.onload=function(event){callback(null,morpheus.Dataset.fromJSON(JSON.parse(event.target.result)))};reader.onerror=function(event){callback(event)};reader.readAsText(fileOrUrl)}}};morpheus.MafFileReader=function(){this.geneFilter=null};morpheus.MafFileReader.summarizeMutations=function(options){var dataset=options.dataset;var fields=options.fields;var count=fields.length;var vector=dataset.getRowMetadata().add("mutation_summary");vector.getProperties().set(morpheus.VectorKeys.FIELDS,fields);vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"[number]");for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var bins=new Int32Array(count);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(value>0){bins[value-1]++}}vector.setValue(i,bins)}};morpheus.MafFileReader.getField=function(fieldNames,headerToIndex){var name;var index;for(var i=0;i<fieldNames.length;i++){name=fieldNames[i];var lc=name.toLowerCase();index=headerToIndex[lc];if(index!==undefined){break}}if(index!==undefined){return{name:name,index:index}}};morpheus.MafFileReader.VARIANT_MAP=new morpheus.Map;morpheus.MafFileReader.VARIANT_MAP.set("Silent",1);morpheus.MafFileReader.VARIANT_MAP.set("In_Frame_Del",2);morpheus.MafFileReader.VARIANT_MAP.set("In_Frame_Ins",2);morpheus.MafFileReader.VARIANT_MAP.set("Inframe_Del",2);morpheus.MafFileReader.VARIANT_MAP.set("Inframe_Ins",2);morpheus.MafFileReader.VARIANT_MAP.set("Translation_Start_Site",3);morpheus.MafFileReader.VARIANT_MAP.set("Nonstop_Mutation",3);morpheus.MafFileReader.VARIANT_MAP.set("3'UTR",3);morpheus.MafFileReader.VARIANT_MAP.set("3'Flank",3);morpheus.MafFileReader.VARIANT_MAP.set("5'UTR",3);morpheus.MafFileReader.VARIANT_MAP.set("5'Flank",3);morpheus.MafFileReader.VARIANT_MAP.set("IGR",3);morpheus.MafFileReader.VARIANT_MAP.set("Intron",3);morpheus.MafFileReader.VARIANT_MAP.set("RNA",3);morpheus.MafFileReader.VARIANT_MAP.set("Targeted_Region",3);morpheus.MafFileReader.VARIANT_MAP.set("Unknown",3);morpheus.MafFileReader.VARIANT_MAP.set("1DEL",3);morpheus.MafFileReader.VARIANT_MAP.set("HA",3);morpheus.MafFileReader.VARIANT_MAP.set("Missense_Mutation",4);morpheus.MafFileReader.VARIANT_MAP.set("Missense",4);morpheus.MafFileReader.VARIANT_MAP.set("Splice_Site",5);morpheus.MafFileReader.VARIANT_MAP.set("Splice_Acceptor",5);morpheus.MafFileReader.VARIANT_MAP.set("Splice_Region",5);morpheus.MafFileReader.VARIANT_MAP.set("Frame_Shift_Del",6);morpheus.MafFileReader.VARIANT_MAP.set("Frame_Shift_Ins",6);morpheus.MafFileReader.VARIANT_MAP.set("Frameshift",6);morpheus.MafFileReader.VARIANT_MAP.set("Nonsense_Mutation",7);morpheus.MafFileReader.VARIANT_MAP.set("Nonsense",7);morpheus.MafFileReader.VARIANT_MAP.set("2DEL",7);morpheus.MafFileReader.FIELD_NAMES=["Synonymous","In Frame Indel","Other Non-Synonymous","Missense","Splice Site","Frame Shift","Nonsense"];morpheus.MafFileReader.prototype={setGeneFilter:function(geneFilter){this.geneFilter=geneFilter},getFormatName:function(){return"maf"},_getGeneLevelDataset:function(datasetName,reader){var _this=this;var tab=/\t/;var header=reader.readLine().split(tab);var headerToIndex={};for(var i=0,length=header.length;i<length;i++){headerToIndex[header[i].toLowerCase()]=i}var sampleField=morpheus.MafFileReader.getField(["Tumor_Sample_Barcode","tumor_name","Tumor_Sample_UUID"],headerToIndex);var encodingField=morpheus.MafFileReader.getField(["encoding"],headerToIndex);if(sampleField==null){throw new Error("Sample id column not found.")}var encodingColumnIndex=encodingField==null?-1:encodingField.index;var sampleColumnName=sampleField.name;var sampleIdColumnIndex=sampleField.index;var tumorFractionField=morpheus.MafFileReader.getField(["ccf_hat","tumor_f","i_tumor_f"],headerToIndex);var ccfColumnName;var ccfColumnIndex;if(tumorFractionField!==undefined){ccfColumnName=tumorFractionField.name;ccfColumnIndex=tumorFractionField.index}var chromosomeColumn=headerToIndex["Chromosome".toLowerCase()];var startPositionColumn=headerToIndex["Start_position".toLowerCase()];var refAlleleColumn=headerToIndex["Reference_Allele".toLowerCase()];var tumorAllelColumn=headerToIndex["Tumor_Seq_Allele2".toLowerCase()];var proteinChangeColumn=headerToIndex["Protein_Change".toLowerCase()];if(proteinChangeColumn==null){proteinChangeColumn=headerToIndex["Protein".toLowerCase()]}var geneSymbolColumn=headerToIndex["Hugo_Symbol".toLowerCase()];if(geneSymbolColumn==null){geneSymbolColumn=headerToIndex["gene"]}if(geneSymbolColumn==null){throw new Error("Gene symbol column not found.")}var variantColumnIndex=headerToIndex["Variant_Classification".toLowerCase()];if(variantColumnIndex==null){variantColumnIndex=headerToIndex["variant".toLowerCase()]}if(variantColumnIndex==null){throw new Error("Variant_Classification not found")}var geneSymbolToIndex=new morpheus.Map;var sampleIdToIndex=new morpheus.Map;var variantMatrix=[];var ccfMatrix=[];var s;var customNumberToValueMap=new morpheus.Map;var hasMutationInfo=chromosomeColumn!==undefined&&startPositionColumn!==undefined&&refAlleleColumn!==undefined&&tumorAllelColumn!==undefined;while((s=reader.readLine())!==null){var tokens=s.split(tab);var sample=String(tokens[sampleIdColumnIndex]);var columnIndex=sampleIdToIndex.get(sample);if(columnIndex===undefined){columnIndex=sampleIdToIndex.size();sampleIdToIndex.set(sample,columnIndex)}var gene=String(tokens[geneSymbolColumn]);if(gene==="Unknown"){continue}if(this.geneFilter==null||this.geneFilter.has(tokens[geneSymbolColumn])){var rowIndex=geneSymbolToIndex.get(gene);if(rowIndex===undefined){rowIndex=geneSymbolToIndex.size();geneSymbolToIndex.set(gene,rowIndex)}var value=String(tokens[variantColumnIndex]);var variantCode;if(encodingColumnIndex===-1){variantCode=morpheus.MafFileReader.VARIANT_MAP.get(value);if(variantCode===undefined){variantCode=3}}else{variantCode=parseInt(tokens[encodingColumnIndex]);customNumberToValueMap.set(variantCode,value)}var variantObject={};var Protein_Change=tokens[proteinChangeColumn];if(Protein_Change){variantObject.Protein=String(Protein_Change)}variantObject.__v=variantCode;variantObject.Variant=value;if(hasMutationInfo){variantObject.Mutation=String(tokens[chromosomeColumn])+":"+String(tokens[startPositionColumn])+" "+String(tokens[refAlleleColumn])+" > "+String(tokens[tumorAllelColumn])}var wrappedVariant=morpheus.Util.wrapNumber(variantCode,variantObject);var variantRow=variantMatrix[rowIndex];if(variantRow===undefined){variantRow=[];variantMatrix[rowIndex]=variantRow}var ccf=-1;var priorCcf=-1;if(ccfColumnIndex!==undefined){var ccfRow=ccfMatrix[rowIndex];if(ccfRow===undefined){ccfRow=[];ccfMatrix[rowIndex]=ccfRow}ccf=parseFloat(tokens[ccfColumnIndex]);priorCcf=ccfRow[columnIndex]||-1}var priorValue=variantRow[columnIndex]||-1;if(variantCode>priorValue){variantRow[columnIndex]=wrappedVariant;if(ccfColumnIndex!==undefined){ccfRow[columnIndex]=ccf}}else if(variantCode===priorValue&&ccf>priorCcf){variantRow[columnIndex]=wrappedVariant;ccfRow[columnIndex]=ccf}}}var dataset=new morpheus.Dataset({name:datasetName,array:variantMatrix,dataType:"Number",rows:geneSymbolToIndex.size(),columns:sampleIdToIndex.size()});var columnIds=dataset.getColumnMetadata().add("id");sampleIdToIndex.forEach(function(index,id){columnIds.setValue(index,id)});var rowIds=dataset.getRowMetadata().add("id");geneSymbolToIndex.forEach(function(index,id){rowIds.setValue(index,id)});for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){if(variantMatrix[i][j]===undefined){variantMatrix[i][j]=0}}}if(ccfColumnIndex!==undefined){dataset.addSeries({dataType:"Float32",name:"allelic_fraction",array:ccfMatrix})}if(this.geneFilter){var orderVector=dataset.getRowMetadata().add("order");for(var i=0,size=orderVector.size();i<size;i++){var gene=rowIds.getValue(i);var order=this.geneFilter.get(gene);orderVector.setValue(i,order)}var project=new morpheus.Project(dataset);project.setRowSortKeys([new morpheus.SortKey("order",morpheus.SortKey.SortOrder.ASCENDING)],true);var tmp=project.getSortedFilteredDataset();project=new morpheus.Project(tmp);var columnIndices=morpheus.Util.seq(tmp.getColumnCount());columnIndices.sort(function(a,b){for(var i=0,nrows=tmp.getRowCount();i<nrows;i++){for(var seriesIndex=0,nseries=tmp.getSeriesCount();seriesIndex<nseries;seriesIndex++){var f1=tmp.getValue(i,a,seriesIndex);if(isNaN(f1)){f1=Number.NEGATIVE_INFINITY}f1=f1.valueOf();var f2=tmp.getValue(i,b,seriesIndex);if(isNaN(f2)){f2=Number.NEGATIVE_INFINITY}f2=f2.valueOf();var returnVal=f1===f2?0:f1<f2?1:-1;if(returnVal!==0){return returnVal}}}return 0});dataset=new morpheus.SlicedDatasetView(dataset,null,columnIndices)}var fieldNames=morpheus.MafFileReader.FIELD_NAMES;if(customNumberToValueMap.size()>0){var pairs=[];customNumberToValueMap.forEach(function(value,key){pairs.push({key:key,value:value})});pairs.sort(function(a,b){return a.key===b.key?0:a.key<b.key?-1:1});fieldNames=pairs.map(function(p){return p.value})}var numUniqueValues=fieldNames.length;morpheus.MafFileReader.summarizeMutations({dataset:dataset,fields:fieldNames});morpheus.MafFileReader.summarizeMutations({dataset:new morpheus.TransposedDatasetView(dataset),fields:fieldNames});var mutationSummarySelectionVector=dataset.getColumnMetadata().add("mutation_summary_selection");mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.FIELDS,fieldNames);mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"[number]");mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.RECOMPUTE_FUNCTION_SELECTION,true);var datasetName=dataset.getName();mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.FUNCTION,{binSize:1,domain:[1,8],cumulative:false});return dataset},read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,_this._getGeneLevelDataset(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}catch(err){callback(err)}}})}};morpheus.SegTabReader=function(){this.regions=null};morpheus.SegTabReader.binByRegion=function(dataset,regions){var chromosomeVector=dataset.getRowMetadata().getByName("Chromosome");var startVector=dataset.getRowMetadata().getByName("Start_bp");var endVector=dataset.getRowMetadata().getByName("End_bp");var collapsedDataset=new morpheus.Dataset({name:dataset.getName(),rows:regions.length,columns:dataset.getColumnCount(),dataType:"Float32"});morpheus.DatasetUtil.fill(collapsedDataset,NaN);var regionIdVector=collapsedDataset.getRowMetadata().add("id");var newChromosomeVector=collapsedDataset.getRowMetadata().add("chromosome");var newStartVector=collapsedDataset.getRowMetadata().add("start");var newEndVector=collapsedDataset.getRowMetadata().add("end");var nsegmentsVector=collapsedDataset.getRowMetadata().add("nsegments");var nseries=dataset.getSeriesCount();for(var series=1;series<nseries;series++){collapsedDataset.addSeries({name:dataset.getName(series),dataType:"Float32"})}var summarizeFunction=morpheus.Mean;collapsedDataset.setColumnMetadata(dataset.getColumnMetadata());for(var regionIndex=0;regionIndex<regions.length;regionIndex++){var region=regions[regionIndex];var rowIndices=[];for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var chromosome=chromosomeVector.getValue(i);var start=startVector.getValue(i);var end=endVector.getValue(i);if(region.chromosome==chromosome&&start>=region.start&&end<=region.end){rowIndices.push(i)}}if(rowIndices.length>0){var slice=morpheus.DatasetUtil.slicedView(dataset,rowIndices,null);var columnView=new morpheus.DatasetColumnView(slice);for(var j=0;j<dataset.getColumnCount();j++){columnView.setIndex(j);for(var series=0;series<nseries;series++){columnView.setSeriesIndex(series);collapsedDataset.setValue(regionIndex,j,summarizeFunction(columnView),series)}}}nsegmentsVector.setValue(regionIndex,rowIndices.length);regionIdVector.setValue(regionIndex,region.id);newChromosomeVector.setValue(regionIndex,region.chromosome);newStartVector.setValue(regionIndex,region.start);newEndVector.setValue(regionIndex,region.end)}return collapsedDataset};morpheus.SegTabReader.prototype={getFormatName:function(){return"seg"},setRegions:function(regions){this.regions=regions},_read:function(datasetName,reader){var tab=/\t/;var header=reader.readLine().split(tab);var fieldNameToIndex={};for(var i=0,length=header.length;i<length;i++){var name=header[i].toLowerCase();fieldNameToIndex[name]=i}var sampleField=morpheus.MafFileReader.getField(["pair_id","Tumor_Sample_Barcode","tumor_name","Tumor_Sample_UUID","Sample"],fieldNameToIndex);var sampleColumnName=sampleField.name;var sampleIdColumnIndex=sampleField.index;var tumorFractionField=morpheus.MafFileReader.getField(["ccf_hat","tumor_f","i_tumor_f"],fieldNameToIndex);var ccfColumnName;var ccfColumnIndex;if(tumorFractionField!==undefined){ccfColumnName=tumorFractionField.name;ccfColumnIndex=tumorFractionField.index}var chromosomeColumn=fieldNameToIndex.Chromosome;var startPositionColumn=morpheus.MafFileReader.getField(["Start_bp","Start"],fieldNameToIndex).index;var endPositionColumn=morpheus.MafFileReader.getField(["End_bp","End"],fieldNameToIndex,{remove:false,lc:true}).index;var valueField=morpheus.MafFileReader.getField(["tau","Segment_Mean"]).index;var s;var matrix=[];var ccfMatrix=[];var sampleIdToIndex=new morpheus.Map;var chromosomeStartEndToIndex=new morpheus.Map;while((s=reader.readLine())!==null){if(s===""){continue}var tokens=s.split(tab);var sample=String(tokens[sampleIdColumnIndex]);var columnIndex=sampleIdToIndex.get(sample);if(columnIndex===undefined){columnIndex=sampleIdToIndex.size();sampleIdToIndex.set(sample,columnIndex)}var rowId=new morpheus.Identifier([String(tokens[chromosomeColumn]),String(tokens[startPositionColumn]),String(tokens[endPositionColumn])]);var rowIndex=chromosomeStartEndToIndex.get(rowId);if(rowIndex===undefined){rowIndex=chromosomeStartEndToIndex.size();chromosomeStartEndToIndex.set(rowId,rowIndex)}var value=parseFloat(String(tokens[valueField]));value=isNaN(value)?value:morpheus.Log2(value)-1;var matrixRow=matrix[rowIndex];if(matrixRow===undefined){matrixRow=[];matrix[rowIndex]=matrixRow;if(ccfColumnIndex!==undefined){ccfMatrix[rowIndex]=[]}}matrixRow[columnIndex]=value;if(ccfColumnIndex!==undefined){ccfMatrix[rowIndex][columnIndex]=parseFloat(tokens[ccfColumnIndex])}}var dataset=new morpheus.Dataset({name:datasetName,array:matrix,dataType:"number",rows:chromosomeStartEndToIndex.size(),columns:sampleIdToIndex.size()});var columnIds=dataset.getColumnMetadata().add("id");sampleIdToIndex.forEach(function(index,id){columnIds.setValue(index,id)});var chromosomeVector=dataset.getRowMetadata().add("Chromosome");var startVector=dataset.getRowMetadata().add("Start_bp");var endVector=dataset.getRowMetadata().add("End_bp");chromosomeStartEndToIndex.forEach(function(index,id){chromosomeVector.setValue(index,id.getArray()[0]);startVector.setValue(index,id.getArray()[1]);endVector.setValue(index,id.getArray()[2])});if(ccfColumnIndex!==undefined){dataset.addSeries({dataType:"number",name:"ccf",array:ccfMatrix})}if(this.regions!=null&&this.regions.length>0){dataset=morpheus.SegTabReader.binByRegion(dataset,this.regions)}return dataset},read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}})}};morpheus.TcgaUtil=function(){};morpheus.TcgaUtil.DISEASE_STUDIES={ACC:"Adrenocortical carcinoma",BLCA:"Bladder Urothelial Carcinoma",BRCA:"Breast invasive carcinoma",CESC:"Cervical squamous cell carcinoma and endocervical adenocarcinoma",CHOL:"Cholangiocarcinoma",COAD:"Colon adenocarcinoma",COADREAD:"Colonrectal adenocarcinoma",DLBC:"Lymphoid Neoplasm Diffuse Large B-cell Lymphoma",ESCA:"Esophageal carcinoma ",GBM:"Glioblastoma multiforme",GBMLGG:"Glioma",HNSC:"Head and Neck squamous cell carcinoma",KICH:"Kidney Chromophobe",KIPAN:"Pan-Kidney Cohort",KIRC:"Kidney renal clear cell carcinoma",KIRP:"Kidney renal papillary cell carcinoma",LAML:"Acute Myeloid Leukemia",LCML:"Chronic Myelogenous Leukemia",LGG:"Brain Lower Grade Glioma",LIHC:"Liver hepatocellular carcinoma",LUAD:"Lung adenocarcinoma",LUSC:"Lung squamous cell carcinoma",MESO:"Mesothelioma",OV:"Ovarian serous cystadenocarcinoma",PAAD:"Pancreatic adenocarcinoma",PCPG:"Pheochromocytoma and Paraganglioma",PRAD:"Prostate adenocarcinoma",READ:"Rectum adenocarcinoma",SARC:"Sarcoma",SKCM:"Skin Cutaneous Melanoma",STAD:"Stomach adenocarcinoma",STES:"Stomach and Esophageal Carcinoma",TGCT:"Testicular Germ Cell Tumors",THCA:"Thyroid carcinoma",THYM:"Thymoma",UCEC:"Uterine Corpus Endometrial Carcinoma",UCS:"Uterine Carcinosarcoma",UVM:"Uveal Melanoma"};morpheus.TcgaUtil.SAMPLE_TYPES={"01":"Primary solid Tumor","02":"Recurrent Solid Tumor","03":"Primary Blood Derived Cancer - Peripheral Blood","04":"Recurrent Blood Derived Cancer - Bone Marrow","05":"Additional - New Primary","06":"Metastatic","07":"Additional Metastatic","08":"Human Tumor Original Cells","09":"Primary Blood Derived Cancer - Bone Marrow",10:"Blood Derived Normal",11:"Solid Tissue Normal",12:"Buccal Cell Normal",13:"EBV Immortalized Normal",14:"Bone Marrow Normal",20:"Control Analyte",40:"Recurrent Blood Derived Cancer - Peripheral Blood",50:"Cell Lines",60:"Primary Xenograft Tissue",61:"Cell Line Derived Xenograft Tissue"};morpheus.TcgaUtil.barcode=function(s){var tokens=s.split("-");var id=tokens[2];var sampleType;if(tokens.length>3){sampleType=tokens[3];if(sampleType.length>2){sampleType=sampleType.substring(0,2)}sampleType=morpheus.TcgaUtil.SAMPLE_TYPES[sampleType]}else{sampleType=morpheus.TcgaUtil.SAMPLE_TYPES["01"]}return{id:id.toLowerCase(),sampleType:sampleType}};morpheus.TcgaUtil.setIdAndSampleType=function(dataset){var idVector=dataset.getColumnMetadata().get(0);var participantId=dataset.getColumnMetadata().add("participant_id");var sampleType=dataset.getColumnMetadata().add("sample_type");for(var i=0,size=idVector.size();i<size;i++){var barcode=morpheus.TcgaUtil.barcode(idVector.getValue(i));idVector.setValue(i,barcode.id+"-"+barcode.sampleType);sampleType.setValue(i,barcode.sampleType);participantId.setValue(i,barcode.id)}};morpheus.TcgaUtil.getDataset=function(options){var promises=[];var datasets=[];var returnDeferred=$.Deferred();if(options.mrna){var mrna=$.Deferred();promises.push(mrna);(new morpheus.TxtReader).read(options.mrna,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}mrna.resolve()})}var sigGenesLines;if(options.mutation){var mutation=$.Deferred();promises.push(mutation);(new morpheus.MafFileReader).read(options.mutation,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}mutation.resolve()});var sigGenesAnnotation=morpheus.Util.readLines(options.sigGenes);sigGenesAnnotation.done(function(lines){sigGenesLines=lines});promises.push(sigGenesAnnotation)}if(options.gistic){var gistic=$.Deferred();promises.push(gistic);(new morpheus.GisticReader).read(options.gistic,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}gistic.resolve()})}if(options.gisticGene){var gisticGene=$.Deferred();promises.push(gisticGene);new morpheus.TxtReader({dataColumnStart:3}).read(options.gisticGene,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}gisticGene.resolve()})}if(options.seg){var seg=$.Deferred();promises.push(seg);(new morpheus.SegTabReader).read(options.seg,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}seg.resolve()})}if(options.rppa){var rppa=$.Deferred();promises.push(rppa);new morpheus.TxtReader({dataColumnStart:2}).read(options.rppa,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}rppa.resolve()})}if(options.methylation){var methylation=$.Deferred();promises.push(methylation);new morpheus.TxtReader({}).read(options.methylation,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}methylation.resolve()})}var mrnaClustPromise=morpheus.Util.readLines(options.mrnaClust);promises.push(mrnaClustPromise);var sampleIdToClusterId;mrnaClustPromise.done(function(lines){sampleIdToClusterId=new morpheus.Map;var lineNumber=0;while(lines[lineNumber].indexOf("SampleName")!==-1){lineNumber++}var tab=/\t/;for(;lineNumber<lines.length;lineNumber++){var tokens=lines[lineNumber].split(tab);var barcode=morpheus.TcgaUtil.barcode(tokens[0]);sampleIdToClusterId.set(barcode.id+"-"+barcode.sampleType,tokens[1])}});var annotationCallbacks=[];var annotationDef=null;if(options.columnAnnotations){annotationDef=morpheus.DatasetUtil.annotate({annotations:options.columnAnnotations,isColumns:true});promises.push(annotationDef);annotationDef.done(function(array){annotationCallbacks=array})}$.when.apply($,promises).then(function(){var datasetToReturn=null;if(datasets.length===1){var sourceName=datasets[0].getName();var sourceVector=datasets[0].getRowMetadata().add("Source");for(var i=0;i<sourceVector.size();i++){sourceVector.setValue(i,sourceName)}datasetToReturn=datasets[0]}else{var maxIndex=0;var maxColumns=datasets[0].getColumnCount();for(var i=1;i<datasets.length;i++){if(datasets[i].getColumnCount()>maxColumns){maxColumns=datasets[i].getColumnCount();maxIndex=i}if(datasets[i].getName()==="mutations_merged.maf"){maxColumns=Number.MAX_VALUE;maxIndex=i}}var datasetIndices=[];datasetIndices.push(maxIndex);for(var i=0;i<datasets.length;i++){if(i!==maxIndex){datasetIndices.push(i)}}var joined=new morpheus.JoinedDataset(datasets[datasetIndices[0]],datasets[datasetIndices[1]],"id","id");for(var i=2;i<datasetIndices.length;i++){joined=new morpheus.JoinedDataset(joined,datasets[datasetIndices[i]],"id","id")}datasetToReturn=joined}var clusterIdVector=datasetToReturn.getColumnMetadata().add("mRNAseq_cluster");var idVector=datasetToReturn.getColumnMetadata().getByName("id");for(var j=0,size=idVector.size();j<size;j++){clusterIdVector.setValue(j,sampleIdToClusterId.get(idVector.getValue(j)))}if(options.mutation){var sourceToIndices=morpheus.VectorUtil.createValueToIndicesMap(datasetToReturn.getRowMetadata().getByName("Source"));var mutationDataset=new morpheus.SlicedDatasetView(datasetToReturn,sourceToIndices.get("mutations_merged.maf"));(new morpheus.OpenFileTool).annotate(sigGenesLines,mutationDataset,false,null,"id","gene",["q"]);var qVector=mutationDataset.getRowMetadata().getByName("q");var qValueVector=mutationDataset.getRowMetadata().getByName("q_value");if(qValueVector==null){qValueVector=mutationDataset.getRowMetadata().add("q_value")}for(var i=0,size=qValueVector.size();i<size;i++){qValueVector.setValue(i,qVector.getValue(i))}mutationDataset.getRowMetadata().remove(morpheus.MetadataUtil.indexOf(mutationDataset.getRowMetadata(),"q"))}if(annotationDef){annotationCallbacks.forEach(function(f){f(datasetToReturn)})}returnDeferred.resolve(datasetToReturn)});return returnDeferred};morpheus.TxtReader=function(options){if(options==null){options={}}this.options=options};morpheus.TxtReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}catch(x){callback(x)}}})},_read:function(datasetName,reader){var dataColumnStart=this.options.dataColumnStart;var dataRowStart=this.options.dataRowStart;if(dataRowStart==null){dataRowStart=1}var tab=/\t/;var header=reader.readLine().trim().split(tab);if(dataRowStart>1){for(var i=1;i<dataRowStart;i++){reader.readLine()}}var testLine=null;if(dataColumnStart==null){testLine=reader.readLine().trim();var tokens=testLine.split(tab);for(var i=1;i<tokens.length;i++){var token=tokens[i];if(token===""||token==="NA"||token==="NaN"||$.isNumeric(token)){dataColumnStart=i;break}}if(dataColumnStart==null){dataColumnStart=1}}var ncols=header.length-dataColumnStart;var matrix=[];var s;var arrayOfRowArrays=[];for(var i=0;i<dataColumnStart;i++){arrayOfRowArrays.push([])}if(testLine!=null){var array=new Float32Array(ncols);matrix.push(array);var tokens=testLine.split(tab);for(var j=0;j<dataColumnStart;j++){arrayOfRowArrays[j].push(morpheus.Util.copyString(tokens[j]))}for(var j=dataColumnStart,k=0;k<ncols;j++,k++){var token=tokens[j];array[j-dataColumnStart]=parseFloat(token)}}while((s=reader.readLine())!==null){s=s.trim();if(s!==""){var array=new Float32Array(ncols);matrix.push(array);var tokens=s.split(tab);for(var j=0;j<dataColumnStart;j++){arrayOfRowArrays[j].push(morpheus.Util.copyString(tokens[j]))}for(var j=dataColumnStart,k=0;k<ncols;j++,k++){var token=tokens[j];array[j-dataColumnStart]=parseFloat(token)}}}var dataset=new morpheus.Dataset({name:datasetName,rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});var columnIds=dataset.getColumnMetadata().add("id");for(var i=0,j=dataColumnStart;i<ncols;i++,j++){columnIds.setValue(i,morpheus.Util.copyString(header[j]))}var rowIdVector=dataset.getRowMetadata().add("id");rowIdVector.array=arrayOfRowArrays[0];for(var i=1;i<dataColumnStart;i++){var v=dataset.getRowMetadata().add(header[i]);v.array=arrayOfRowArrays[i]}return dataset}};morpheus.XlsxDatasetReader=function(){};morpheus.XlsxDatasetReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{var data=new Uint8Array(arrayBuffer);var arr=[];for(var i=0;i!=data.length;++i){arr[i]=String.fromCharCode(data[i])}var bstr=arr.join("");_this._read(name,bstr,callback)}catch(x){callback(x)}}})},_read:function(datasetName,bstr,callback){morpheus.Util.xlsxTo2dArray({data:bstr},function(err,lines){var nrows=lines.length-1;var header=lines[0];var ncols=header.length-1;var dataset=new morpheus.Dataset({name:datasetName,rows:nrows,columns:ncols});var columnIds=dataset.getColumnMetadata().add("id");for(var j=1;j<=ncols;j++){columnIds.setValue(j-1,header[j])}var rowIds=dataset.getRowMetadata().add("id");for(var i=1;i<lines.length;i++){var tokens=lines[i];rowIds.setValue(i-1,tokens[0]);for(var j=1;j<=ncols;j++){var token=tokens[j];var value=parseFloat(token);dataset.setValue(i-1,j-1,value)}}callback(null,dataset)})}};morpheus.VectorAdapter=function(v){if(v==null){throw"vector is null"}this.v=v};morpheus.VectorAdapter.prototype={setValue:function(i,value){this.v.setValue(i,value)},getValue:function(i){return this.v.getValue(i)},getProperties:function(){return this.v.getProperties()},size:function(){return this.v.size()},getName:function(){return this.v.getName()},setName:function(name){this.v.setName(name)}};morpheus.AbstractDataset=function(rows,columns){this.seriesNames=[];this.seriesArrays=[];this.seriesDataTypes=[];this.rows=rows;this.columns=columns;this.rowMetadataModel=new morpheus.MetadataModel(rows);this.columnMetadataModel=new morpheus.MetadataModel(columns)};morpheus.AbstractDataset.prototype={setRowMetadata:function(metadata){this.rowMetadataModel=metadata},setColumnMetadata:function(metadata){this.columnMetadataModel=metadata},getName:function(seriesIndex){return this.seriesNames[seriesIndex||0]},setName:function(seriesIndex,name){this.seriesNames[seriesIndex||0]=name},getRowMetadata:function(){return this.rowMetadataModel},getColumnMetadata:function(){return this.columnMetadataModel},getRowCount:function(){return this.rows},getColumnCount:function(){return this.columns},getValue:function(rowIndex,columnIndex,seriesIndex){},setValue:function(rowIndex,columnIndex,value,seriesIndex){},addSeries:function(options){},removeSeries:function(seriesIndex){this.seriesArrays.splice(seriesIndex,1);this.seriesNames.splice(seriesIndex,1);this.seriesDataTypes.splice(seriesIndex,1)},getSeriesCount:function(){return this.seriesArrays.length},getDataType:function(seriesIndex){return this.seriesDataTypes[seriesIndex||0]},toString:function(){return this.getName()}};morpheus.AbstractVector=function(name,size){this.name=name;this.n=size;this.properties=new morpheus.Map};morpheus.AbstractVector.prototype={getValue:function(index){throw new Error("Not implemented")},getProperties:function(){return this.properties},size:function(){return this.n},getName:function(){return this.name}};morpheus.SignalToNoise=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var s1=Math.sqrt(morpheus.Variance(list1,m1));var s2=Math.sqrt(morpheus.Variance(list2,m2));return(m1-m2)/(s1+s2)};morpheus.SignalToNoise.toString=function(){return"Signal to noise"};morpheus.createSignalToNoiseAdjust=function(percent){percent=percent||.2;var f=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var s1=Math.sqrt(morpheus.Variance(list1,m1));var s2=Math.sqrt(morpheus.Variance(list2,m2));s1=morpheus.SignalToNoise.thresholdStandardDeviation(m1,s1,percent);s2=morpheus.SignalToNoise.thresholdStandardDeviation(m2,s2,percent);return(m1-m2)/(s1+s2)};f.toString=function(){return"Signal to noise (adjust standard deviation)"};return f};morpheus.SignalToNoise.thresholdStandardDeviation=function(mean,standardDeviation,percent){var returnValue=standardDeviation;var absMean=Math.abs(mean);var minStdev=percent*absMean;if(minStdev>standardDeviation){returnValue=minStdev}if(returnValue<percent){returnValue=percent}return returnValue};morpheus.createContingencyTable=function(listOne,listTwo,groupingValue){if(groupingValue==null||isNaN(groupingValue)){groupingValue=1}var aHit=0;var aMiss=0;for(var j=0,size=listOne.size();j<size;j++){var val=listOne.getValue(j);if(!isNaN(val)){if(val>=groupingValue){aHit++}else{aMiss++}}}var bHit=0;var bMiss=0;for(var j=0,size=listTwo.size();j<size;j++){var val=listTwo.getValue(j);if(!isNaN(val)){if(val>=groupingValue){bHit++}else{bMiss++}}}var N=aHit+aMiss+bHit+bMiss;var K=aHit+bHit;var n=aHit+aMiss;var k=aHit;var a=k;var b=K-k;var c=n-k;var d=N+k-n-K;return[a,b,c,d]};morpheus.FisherExact=function(listOne,listTwo){var abcd=morpheus.createContingencyTable(listOne,listTwo,1);return morpheus.FisherExact.fisherTest(abcd[0],abcd[1],abcd[2],abcd[3])};morpheus.createFisherExact=function(groupingValue){var f=function(listOne,listTwo){var abcd=morpheus.createContingencyTable(listOne,listTwo,groupingValue);return morpheus.FisherExact.fisherTest(abcd[0],abcd[1],abcd[2],abcd[3])};return f};morpheus.FisherExact.phyper=function(a,b,c,d){return Math.exp(morpheus.FisherExact.logFactorial(a+b)+morpheus.FisherExact.logFactorial(c+d)+morpheus.FisherExact.logFactorial(a+c)+morpheus.FisherExact.logFactorial(b+d)-(morpheus.FisherExact.logFactorial(a)+morpheus.FisherExact.logFactorial(b)+morpheus.FisherExact.logFactorial(c)+morpheus.FisherExact.logFactorial(d)+morpheus.FisherExact.logFactorial(a+b+c+d)))};morpheus.FisherExact.logFactorials=[0,0,.6931471805599453,1.791759469228055,3.1780538303479458,4.787491742782046,6.579251212010101,8.525161361065415,10.60460290274525,12.801827480081469,15.104412573075516,17.502307845873887,19.987214495661885,22.552163853123425,25.19122118273868,27.89927138384089,30.671860106080672,33.50507345013689,36.39544520803305,39.339884187199495,42.335616460753485,45.38013889847691,48.47118135183523,51.60667556776438,54.78472939811232,58.00360522298052,61.261701761002,64.55753862700634,67.88974313718154,71.25703896716801];morpheus.FisherExact.logFactorial=function(k){if(k>=30){var C0=.9189385332046728;var C1=.08333333333333333;var C3=-.002777777777777778;var C5=.0007936507936507937;var C7=-.0005952380952380953;var r=1/k;var rr=r*r;return(k+.5)*Math.log(k)-k+C0+r*(C1+rr*(C3+rr*(C5+rr*C7)))}return morpheus.FisherExact.logFactorials[k]};morpheus.FisherExact.fisherTest=function(a,b,c,d){var p=morpheus.FisherExact.phyper(a,b,c,d);var sum=p;for(var _a=0,n=a+b+c+d;_a<=n;_a++){var _b=a+b-_a;var _c=a+c-_a;var _d=b+d-_b;if(_a!==a&&_b>=0&&_c>=0&&_d>=0){var _p=morpheus.FisherExact.phyper(_a,_b,_c,_d);if(_p<=p){sum+=_p}}}return Math.min(1,sum)};morpheus.FisherExact.toString=function(){return"Fisher Exact Test"};morpheus.FoldChange=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);return m1/m2};morpheus.FoldChange.toString=function(){return"Fold Change"};morpheus.MeanDifference=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var diff=m1-m2;return diff};morpheus.MeanDifference.toString=function(){return"Mean Difference"};morpheus.TTest=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var s1=Math.sqrt(morpheus.Variance(list1,m1));var s2=Math.sqrt(morpheus.Variance(list2,m2));var n1=morpheus.CountNonNaN(list1);var n2=morpheus.CountNonNaN(list2);return(m1-m2)/Math.sqrt(s1*s1/n1+s2*s2/n2)};morpheus.TTest.toString=function(){return"T-Test"};morpheus.DegreesOfFreedom=function(v1,v2,n1,n2){return(v1/n1+v2/n2)*(v1/n1+v2/n2)/(v1*v1/(n1*n1*(n1-1))+v2*v2/(n2*n2*(n2-1)))};morpheus.Spearman=function(list1,list2){var flist1=[];var flist2=[];for(var i=0,n=list1.size();i<n;i++){var v1=list1.getValue(i);var v2=list2.getValue(i);if(isNaN(v1)||isNaN(v2)){continue}flist1.push(v1);flist2.push(v2)}var rank1=morpheus.Ranking(flist1);var rank2=morpheus.Ranking(flist2);return morpheus.Pearson(new morpheus.Vector("",rank1.length).setArray(rank1),new morpheus.Vector("",rank2.length).setArray(rank2))};morpheus.Spearman.toString=function(){return"Spearman rank correlation"};morpheus.WeightedMean=function(weights,values){var numerator=0;var denom=0;for(var i=0,size=values.size();i<size;i++){var value=values.getValue(i);if(!isNaN(value)){var weight=Math.abs(weights.getValue(i));if(!isNaN(weight)){numerator+=weight*value;denom+=weight}}}return denom===0?NaN:numerator/denom};morpheus.WeightedMean.toString=function(){return"Weighted average"};morpheus.createOneMinusMatrixValues=function(dataset){var f=function(listOne,listTwo){return 1-dataset.getValue(listOne.getIndex(),listTwo.getIndex())};f.toString=function(){return"One minus matrix values (for a precomputed similarity matrix)"};return f};morpheus.Pearson=function(listOne,listTwo){var sumx=0;var sumxx=0;var sumy=0;var sumyy=0;var sumxy=0;var N=0;for(var i=0,size=listOne.size();i<size;i++){var x=listOne.getValue(i);var y=listTwo.getValue(i);if(isNaN(x)||isNaN(y)){continue}sumx+=x;sumxx+=x*x;sumy+=y;sumyy+=y*y;sumxy+=x*y;N++}var numr=sumxy-sumx*sumy/N;var denr=Math.sqrt((sumxx-sumx*sumx/N)*(sumyy-sumy*sumy/N));return denr==0?1:numr/denr};morpheus.Pearson.toString=function(){return"Pearson correlation"};morpheus.Jaccard=function(listOne,listTwo){var orCount=0;var andCount=0;for(var i=0,size=listOne.size();i<size;i++){var xval=listOne.getValue(i);var yval=listTwo.getValue(i);if(isNaN(xval)||isNaN(yval)){continue}var x=xval>0;var y=yval>0;if(x&&y){andCount++}else if(x||y){orCount++}}if(orCount===0){return 1}return 1-andCount/orCount};morpheus.Jaccard.toString=function(){return"Jaccard distance"};morpheus.Cosine=function(listOne,listTwo){var sumX2=0;var sumY2=0;var sumXY=0;for(var i=0,size=listOne.size();i<size;i++){var x=listOne.getValue(i);var y=listTwo.getValue(i);if(isNaN(x)||isNaN(y)){continue}sumX2+=x*x;sumY2+=y*y;sumXY+=x*y}return sumXY/Math.sqrt(sumX2*sumY2)};morpheus.Cosine.toString=function(){return"Cosine similarity"};morpheus.Euclidean=function(x,y){var dist=0;for(var i=0,size=x.size();i<size;++i){var x_i=x.getValue(i);var y_i=y.getValue(i);if(isNaN(x_i)||isNaN(y_i)){continue}dist+=(x_i-y_i)*(x_i-y_i)}return Math.sqrt(dist)};morpheus.Euclidean.toString=function(){return"Euclidean distance"};morpheus.OneMinusFunction=function(f){var dist=function(x,y){return 1-f(x,y)};dist.toString=function(){var s=f.toString();return"One minus "+s[0].toLowerCase()+s.substring(1)};return dist};morpheus.LinearRegression=function(xVector,yVector){var sumX=0;var sumY=0;var sumXX=0;var sumXY=0;var count=0;for(var i=0,size=xVector.size();i<size;i++){var x=xVector.getValue(i);var y=yVector.getValue(i);if(!isNaN(x)&&!isNaN(y)){sumX+=x;sumY+=y;sumXX+=x*x;sumXY+=x*y;count++}}var m=(count*sumXY-sumX*sumY)/(count*sumXX-sumX*sumX);var b=sumY/count-m*sumX/count;return{m:m,b:b}};morpheus.KendallsCorrelation=function(x,y){function sum(n){return n*(n+1)/2}var xArray=[];var yArray=[];for(var i=0,size=x.size();i<size;++i){var x_i=x.getValue(i);var y_i=y.getValue(i);if(isNaN(x_i)||isNaN(y_i)){continue}xArray.push(x_i);yArray.push(y_i)}var n=xArray.length;var numPairs=sum(n-1);var pairs=[];for(var i=0;i<n;i++){pairs[i]=[xArray[i],yArray[i]]}pairs.sort(function(pair1,pair2){var a=pair1[0];var b=pair2[0];var compareFirst=a===b?0:a<b?-1:1;if(compareFirst!==0){return compareFirst}a=pair1[1];b=pair2[1];return a===b?0:a<b?-1:1});var tiedXPairs=0;var tiedXYPairs=0;var consecutiveXTies=1;var consecutiveXYTies=1;var prev=pairs[0];for(var i=1;i<n;i++){var curr=pairs[i];if(curr[0]===prev[0]){consecutiveXTies++;if(curr[1]===prev[1]){consecutiveXYTies++}else{tiedXYPairs+=sum(consecutiveXYTies-1);consecutiveXYTies=1}}else{tiedXPairs+=sum(consecutiveXTies-1);consecutiveXTies=1;tiedXYPairs+=sum(consecutiveXYTies-1);consecutiveXYTies=1}prev=curr}tiedXPairs+=sum(consecutiveXTies-1);tiedXYPairs+=sum(consecutiveXYTies-1);var swaps=0;var pairsDestination=[];for(var segmentSize=1;segmentSize<n;segmentSize<<=1){for(var offset=0;offset<n;offset+=2*segmentSize){var i=offset;var iEnd=Math.min(i+segmentSize,n);var j=iEnd;var jEnd=Math.min(j+segmentSize,n);var copyLocation=offset;while(i<iEnd||j<jEnd){if(i<iEnd){if(j<jEnd){var c=pairs[i][1]===pairs[j][1]?0:pairs[i][1]<pairs[j][1]?-1:1;if(c<=0){pairsDestination[copyLocation]=pairs[i];i++}else{pairsDestination[copyLocation]=pairs[j];j++;swaps+=iEnd-i}}else{pairsDestination[copyLocation]=pairs[i];i++}}else{pairsDestination[copyLocation]=pairs[j];j++}copyLocation++}}var pairsTemp=pairs;pairs=pairsDestination;pairsDestination=pairsTemp}var tiedYPairs=0;var consecutiveYTies=1;prev=pairs[0];for(var i=1;i<n;i++){var curr=pairs[i];if(curr[1]===prev[1]){consecutiveYTies++}else{tiedYPairs+=sum(consecutiveYTies-1);consecutiveYTies=1}prev=curr}tiedYPairs+=sum(consecutiveYTies-1);var concordantMinusDiscordant=numPairs-tiedXPairs-tiedYPairs+tiedXYPairs-2*swaps;var nonTiedPairsMultiplied=(numPairs-tiedXPairs)*(numPairs-tiedYPairs);return concordantMinusDiscordant/Math.sqrt(nonTiedPairsMultiplied)};morpheus.KendallsCorrelation.toString=function(){return"Kendall's correlation"};morpheus.ComputedVector=function(name,size,callback){morpheus.AbstractVector.call(this,name,size);this.callback=callback};morpheus.ComputedVector.prototype={getValue:function(index){return this.callback(index)}};morpheus.Util.extend(morpheus.ComputedVector,morpheus.AbstractVector);morpheus.DatasetAdapter=function(dataset,rowMetadata,columnMetadata){if(dataset==null){throw"dataset is null"}this.dataset=dataset;this.rowMetadata=rowMetadata||dataset.getRowMetadata();this.columnMetadata=columnMetadata||dataset.getColumnMetadata()};morpheus.DatasetAdapter.prototype={getDataset:function(){return this.dataset},getName:function(seriesIndex){return this.dataset.getName(seriesIndex)},setName:function(seriesIndex,name){this.dataset.setName(seriesIndex,name)},getRowMetadata:function(){return this.rowMetadata},getColumnMetadata:function(){return this.columnMetadata},getRowCount:function(){return this.dataset.getRowCount()},getColumnCount:function(){return this.dataset.getColumnCount()},getValue:function(rowIndex,columnIndex,seriesIndex){return this.dataset.getValue(rowIndex,columnIndex,seriesIndex)},setValue:function(rowIndex,columnIndex,value,seriesIndex){this.dataset.setValue(rowIndex,columnIndex,value,seriesIndex)},addSeries:function(options){return this.dataset.addSeries(options)},removeSeries:function(seriesIndex){this.dataset.removeSeries(seriesIndex)},getSeriesCount:function(){return this.dataset.getSeriesCount()},getDataType:function(seriesIndex){return this.dataset.getDataType(seriesIndex)},toString:function(){return this.dataset.toString()}};morpheus.DatasetColumnView=function(dataset){this.dataset=dataset;this.columnIndex=0;this.seriesIndex=0};morpheus.DatasetColumnView.prototype={columnIndex:-1,size:function(){return this.dataset.getRowCount()},getValue:function(rowIndex){return this.dataset.getValue(rowIndex,this.columnIndex,this.seriesIndex)},setIndex:function(newColumnIndex){this.columnIndex=newColumnIndex;return this},setSeriesIndex:function(seriesIndex){this.seriesIndex=seriesIndex;return this}};morpheus.DatasetRowView=function(dataset){this.dataset=dataset;this.index=0;this.seriesIndex=0};morpheus.DatasetRowView.prototype={size:function(){return this.dataset.getColumnCount()},getIndex:function(){return this.index},getValue:function(columnIndex){return this.dataset.getValue(this.index,columnIndex,this.seriesIndex)},setIndex:function(newRowIndex){this.index=newRowIndex;return this},setSeriesIndex:function(seriesIndex){this.seriesIndex=seriesIndex;return this},setDataset:function(dataset){this.dataset=dataset;return this}};morpheus.DatasetSeriesView=function(dataset,seriesIndices){morpheus.DatasetAdapter.call(this,dataset);this.seriesIndices=seriesIndices};morpheus.DatasetSeriesView.prototype={getValue:function(i,j,seriesIndex){seriesIndex=seriesIndex||0;return this.dataset.getValue(i,j,this.seriesIndices[seriesIndex])},setValue:function(i,j,value,seriesIndex){seriesIndex=seriesIndex||0;this.dataset.setValue(i,j,value,this.seriesIndices[seriesIndex])},getName:function(seriesIndex){seriesIndex=seriesIndex||0;return this.dataset.getName(this.seriesIndices[seriesIndex])},setName:function(seriesIndex,name){seriesIndex=seriesIndex||0;this.dataset.setName(this.seriesIndices[seriesIndex],name)},addSeries:function(options){var index=this.dataset.addSeries(options);this.seriesIndices.push(index);return index},getSeriesCount:function(){return this.seriesIndices.length},toString:function(){return this.getName()}};morpheus.Util.extend(morpheus.DatasetSeriesView,morpheus.DatasetAdapter);morpheus.DatasetUtil=function(){};morpheus.DatasetUtil.min=function(dataset,seriesIndex){seriesIndex=seriesIndex||0;var min=Number.MAX_VALUE;for(var i=0,rows=dataset.getRowCount();i<rows;i++){for(var j=0,columns=dataset.getColumnCount();j<columns;j++){var d=dataset.getValue(i,j,seriesIndex);if(isNaN(d)){continue}min=Math.min(min,d)}}return min};morpheus.DatasetUtil.slicedView=function(dataset,rows,columns){return new morpheus.SlicedDatasetView(dataset,rows,columns)};morpheus.DatasetUtil.transposedView=function(dataset){return dataset instanceof morpheus.TransposedDatasetView?dataset.getDataset():new morpheus.TransposedDatasetView(dataset)};morpheus.DatasetUtil.max=function(dataset,seriesIndex){seriesIndex=seriesIndex||0;var max=-Number.MAX_VALUE;for(var i=0,rows=dataset.getRowCount();i<rows;i++){for(var j=0,columns=dataset.getColumnCount();j<columns;j++){var d=dataset.getValue(i,j,seriesIndex);if(isNaN(d)){continue}max=Math.max(max,d)}}return max};morpheus.DatasetUtil.getDatasetReader=function(ext,options){if(options==null){options={}}var datasetReader=null;if(ext==="maf"){datasetReader=new morpheus.MafFileReader;if(options&&options.mafGeneFilter){datasetReader.setGeneFilter(options.mafGeneFilter)}}else if(ext==="gct"){datasetReader=new morpheus.GctReader}else if(ext==="gmt"){datasetReader=new morpheus.GmtDatasetReader}else if(ext==="xlsx"||ext==="xls"){datasetReader=options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.XlsxDatasetReader}else if(ext==="segtab"||ext==="seg"){datasetReader=new morpheus.SegTabReader;if(options&&options.regions){datasetReader.setRegions(options.regions)}}else if(ext==="txt"||ext==="tsv"||ext==="csv"){datasetReader=options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.TxtReader}else if(ext==="json"){datasetReader=new morpheus.JsonDatasetReader}else if(ext==="gct"){datasetReader=new morpheus.GctReader}return datasetReader};morpheus.DatasetUtil.readDatasetArray=function(datasets){var retDef=$.Deferred();var loadedDatasets=[];var promises=[];_.each(datasets,function(url,i){var p=morpheus.DatasetUtil.read(url);p.index=i;p.done(function(dataset){loadedDatasets[this.index]=dataset});p.fail(function(err){var message=["Error opening "+morpheus.Util.getFileName(url)+"."];if(err.message){message.push("<br />Cause: ");message.push(err.message)}retDef.reject(message.join(""))});promises.push(p)});if(promises.length===0){retDef.reject("No datasets specified.")}$.when.apply($,promises).then(function(){retDef.resolve(morpheus.DatasetUtil.join(loadedDatasets,"id"))});return retDef};morpheus.DatasetUtil.annotate=function(options){var retDef=$.Deferred();var promises=[];var functions=[];var isColumns=options.isColumns;_.each(options.annotations,function(ann,annotationIndex){if(morpheus.Util.isArray(ann.file)){functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotate(ann.file,dataset,isColumns,null,ann.datasetField,ann.fileField,ann.include)}}else{var result=morpheus.Util.readLines(ann.file);var fileName=morpheus.Util.getFileName(ann.file);var deferred=$.Deferred();promises.push(deferred);result.fail(function(message){deferred.reject(message)});result.done(function(lines){if(morpheus.Util.endsWith(fileName,".gmt")){var sets=(new morpheus.GmtReader).parseLines(lines);functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotate(null,dataset,isColumns,sets,ann.datasetField,ann.fileField)};deferred.resolve()}else if(morpheus.Util.endsWith(fileName,".cls")){functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotateCls(null,dataset,fileName,isColumns,lines)};deferred.resolve()}else{functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotate(lines,dataset,isColumns,null,ann.datasetField,ann.fileField,ann.include,ann.transposed)};deferred.resolve()}})}});$.when.apply($,promises).then(function(){retDef.resolve(functions)});return retDef};morpheus.DatasetUtil.read=function(fileOrUrl,options){if(fileOrUrl==null){throw"File is null"}if(options==null){options={}}var isFile=morpheus.Util.isFile(fileOrUrl);var isString=morpheus.Util.isString(fileOrUrl);var ext=options.extension?options.extension:morpheus.Util.getExtension(morpheus.Util.getFileName(fileOrUrl));var datasetReader;var str=fileOrUrl.toString();if(ext===""&&str!=null&&str.indexOf("blob:")===0){datasetReader=options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.TxtReader}else{datasetReader=morpheus.DatasetUtil.getDatasetReader(ext,options);if(datasetReader==null){datasetReader=isFile?options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.TxtReader:new morpheus.GctReader}}if(isString||isFile){var deferred=$.Deferred();if(options.background){var path=morpheus.Util.getScriptPath();var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.path);"+"var ext = morpheus.Util.getExtension(morpheus.Util"+".getFileName(e.data.fileOrUrl));"+"var datasetReader = morpheus.DatasetUtil.getDatasetReader(ext,"+"\te.data.options);"+"datasetReader.read(e.data.fileOrUrl, function(err,dataset) {"+"\tself.postMessage(dataset);"+"\t});"+"}"]);var blobURL=window.URL.createObjectURL(blob);var worker=new Worker(blobURL);worker.addEventListener("message",function(e){deferred.resolve(morpheus.Dataset.fromJSON(e.data));window.URL.revokeObjectURL(blobURL)},false);worker.postMessage({path:path,fileOrUrl:fileOrUrl,options:options})}else{datasetReader.read(fileOrUrl,function(err,dataset){if(err){deferred.reject(err)}else{deferred.resolve(dataset)}})}var pr=deferred.promise();pr.toString=function(){return""+fileOrUrl};return pr}else if(typeof fileOrUrl.done==="function"){return fileOrUrl}else{if(fileOrUrl.promise){return fileOrUrl}var deferred=$.Deferred();if(fileOrUrl.getRowCount){deferred.resolve(fileOrUrl)}else{deferred.resolve(morpheus.Dataset.fromJSON(fileOrUrl))}return deferred.promise()}};morpheus.DatasetUtil.toObjectArray=function(dataset,options){var columns=options.columns||[0];var columnFields=options.columnFields||["value"];if(columnFields.length!==columns.length){throw"columns.length !== columnFields.length"}var metadataFields=options.metadataFields;var rowMetadata=dataset.getRowMetadata();if(!metadataFields){metadataFields=morpheus.MetadataUtil.getMetadataNames(rowMetadata)}var vectors=morpheus.MetadataUtil.getVectors(rowMetadata,metadataFields);var array=[];for(var i=0;i<dataset.getRowCount();i++){var obj={};for(var j=0;j<columns.length;j++){obj[columnFields[j]]=dataset.getValue(i,columns[j])}for(var j=0;j<vectors.length;j++){obj[vectors[j].getName()]=vectors[j].getValue(i)}array.push(obj)}return array};morpheus.DatasetUtil.fixL1K=function(dataset){var names={cell_id:"Cell Line",pert_idose:"Dose (µM)",pert_iname:"Name",pert_itime:"Time (hr)",distil_ss:"Signature Strength",pert_type:"Type",cell_lineage:"Lineage",cell_histology:"Histology",cell_type:"Cell Type"};var fixNames=function(metadata){for(var i=0,count=metadata.getMetadataCount();i<count;i++){var v=metadata.get(i);var name=v.getName();var mapped=names[name];if(mapped){v.setName(mapped)}}};fixNames(dataset.getRowMetadata());fixNames(dataset.getColumnMetadata());var fix666=function(metadata){for(var i=0,count=metadata.getMetadataCount();i<count;i++){var v=metadata.get(i);if(v.getName()=="Dose (µM)"){for(var j=0,size=v.size();j<size;j++){var value=v.getValue(j);if(value!=null){v.setValue(j,parseFloat(value))}}}var isNumber=false;for(var j=0,size=v.size();j<size;j++){var value=v.getValue(j);if(value!=null){isNumber=_.isNumber(value);break}}var newValue=isNumber||v.getName()=="Dose (µM)"?0:"";for(var j=0,size=v.size();j<size;j++){var value=v.getValue(j);if(value!=null&&value=="-666"){v.setValue(j,newValue)}}}};fix666(dataset.getRowMetadata());fix666(dataset.getColumnMetadata());var fixCommas=function(metadata){var regex=/(,)([^ ])/g;_.each(["Lineage","Histology"],function(name){var v=metadata.getByName(name);if(v!=null){for(var i=0,size=v.size();i<size;i++){var val=v.getValue(i);if(val){v.setValue(i,val.replace(regex,", $2"))}}}})};fixCommas(dataset.getRowMetadata());fixCommas(dataset.getColumnMetadata())};morpheus.DatasetUtil.geneSetsToDataset=function(name,sets){var uniqueIds=new morpheus.Map;for(var i=0,length=sets.length;i<length;i++){var ids=sets[i].ids;for(var j=0,nIds=ids.length;j<nIds;j++){uniqueIds.set(ids[j],1)}}var uniqueIdsArray=uniqueIds.keys();var dataset=new morpheus.Dataset({name:name,rows:uniqueIdsArray.length,columns:sets.length});var columnIds=dataset.getColumnMetadata().add("id");for(var i=0,length=sets.length;i<length;i++){columnIds.setValue(i,sets[i].name)}var rowIds=dataset.getRowMetadata().add("id");for(var i=0,size=uniqueIdsArray.length;i<size;i++){rowIds.setValue(i,uniqueIdsArray[i])}var rowIdToIndex=morpheus.VectorUtil.createValueToIndexMap(rowIds);for(var i=0,length=sets.length;i<length;i++){var ids=sets[i].ids;for(var j=0,nIds=ids.length;j<nIds;j++){dataset.setValue(rowIdToIndex.get(ids[j]),i,1)}}return dataset};morpheus.DatasetUtil.getRootDataset=function(dataset){while(dataset.getDataset){dataset=dataset.getDataset()}return dataset};morpheus.DatasetUtil.getSeriesIndex=function(dataset,name){for(var i=0,nseries=dataset.getSeriesCount();i<nseries;i++){if(name===dataset.getName(i)){return i}}return-1};morpheus.DatasetUtil.getSeriesNames=function(dataset){var names=[];for(var i=0,nseries=dataset.getSeriesCount();i<nseries;i++){names.push(dataset.getName(i))}return names};morpheus.DatasetUtil.searchValues=function(options){if(text===""){return}var dataset=options.dataset;var text=options.text;var tokens=morpheus.Util.getAutocompleteTokens(text);if(tokens.length==0){return}var predicates=morpheus.Util.createSearchPredicates({tokens:tokens,defaultMatchMode:options.defaultMatchMode});var matchAllPredicates=options.matchAllPredicates===true;var npredicates=predicates.length;var viewIndices=new morpheus.Set;function isMatch(object,toObject,predicate){if(object!=null){if(toObject){var filterColumnName=predicate.getField();if(filterColumnName!=null){var value=object[filterColumnName];return predicate.accept(value)}else{for(var name in object){var value=object[name];return predicate.accept(value)}}}else{var filterColumnName=predicate.getField();if(filterColumnName==null||filterColumnName===dataset.getName(k)){return predicate.accept(object)}}}}for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var matches=false;itemSearch:if(matchAllPredicates){matches=true;for(var p=0;p<npredicates;p++){var predicate=predicates[p];var pmatch=false;for(var k=0,nseries=dataset.getSeriesCount();k<nseries;k++){var element=dataset.getValue(i,j,k);var isObject=element!=null&&element.toObject!=null;if(isObject){element=element.toObject()}if(isMatch(element,isObject,predicate)){pmatch=true;break}}if(!pmatch){matches=false;break itemSearch}}}else{for(var k=0,nseries=dataset.getSeriesCount();k<nseries;k++){var element=dataset.getValue(i,j,k);var isObject=element!=null&&element.toObject!=null;if(isObject){element=element.toObject()}for(var p=0;p<npredicates;p++){var predicate=predicates[p];if(isMatch(element,isObject,predicate)){matches=true;break itemSearch}}}}if(matches){viewIndices.add(new morpheus.Identifier([i,j]))}}}return viewIndices};morpheus.DatasetUtil.autocompleteValues=function(dataset){return function(tokens,cb){var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);var seriesIndices=[];for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var k=0,nseries=dataset.getSeriesCount();k<nseries;k++){if(dataset.getDataType(i,k)==="Number"){seriesIndices.push([i,k])}}}if(seriesIndices.length===0){return cb()}var _val;elementSearch:for(var k=0,nseries=seriesIndices.length;k<nseries;k++){var pair=seriesIndices[k];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var element=dataset.getValue(pair[0],j,pair[1]);if(element!=null&&element.toObject){_val=element.toObject();break elementSearch}}}var matches=[];var fields=_val==null?[]:_.keys(_val);if(token===""){fields.sort(function(a,b){return a===b?0:a<b?-1:1});fields.forEach(function(field){matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})});return cb(matches)}var field=null;var semi=token.indexOf(":");if(semi>0){if(token.charCodeAt(semi-1)!==92){var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[token.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}var index=fields.indexOf(possibleField);if(index!==-1){token=$.trim(token.substring(semi+1));field=possibleField}}}var set=new morpheus.Set;var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");var max=10;loop:for(var k=0,nseries=seriesIndices.length;k<nseries;k++){var pair=seriesIndices[k];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var element=dataset.getValue(pair[0],j,pair[1]);if(element&&element.toObject){var object=element.toObject();if(field!==null){var val=object[field];if(val!=null){var id=new morpheus.Identifier([val,field]);if(!set.has(id)&&regex.test(val)){set.add(id);if(set.size()===max){break loop}}}}else{for(var name in object){var val=object[name];var id=new morpheus.Identifier([val,name]);if(!set.has(id)&&regex.test(val)){set.add(id);if(set.size()===max){break loop}}}}}}}set.forEach(function(id){var array=id.getArray();var field=array[1];var val=array[0];matches.push({value:field+":"+val,label:'<span style="font-weight:300;">'+field+":</span>"+'<span style="font-weight:900;">'+val+"</span>"})});if(field==null){fields.forEach(function(field){if(regex.test(field)){matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})}})}cb(matches)}};morpheus.DatasetUtil.fill=function(dataset,value,seriesIndex){seriesIndex=seriesIndex||0;for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){dataset.setValue(i,j,value,seriesIndex)}}};morpheus.DatasetUtil.overlay=function(options){var dataset=options.dataset;var newDataset=options.newDataset;var current_dataset_row_annotation_name=options.rowAnnotationName;var current_dataset_column_annotation_name=options.columnAnnotationName;var new_dataset_row_annotation_name=options.newRowAnnotationName;var new_dataset_column_annotation_name=options.newColumnAnnotationName;var rowValueToIndexMap=morpheus.VectorUtil.createValueToIndexMap(dataset.getRowMetadata().getByName(current_dataset_row_annotation_name));var columnValueToIndexMap=morpheus.VectorUtil.createValueToIndexMap(dataset.getColumnMetadata().getByName(current_dataset_column_annotation_name));var seriesIndex=dataset.addSeries({name:newDataset.getName(),dataType:newDataset.getDataType(0)});var rowVector=newDataset.getRowMetadata().getByName(new_dataset_row_annotation_name);var rowIndices=[];var newDatasetRowIndicesSubset=[];for(var i=0,size=rowVector.size();i<size;i++){var index=rowValueToIndexMap.get(rowVector.getValue(i));if(index!==undefined){rowIndices.push(index);newDatasetRowIndicesSubset.push(i)}}var columnVector=newDataset.getColumnMetadata().getByName(new_dataset_column_annotation_name);var columnIndices=[];var newDatasetColumnIndicesSubset=[];for(var i=0,size=columnVector.size();i<size;i++){var index=columnValueToIndexMap.get(columnVector.getValue(i));if(index!==undefined){columnIndices.push(index);newDatasetColumnIndicesSubset.push(i)}}newDataset=new morpheus.SlicedDatasetView(newDataset,newDatasetRowIndicesSubset,newDatasetColumnIndicesSubset);for(var i=0,nrows=newDataset.getRowCount();i<nrows;i++){for(var j=0,ncols=newDataset.getColumnCount();j<ncols;j++){dataset.setValue(rowIndices[i],columnIndices[j],newDataset.getValue(i,j),seriesIndex)}}};morpheus.DatasetUtil.join=function(datasets,field){if(datasets.length===0){throw"No datasets"}if(datasets.length===1){var name=datasets[0].getName();var sourceVector=datasets[0].getRowMetadata().add("Source");for(var i=0,size=sourceVector.size();i<size;i++){sourceVector.setValue(i,name)}return datasets[0]}var ids=new morpheus.Set;for(var i=0;i<datasets.length;i++){var idVector=datasets[i].getColumnMetadata().getByName(field);for(var j=0,size=idVector.size();j<size;j++){ids.add(idVector.getValue(j))}}var dummyDataset=new morpheus.Dataset({rows:0,columns:ids.size(),name:datasets[0].getName()});var dummyIdVector=dummyDataset.getColumnMetadata().add(field);var counter=0;ids.forEach(function(id){dummyIdVector.setValue(counter++,id)});var dataset=new morpheus.JoinedDataset(dummyDataset,datasets[0],field,field);for(var i=1;i<datasets.length;i++){dataset=new morpheus.JoinedDataset(dataset,datasets[i],field,field)}return dataset};morpheus.DatasetUtil.shallowCopy=function(dataset){var rowMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getRowMetadata());var columnMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata());dataset.getRowMetadata=function(){return rowMetadataModel};dataset.getColumnMetadata=function(){return columnMetadataModel};return dataset};morpheus.DatasetUtil.copy=function(dataset){var newDataset=new morpheus.Dataset({name:dataset.getName(),rows:dataset.getRowCount(),columns:dataset.getColumnCount(),dataType:dataset.getDataType(0)});for(var seriesIndex=0,nseries=dataset.getSeriesCount();seriesIndex<nseries;seriesIndex++){if(seriesIndex>0){newDataset.addSeries({name:dataset.getName(seriesIndex),rows:dataset.getRowCount(),columns:dataset.getColumnCount(),dataType:dataset.getDataType(seriesIndex)})}for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){newDataset.setValue(i,j,dataset.getValue(i,j,seriesIndex),seriesIndex)}}}var rowMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getRowMetadata());var columnMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata());newDataset.getRowMetadata=function(){return rowMetadataModel};newDataset.getColumnMetadata=function(){return columnMetadataModel};return newDataset};morpheus.DatasetUtil.toString=function(dataset,value,seriesIndex){seriesIndex=seriesIndex||0;var s=[];for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){if(j>0){s.push(", ")}s.push(morpheus.Util.nf(dataset.getValue(i,j,seriesIndex)))}s.push("\n")}return s.join("")};morpheus.DatasetUtil.getNonEmptyRows=function(dataset){var rowsToKeep=[];for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var keep=false;for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(!isNaN(value)){keep=true;break}}if(keep){rowsToKeep.push(i)}}return rowsToKeep};morpheus.Dataset=function(options){morpheus.AbstractDataset.call(this,options.rows,options.columns);if(options.dataType==null){options.dataType="Float32"}this.seriesNames.push(options.name);this.seriesArrays.push(options.array?options.array:morpheus.Dataset.createArray(options));this.seriesDataTypes.push(options.dataType)};morpheus.Dataset.toJSON=function(dataset,options){options=options||{};var seriesArrays=[];var seriesDataTypes=[];var seriesNames=[];var seriesIndices=options.seriesIndices;if(seriesIndices==null){seriesIndices=morpheus.Util.sequ32(dataset.getSeriesCount())}for(var series=0;series<seriesIndices.length;series++){var seriesIndex=seriesIndices[series];seriesNames.push(dataset.getName(seriesIndex));seriesDataTypes.push(dataset.getDataType(seriesIndex));var data=[];seriesArrays.push(data);for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var row=[];data.push(row);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){row[j]=dataset.getValue(i,j,seriesIndex)}}}var vectorToJSON=function(vector){var array=[];for(var i=0,size=vector.size();i<size;i++){array[i]=vector.getValue(i)}var properties=new morpheus.Map;vector.getProperties().forEach(function(value,key){if(morpheus.VectorKeys.JSON_WHITELIST.has(key)){properties.set(key,value)}});return{properties:properties,name:vector.getName(),array:array}};var metadatatoJSON=function(metadata,fields){var vectors=[];var filter;if(fields){filter=new morpheus.Set;fields.forEach(function(field){filter.add(field)})}for(var i=0,count=metadata.getMetadataCount();i<count;i++){var v=metadata.get(i);if(!v.getProperties().has(morpheus.VectorKeys.IS_INDEX)){if(filter){if(filter.has(v.getName())){vectors.push(vectorToJSON(v))}}else{vectors.push(vectorToJSON(v))}}}return vectors};return{rows:dataset.getRowCount(),columns:dataset.getColumnCount(),seriesArrays:seriesArrays,seriesDataTypes:seriesDataTypes,seriesNames:seriesNames,rowMetadataModel:{vectors:metadatatoJSON(dataset.getRowMetadata(),options.rowFields)},columnMetadataModel:{vectors:metadatatoJSON(dataset.getColumnMetadata(),options.columnFields)}}};morpheus.Dataset.fromJSON=function(options){if(options.seriesMappings){for(var seriesIndex=0;seriesIndex<options.seriesMappings.length;seriesIndex++){if(options.seriesMappings[seriesIndex]){var map=options.seriesMappings[seriesIndex];var valueMap=new morpheus.Map;for(var key in map){var value=map[key];valueMap.set(value,morpheus.Util.wrapNumber(value,key))}var array=options.seriesArrays[seriesIndex];for(var i=0;i<options.rows;i++){for(var j=0;j<options.columns;j++){var value=array[i][j];array[i][j]=valueMap.get(value)}}options.seriesDataTypes[seriesIndex]="Number"}}}for(var seriesIndex=0;seriesIndex<options.seriesArrays.length;seriesIndex++){var array=options.seriesArrays[seriesIndex];for(var i=0;i<options.rows;i++){for(var j=0;j<options.columns;j++){var value=array[i][j];if(value==null){array[i][j]=NaN}}}}var dataset=new morpheus.Dataset({name:options.seriesNames[0],dataType:options.seriesDataTypes[0],array:options.seriesArrays[0],rows:options.rows,columns:options.columns});if(options.rowMetadataModel){options.rowMetadataModel.vectors.forEach(function(v){var vector=new morpheus.Vector(v.name,dataset.getRowCount());vector.array=v.array;vector.properties=morpheus.Map.fromJSON(v.properties);dataset.rowMetadataModel.vectors.push(vector)})}if(options.columnMetadataModel){options.columnMetadataModel.vectors.forEach(function(v){var vector=new morpheus.Vector(v.name,dataset.getColumnCount());vector.array=v.array;vector.properties=morpheus.Map.fromJSON(v.properties);dataset.columnMetadataModel.vectors.push(vector)})}for(var i=1;i<options.seriesArrays.length;i++){dataset.addSeries({name:options.seriesNames[i],dataType:options.seriesDataTypes[i],array:options.seriesArrays[i]})}return dataset};morpheus.Dataset.createArray=function(options){var array=[];if(options.dataType==null||options.dataType==="Float32"){for(var i=0;i<options.rows;i++){array.push(new Float32Array(options.columns))}}else if(options.dataType==="Int8"){for(var i=0;i<options.rows;i++){array.push(new Int8Array(options.columns))}}else if(options.dataType==="Int16"){for(var i=0;i<options.rows;i++){array.push(new Int16Array(options.columns))}}else{for(var i=0;i<options.rows;i++){array.push([])}}return array};morpheus.Dataset.prototype={getValue:function(i,j,seriesIndex){seriesIndex=seriesIndex||0;return this.seriesArrays[seriesIndex][i][j]},toString:function(){return this.getName()},setValue:function(i,j,value,seriesIndex){seriesIndex=seriesIndex||0;this.seriesArrays[seriesIndex][i][j]=value},addSeries:function(options){options=$.extend({},{rows:this.getRowCount(),columns:this.getColumnCount(),dataType:"Float32"},options);this.seriesDataTypes.push(options.dataType);this.seriesNames.push(options.name);this.seriesArrays.push(options.array!=null?options.array:morpheus.Dataset.createArray(options));return this.seriesNames.length-1}};morpheus.Util.extend(morpheus.Dataset,morpheus.AbstractDataset);morpheus.ElementSelectionModel=function(project){this.viewIndices=new morpheus.Set;this.project=project};morpheus.ElementSelectionModel.prototype={click:function(rowIndex,columnIndex,add){var id=new morpheus.Identifier([rowIndex,columnIndex]);var isSelected=this.viewIndices.has(id);if(add){isSelected?this.viewIndices.remove(id):this.viewIndices.add(id)}else{this.viewIndices.clear();if(!isSelected){this.viewIndices.add(id)}}this.trigger("selectionChanged")},getProject:function(){return this.project},setViewIndices:function(indices){this.viewIndices=indices;this.trigger("selectionChanged")},clear:function(){this.viewIndices=new morpheus.Set},getViewIndices:function(){return this.viewIndices},count:function(){return this.viewIndices.size()},toModelIndices:function(){var project=this.project;var modelIndices=[];this.viewIndices.forEach(function(id){modelIndices.push(project.convertViewRowIndexToModel(id.getArray()[0]),project.convertViewColumnIndexToModel(id.getArray()[1]))});return modelIndices},save:function(){this.modelIndices=this.toModelIndices()},restore:function(){var project=this.project;this.viewIndices=new morpheus.Set;for(var i=0,length=this.modelIndices.length;i<length;i++){var rowIndex=project.convertModelRowIndexToView(this.modelIndices[i][0]);var columnIndex=project.convertModelColumnIndexToView(this.modelIndices[i][1]);if(rowIndex!==-1&&columnIndex!==-1){this.viewIndices.add(new morpheus.Identifier([rowIndex,columnIndex]))}}}};morpheus.Util.extend(morpheus.ElementSelectionModel,morpheus.Events);morpheus.CombinedFilter=function(isAndFilter){this.filters=[];this.isAndFilter=isAndFilter;this.enabledFilters=[];this.name="combined filter"};morpheus.CombinedFilter.prototype={shallowClone:function(){var f=new morpheus.CombinedFilter(this.isAndFilter);f.filters=this.filters.slice(0);return f},isColumns:function(){return this.filters[0].isColumns()},toString:function(){return this.name},setAnd:function(isAndFilter,notify){this.isAndFilter=isAndFilter;if(notify){this.trigger("and",{})}},isAnd:function(){return this.isAndFilter},equals:function(f){if(!(f instanceof morpheus.CombinedFilter)){return false}if(this.isAndFilter!==f.isAndFilter){return false}if(this.filters.length!==f.filters.length){return false}for(var i=0,length=this.filters.length;i<length;i++){if(!this.filters[i].equals(f.filters[i])){return false}}return true},add:function(filter,notify){this.filters.push(filter);if(notify){this.trigger("add",{filter:filter})}},getFilters:function(){return this.filters},get:function(index){return this.filters[index]},indexOf:function(name,type){for(var i=0,length=this.filters.length;i<length;i++){if(this.filters[i].toString()===name&&(type==null?true:this.filters[i]instanceof type)){return i}}return-1},remove:function(index,notify){this.filters.splice(index,1);if(notify){this.trigger("remove",{index:index})}},set:function(index,filter){this.filters[index]=filter},insert:function(index,filter){this.filters.splice(index,0,filter)},clear:function(){this.filters=[]},init:function(dataset){for(var i=0,nfilters=this.filters.length;i<nfilters;i++){if(this.filters[i].isColumns()){this.filters[i].init(new morpheus.TransposedDatasetView(dataset))}else{this.filters[i].init(dataset)}}this.enabledFilters=this.filters.filter(function(filter){return filter.isEnabled()})},accept:function(index){var filters=this.enabledFilters;if(this.isAndFilter){for(var i=0,nfilters=filters.length;i<nfilters;i++){if(filters[i].accept(index)===false){return false}}return true}else{for(var i=0,nfilters=filters.length;i<nfilters;i++){if(filters[i].accept(index)){return true}}return false}},isEnabled:function(){return this.enabledFilters.length>0}};morpheus.Util.extend(morpheus.CombinedFilter,morpheus.Events);morpheus.IndexFilter=function(acceptIndicesSet,name,isColumns){this.acceptIndicesSet=acceptIndicesSet;this.name=name;this.columns=isColumns};morpheus.IndexFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled},setAcceptIndicesSet:function(acceptIndicesSet){this.acceptIndicesSet=acceptIndicesSet},setEnabled:function(enabled){this.enabled=enabled},equals:function(filter){return filter instanceof morpheus.IndexFilter&&this.acceptIndicesSet.equals(filter.acceptIndicesSet)},init:function(dataset){},toString:function(){return this.name},accept:function(index){return this.acceptIndicesSet.has(index)}};morpheus.VectorFilter=function(set,maxSetSize,name,isColumns){this.set=set;this.name=name;this.maxSetSize=maxSetSize;this.columns=isColumns};morpheus.VectorFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&this.set.size()>0&&this.set.size()!==this.maxSetSize&&this.vector!=null},setEnabled:function(enabled){this.enabled=enabled},equals:function(filter){return filter instanceof morpheus.VectorFilter&&this.name===filter.name},init:function(dataset){this.vector=dataset.getRowMetadata().getByName(this.name)},toString:function(){return this.name},accept:function(index){return this.set.has(this.vector.getValue(index))}};morpheus.NotNullFilter=function(name,isColumns){this.name=name;this.columns=isColumns};morpheus.NotNullFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&this.vector!=null},setEnabled:function(enabled){this.enabled=enabled},equals:function(filter){return filter instanceof morpheus.NotNullFilter&&this.name===filter.name},init:function(dataset){this.vector=dataset.getRowMetadata().getByName(this.name)},toString:function(){return this.name},accept:function(index){return this.vector.getValue(index)!=null}};morpheus.RangeFilter=function(min,max,name,isColumns){this.min=min;this.max=max;this.name=name;this.columns=isColumns};morpheus.RangeFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&(!isNaN(this.min)||!isNaN(this.max))&&this.vector},setEnabled:function(enabled){this.enabled=enabled},setMin:function(value){this.min=isNaN(value)?-Number.MAX_VALUE:value},setMax:function(value){this.max=isNaN(value)?Number.MAX_VALUE:value},equals:function(filter){return filter instanceof morpheus.RangeFilter&&this.name===filter.name},init:function(dataset){this.vector=dataset.getRowMetadata().getByName(this.name)},toString:function(){return this.name},accept:function(index){var value=this.vector.getValue(index);return value>=this.min&&value<=this.max}};morpheus.TopNFilter=function(n,direction,name,isColumns){this.n=n;this.direction=direction;this.name=name;this.columns=isColumns};morpheus.TopNFilter.TOP=0;morpheus.TopNFilter.BOTTOM=1;morpheus.TopNFilter.TOP_BOTTOM=2;morpheus.TopNFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&this.n>0&&this.vector},setEnabled:function(enabled){this.enabled=enabled},setN:function(value){this.n=value},setDirection:function(direction){this.direction=direction},equals:function(filter){return filter instanceof morpheus.TopNFilter&&this.name===filter.name&&this.n===filter.n&&this.direction===filter.direction},init:function(dataset){if(!this.vector||this.vector!==dataset.getRowMetadata().getByName(this.name)){var vector=dataset.getRowMetadata().getByName(this.name);if(vector==null){vector={getValue:function(){},size:function(){return 0}}}this.vector=vector;var set=new morpheus.Set;for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(!isNaN(value)){set.add(value)}}var values=set.values();values.sort(function(a,b){return a===b?0:a<b?-1:1});this.sortedValues=values}var topAndBottomIndices=[this.sortedValues.length-this.n,this.n-1];for(var i=0;i<topAndBottomIndices.length;i++){topAndBottomIndices[i]=Math.max(0,topAndBottomIndices[i]);topAndBottomIndices[i]=Math.min(this.sortedValues.length-1,topAndBottomIndices[i])}var topAndBottomValues=[this.sortedValues[topAndBottomIndices[0]],this.sortedValues[topAndBottomIndices[1]]];if(this.direction===morpheus.TopNFilter.TOP){this.f=function(val){return isNaN(val)?false:val>=topAndBottomValues[0]}}else if(this.direction===morpheus.TopNFilter.BOTTOM){this.f=function(val){return isNaN(val)?false:val<=topAndBottomValues[1]}}else{this.f=function(val){return isNaN(val)?false:val>=topAndBottomValues[0]||val<=topAndBottomValues[1]}}},accept:function(index){return this.f(this.vector.getValue(index))},toString:function(){return this.name}};morpheus.AlwaysTrueFilter=function(){};morpheus.AlwaysTrueFilter.prototype={isEnabled:function(){return false},setEnabled:function(enabled){},equals:function(filter){return filter instanceof morpheus.AlwaysTrueFilter},init:function(dataset){},toString:function(){return"AlwaysTrue"},accept:function(index){return true}};morpheus.CombinedFilter.fromJSON=function(combinedFilter,json){combinedFilter.setAnd(json.isAnd);json.filters.forEach(function(filter){var name=filter.name!=null?filter.name:filter.field;if(filter.type==="set"){var set=new morpheus.Set;filter.values.forEach(function(value){set.add(value)});combinedFilter.add(new morpheus.VectorFilter(set,filter.maxSetSize,name,filter.isColumns))}else if(filter.type==="range"){combinedFilter.add(new morpheus.RangeFilter(filter.min,filter.max,name,filter.isColumns))}else if(filter.type==="top"){if(_.isString(filter.direction)){if(filter.direction==="top"){filter.direction=morpheus.TopNFilter.TOP}else if(filter.direction==="bottom"){filter.direction=morpheus.TopNFilter.BOTTOM}else if(filter.direction==="topAndBottom"){filter.direction=morpheus.TopNFilter.TOP_BOTTOM}}combinedFilter.add(new morpheus.TopNFilter(filter.n,filter.direction,name,filter.isColumns))}else if(filter.type==="index"){var set=new morpheus.Set;filter.indices.forEach(function(value){set.add(value)});combinedFilter.add(new morpheus.IndexFilter(set,name,filter.isColumns))}else{console.log("Unknown filter type")}})};morpheus.CombinedFilter.toJSON=function(filter){var json={isAnd:filter.isAnd(),filters:[]};filter.getFilters().forEach(function(filter){if(filter.isEnabled()){if(filter instanceof morpheus.VectorFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),values:filter.set.values(),maxSetSize:filter.maxSetSize,type:"set"})}else if(filter instanceof morpheus.RangeFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),min:filter.min,max:filter.max,type:"range"})}else if(filter instanceof morpheus.TopNFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),n:filter.n,direction:filter.direction,type:"top"})}else if(filter instanceof morpheus.IndexFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),indices:filter.acceptIndicesSet.values(),type:"index"})}}});return json};morpheus.IndexMapper=function(project,isRows){this.project=project;this.isRows=isRows;this.sortKeys=[];this.modelToView=null;this.filteredModelIndices=null;this.filteredSortedModelIndices=null;this.filter=new morpheus.CombinedFilter(true);this._filter();this._sort()};morpheus.IndexMapper.prototype={convertModelIndexToView:function(modelIndex){var index=this.modelToView.get(modelIndex);return index!==undefined?index:-1},convertViewIndexToModel:function(viewIndex){return viewIndex<this.filteredSortedModelIndices.length&&viewIndex>=0?this.filteredSortedModelIndices[viewIndex]:-1},convertToView:function(){return this.filteredSortedModelIndices},setFilter:function(filter){this.filter=filter;this._filter();this._sort()},_filter:function(){var filter=this.filter;var dataset=this.project.getFullDataset();var count=this.isRows?dataset.getRowCount():dataset.getColumnCount();var filteredModelIndices;if(filter!=null){filter.init(dataset);if(filter.isEnabled()){filteredModelIndices=[];for(var i=0;i<count;i++){if(filter.accept(i)){filteredModelIndices.push(i)}}}}this.filteredModelIndices=filteredModelIndices!=null?filteredModelIndices:morpheus.Util.seq(count)},_sort:function(){var sortKeys=this.sortKeys;if(sortKeys.length>0){var dataset=this.project.getFullDataset();var nkeys=sortKeys.length;for(var i=0;i<nkeys;i++){sortKeys[i].init(sortKeys[i].isColumns()?new morpheus.TransposedDatasetView(dataset):dataset,this.filteredSortedModelIndices)}this.filteredSortedModelIndices=this.filteredModelIndices.slice(0);this.filteredSortedModelIndices.sort(function(a,b){for(var i=0;i<nkeys;i++){var key=sortKeys[i];var comparator=key.getComparator();var val1=key.getValue(a);var val2=key.getValue(b);var c=comparator(val1,val2);if(c!==0){return c}}return 0})}else{this.filteredSortedModelIndices=this.filteredModelIndices}var modelToView=new morpheus.Map;for(var i=0,length=this.filteredSortedModelIndices.length;i<length;i++){modelToView.set(this.filteredSortedModelIndices[i],i)}this.modelToView=modelToView},getFilter:function(){return this.filter},getViewCount:function(){if(this.project.getFullDataset()==null){return 0}return this.filteredSortedModelIndices.length},setSelectedModelIndices:function(selectedModelIndices){this.selectionModel.setSelectedModelIndices(selectedModelIndices)},setSortKeys:function(sortKeys){if(sortKeys==null){sortKeys=[]}this.sortKeys=sortKeys;this._sort()}};morpheus.JoinedDataset=function(dataset1,dataset2,dataset1Field,dataset2Field,sourceFieldName){sourceFieldName=sourceFieldName||"Source";this.dataset1Field=dataset1Field;this.dataset2Field=dataset2Field;if(dataset1==null){throw"dataset1 is null"}if(dataset2==null){throw"dataset2 is null"}if(dataset1Field){var v1=dataset1.getColumnMetadata().getByName(dataset1Field);var dataset2ValueToIndex=morpheus.VectorUtil.createValueToIndexMap(dataset2.getColumnMetadata().getByName(dataset2Field));var dataset2ColumnIndices=[];for(var i=0;i<v1.size();i++){dataset2ColumnIndices[i]=dataset2ValueToIndex.get(v1.getValue(i))}dataset2=new morpheus.SlicedDatasetWithNulls(dataset2,dataset2ColumnIndices,dataset1.getColumnCount(),dataset1.getColumnMetadata())}if(!dataset1.getRowMetadata().getByName(sourceFieldName)){var sourceVector=dataset1.getRowMetadata().add(sourceFieldName);var name=dataset1.getName();for(var i=0,nrows=sourceVector.size();i<nrows;i++){sourceVector.setValue(i,name)}}if(!dataset2.getRowMetadata().getByName(sourceFieldName)){var sourceVector=dataset2.getRowMetadata().add(sourceFieldName);var name=dataset2.getName();for(var i=0,nrows=sourceVector.size();i<nrows;i++){sourceVector.setValue(i,name)}}for(var i=0,count=dataset1.getRowMetadata().getMetadataCount();i<count;i++){var name=dataset1.getRowMetadata().get(i).getName();if(dataset2.getRowMetadata().getByName(name)==null){dataset2.getRowMetadata().add(name)}}for(var i=0,count=dataset2.getRowMetadata().getMetadataCount();i<count;i++){var name=dataset2.getRowMetadata().get(i).getName();if(dataset1.getRowMetadata().getByName(name)==null){dataset1.getRowMetadata().add(name)}}var dataset2RowMetadataOrder=[];var metadataInDifferentOrder=false;for(var i=0,count=dataset1.getRowMetadata().getMetadataCount();i<count;i++){var name=dataset1.getRowMetadata().get(i).getName();var index=morpheus.MetadataUtil.indexOf(dataset2.getRowMetadata(),name);dataset2RowMetadataOrder.push(index);if(index!==i){metadataInDifferentOrder=true}}this.dataset1=dataset1;this.dataset2=dataset2;var maxSeriesCount=Math.max(this.dataset1.getSeriesCount(),this.dataset2.getSeriesCount());for(var i=this.dataset1.getSeriesCount();i<maxSeriesCount;i++){this.dataset1.addSeries({name:this.dataset2.getName(i)})}for(var i=this.dataset2.getSeriesCount();i<maxSeriesCount;i++){this.dataset2.addSeries({name:this.dataset1.getName(i)})}this.rowMetadata=new morpheus.JoinedMetadataModel(this.dataset1.getRowMetadata(),!metadataInDifferentOrder?this.dataset2.getRowMetadata():new morpheus.MetadataModelColumnView(this.dataset2.getRowMetadata(),dataset2RowMetadataOrder))};morpheus.JoinedDataset.prototype={getName:function(seriesIndex){return this.dataset1.getName(seriesIndex)},setName:function(seriesIndex,name){this.dataset1.setName(seriesIndex,name)},getDataType:function(seriesIndex){return this.dataset1.getDataType(seriesIndex)},getDatasets:function(){return[this.dataset1,this.dataset2]},getDataset1:function(){return this.dataset1},getRowMetadata:function(){return this.rowMetadata},getColumnMetadata:function(){return this.dataset1.getColumnMetadata()},getRowCount:function(){return this.dataset1.getRowCount()+this.dataset2.getRowCount()},getColumnCount:function(){return this.dataset1.getColumnCount()},getValue:function(i,j,seriesIndex){return i<this.dataset1.getRowCount()?this.dataset1.getValue(i,j,seriesIndex):this.dataset2.getValue(i-this.dataset1.getRowCount(),j,seriesIndex)},setValue:function(i,j,value,seriesIndex){i<this.dataset1.getRowCount()?this.dataset1.setValue(i,j,value,seriesIndex):this.dataset2.setValue(i-this.dataset1.getRowCount(),j,value,seriesIndex)},getSeriesCount:function(){return this.dataset1.getSeriesCount()},addSeries:function(options){this.dataset1.addSeries(options);return this.dataset2.addSeries(options)},removeSeries:function(seriesIndex){this.dataset1.removeSeries(seriesIndex);this.dataset2.removeSeries(seriesIndex)},toString:function(){return this.getName()}};morpheus.SlicedDatasetWithNulls=function(dataset,columnIndices,columnCount,columnMetadata){morpheus.DatasetAdapter.call(this,dataset);this.columnIndices=columnIndices;this.columnCount=columnCount;this.columnMetadata=columnMetadata};morpheus.SlicedDatasetWithNulls.prototype={getColumnMetadata:function(){return this.columnMetadata},getColumnCount:function(){return this.columnCount},getValue:function(i,j,seriesIndex){var index=this.columnIndices[j];return index===undefined?undefined:this.dataset.getValue(i,index,seriesIndex)},setValue:function(i,j,value,seriesIndex){var index=this.columnIndices[j];if(index!==undefined){this.dataset.setValue(i,index,value,seriesIndex)}else{console.log(j+" out of range")}}};morpheus.Util.extend(morpheus.SlicedDatasetWithNulls,morpheus.DatasetAdapter);morpheus.JoinedVector=function(v1,v2){this.v1=v1;this.v2=v2;morpheus.VectorAdapter.call(this,v1);this.properties=new morpheus.Map};morpheus.JoinedVector.prototype={setValue:function(i,value){i<this.v1.size()?this.v1.setValue(i,value):this.v2.setValue(i-this.v1.size(),value)},getValue:function(i){return i<this.v1.size()?this.v1.getValue(i):this.v2.getValue(i-this.v1.size())},size:function(){return this.v1.size()+this.v2.size()},getProperties:function(){return this.properties}};morpheus.Util.extend(morpheus.JoinedVector,morpheus.VectorAdapter);morpheus.JoinedMetadataModel=function(m1,m2){this.m1=m1;this.m2=m2;this.vectors=[];for(var i=0,count=m1.getMetadataCount();i<count;i++){var v1=this.m1.get(i);var v2=this.m2.get(i);var v=new morpheus.JoinedVector(v1,v2);v1.getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){v.properties.set(key,val)}});v2.getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){v.properties.set(key,val)}});this.vectors.push(v)}};morpheus.JoinedMetadataModel.prototype={add:function(name){var index=morpheus.MetadataUtil.indexOf(this,name);var oldVector;if(index!==-1){oldVector=this.remove(index)}var v=new morpheus.Vector(name,this.getItemCount());if(oldVector!=null){oldVector.getProperties().forEach(function(val,key){v.getProperties().set(key,val)});for(var i=0,size=oldVector.size();i<size;i++){v.setValue(i,oldVector.getValue(i))}}this.vectors.push(v);return v},getItemCount:function(){return this.m1.getItemCount()+this.m2.getItemCount()},get:function(index){return this.vectors[index]},remove:function(index){return this.vectors.splice(index,1)[0]},getByName:function(name){for(var i=0,length=this.vectors.length;i<length;i++){if(name===this.vectors[i].getName()){return this.vectors[i]}}},getMetadataCount:function(){return this.vectors.length}};morpheus.MetadataModelAdapter=function(model){this.model=model};morpheus.MetadataModelAdapter.prototype={add:function(name){return this.model.add(name)},getItemCount:function(){return this.model.getItemCount()},get:function(index){return this.model.get(index)},remove:function(index){return this.model.remove(index)},getByName:function(name){return this.model.getByName(name)},getMetadataCount:function(){return this.model.getMetadataCount()}};morpheus.MetadataModelColumnView=function(model,indices){this.model=model;this.indices=indices};morpheus.MetadataModelColumnView.prototype={add:function(name){var vector=this.model.add(name);var index=morpheus.MetadataUtil.indexOf(this.model,name);this.indices.push(index);return vector},getMetadataCount:function(){return this.indices.length},get:function(index){if(index<0||index>=this.indices.length){throw"index out of bounds"}return this.model.get(this.indices[index])},remove:function(index){if(index<0||index>=this.indices.length){throw"index out of bounds"}var v=this.model.remove(this.indices[index]);this.indices.splice(index,1);return v},getByName:function(name){var index=morpheus.MetadataUtil.indexOf(this,name);return index!==-1?this.get(index):undefined}};morpheus.Util.extend(morpheus.MetadataModelColumnView,morpheus.MetadataModelAdapter);morpheus.MetadataModelItemView=function(model,indices){this.model=model;this.indices=indices};morpheus.MetadataModelItemView.prototype={add:function(name){var v=this.model.add(name);return new morpheus.SlicedVector(v,this.indices)},getItemCount:function(){return this.indices.length},get:function(index){var v=this.model.get(index);if(v===undefined){return undefined}return new morpheus.SlicedVector(v,this.indices)},getByName:function(name){var v=this.model.getByName(name);if(v===undefined){return undefined}return new morpheus.SlicedVector(v,this.indices)},getMetadataCount:function(){return this.model.getMetadataCount()}};morpheus.Util.extend(morpheus.MetadataModelItemView,morpheus.MetadataModelAdapter);morpheus.MetadataModel=function(itemCount){this.itemCount=itemCount;this.vectors=[]};morpheus.MetadataModel.prototype={add:function(name,options){var index=morpheus.MetadataUtil.indexOf(this,name);var oldVector;if(index!==-1){oldVector=this.get(index)}var v=new morpheus.Vector(name,this.getItemCount());if(oldVector!=null){for(var i=0,size=oldVector.size();i<size;i++){var val=oldVector.getValue(i);v.setValue(i,val)}}if(index!==-1){this.vectors.splice(index,1,v)}else{this.vectors.push(v)}return v},getItemCount:function(){return this.itemCount},get:function(index){return this.vectors[index]},remove:function(index){return this.vectors.splice(index,1)[0]},getByName:function(name){var index=morpheus.MetadataUtil.indexOf(this,name);return index!==-1?this.get(index):undefined},getMetadataCount:function(){return this.vectors.length}};morpheus.MetadataUtil=function(){};morpheus.MetadataUtil.renameFields=function(dataset,options){_.each(options.rows,function(item){if(item.renameTo){var v=dataset.getRowMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}});_.each(options.columns,function(item){if(item.renameTo){var v=dataset.getColumnMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}})};morpheus.MetadataUtil.search=function(options){var model=options.model;var fullModel=options.fullModel;if(!fullModel){fullModel=model}var text=options.text;var isColumns=options.isColumns;text=$.trim(text);if(text===""){return null}var tokens=morpheus.Util.getAutocompleteTokens(text);if(tokens.length==0){return null}var indexField="#";var fieldNames=morpheus.MetadataUtil.getMetadataNames(fullModel);fieldNames.push(indexField);var predicates=morpheus.Util.createSearchPredicates({tokens:tokens,fields:fieldNames,defaultMatchMode:options.defaultMatchMode});var vectors=[];var nameToVector=new morpheus.Map;for(var j=0;j<fullModel.getMetadataCount();j++){var v=fullModel.get(j);var dataType=morpheus.VectorUtil.getDataType(v);var wrapper={vector:v,dataType:dataType,isArray:dataType.indexOf("[")===0};nameToVector.set(v.getName(),wrapper);if(model.getByName(v.getName())!=null){vectors.push(wrapper)}}var indices=[];var npredicates=predicates.length;for(var p=0;p<npredicates;p++){var predicate=predicates[p];var filterColumnName=predicate.getField();if(filterColumnName!=null&&!predicate.isNumber()){var wrapper=nameToVector.get(filterColumnName);if(wrapper&&(wrapper.dataType==="number"||wrapper.dataType==="[number]")){if(predicate.getText){predicates[p]=new morpheus.Util.EqualsPredicate(filterColumnName,parseFloat(predicate.getText()))}else if(predicate.getValues){var values=[];predicate.getValues().forEach(function(val){values.push(parseFloat(val))});predicate[p]=new morpheus.Util.ExactTermsPredicate(filterColumnName,values)}}}}var matchAllPredicates=options.matchAllPredicates===true;function isPredicateMatch(predicate){var filterColumnName=predicate.getField();if(filterColumnName!=null){var value=null;if(filterColumnName===indexField){value=i+1;if(predicate.accept(value)){return true}}else{var wrapper=nameToVector.get(filterColumnName);if(wrapper){value=wrapper.vector.getValue(i);if(wrapper.isArray){if(value!=null){for(var k=0;k<value.length;k++){if(predicate.accept(value[k])){return true}}}}else{if(predicate.accept(value)){return true}}}}}else{for(var j=0;j<nfields;j++){var wrapper=vectors[j];var value=wrapper.vector.getValue(i);if(wrapper.isArray){if(value!=null){for(var k=0;k<value.length;k++){if(predicate.accept(value[k])){return true}}}}else{if(predicate.accept(value)){return true}}}}}var nfields=vectors.length;for(var i=0,nitems=model.getItemCount();i<nitems;i++){if(!matchAllPredicates){for(var p=0;p<npredicates;p++){var predicate=predicates[p];if(isPredicateMatch(predicate)){indices.push(i);break}}}else{var matches=true;for(var p=0;p<npredicates;p++){var predicate=predicates[p];if(!isPredicateMatch(predicate)){matches=false;break}}if(matches){indices.push(i)}}}return indices};morpheus.MetadataUtil.shallowCopy=function(model){var copy=new morpheus.MetadataModel(model.getItemCount());for(var i=0;i<model.getMetadataCount();i++){var v=model.get(i);var newVector=new morpheus.VectorAdapter(v);newVector.properties=new morpheus.Map;newVector.getProperties=function(){return this.properties};v.getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){newVector.properties.set(key,val)}});copy.vectors.push(newVector)}return copy};morpheus.MetadataUtil.autocomplete=function(model){return function(tokens,cb){var matches=[];var regex=null;var regexMatch=null;var searchModel=model;var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);var fieldSearchFieldName=null;if(token!==""){var semi=token.indexOf(":");if(semi>0){if(token.charCodeAt(semi-1)!==92){var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[token.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}var index=morpheus.MetadataUtil.indexOf(searchModel,possibleField);if(index!==-1){fieldSearchFieldName=possibleField;token=$.trim(token.substring(semi+1));searchModel=new morpheus.MetadataModelColumnView(model,[index])}}}var set=new morpheus.Set;regex=new RegExp(morpheus.Util.escapeRegex(token),"i");regexMatch=new RegExp("("+morpheus.Util.escapeRegex(token)+")","i");var max=10;var vectors=[];var isArray=[];for(var j=0;j<searchModel.getMetadataCount();j++){var v=searchModel.get(j);var dataType=morpheus.VectorUtil.getDataType(v);if(dataType==="string"||dataType==="[string]"){vectors.push(v);isArray.push(dataType==="[string]")}}var nfields=vectors.length;loop:for(var i=0,nitems=searchModel.getItemCount();i<nitems;i++){for(var j=0;j<nfields;j++){var v=vectors[j];var val=v.getValue(i);if(val!=null){if(isArray[j]){for(var k=0;k<val.length;k++){var id=new morpheus.Identifier([val[k],v.getName()]);if(!set.has(id)&&regex.test(val[k])){set.add(id);if(set.size()===max){break loop}}}}else{var id=new morpheus.Identifier([val,v.getName()]);if(!set.has(id)&&regex.test(val)){set.add(id);if(set.size()===max){break loop}}}}}}set.forEach(function(id){var array=id.getArray();var field=array[1];var val=array[0];var quotedField=field;if(quotedField.indexOf(" ")!==-1){quotedField='"'+quotedField+'"'}var quotedValue=val;if(quotedValue.indexOf(" ")!==-1){quotedValue='"'+quotedValue+'"'}matches.push({value:quotedField+":"+quotedValue,label:'<span style="font-weight:300;">'+field+":</span>"+"<span>"+val.replace(regexMatch,"<b>$1</b>")+"</span>"})})}if(regex==null){regex=new RegExp(".*","i")}for(var j=0;j<searchModel.getMetadataCount();j++){var v=searchModel.get(j);var dataType=morpheus.VectorUtil.getDataType(v);var field=v.getName();if(dataType==="number"||dataType==="string"||dataType==="[string]"){if(regex.test(field)&&field!==fieldSearchFieldName){var quotedField=field;if(quotedField.indexOf(" ")!==-1){quotedField='"'+quotedField+'"'}matches.push({value:quotedField+":",label:'<span style="font-weight:300;">'+(regexMatch==null?field:field.replace(regexMatch,"<b>$1</b>"))+":</span>"+(dataType==="number"?"<span"+' style="font-weight:300;font-size:85%;">.., >, <, >=, <=,'+" =</span>":""),show:true})}}}cb(matches)}};morpheus.MetadataUtil.getMetadataNames=function(metadataModel){var names=[];for(var i=0,count=metadataModel.getMetadataCount();i<count;i++){names.push(metadataModel.get(i).getName(i))}names.sort(function(a,b){a=a.toLowerCase();b=b.toLowerCase();return a<b?-1:a===b?0:1});return names};morpheus.MetadataUtil.getVectors=function(metadataModel,names){var vectors=[];names.forEach(function(name){var v=metadataModel.getByName(name);if(!v){throw name+" not found. Available fields are "+morpheus.MetadataUtil.getMetadataNames(metadataModel)}vectors.push(v)});return vectors};morpheus.MetadataUtil.indexOf=function(metadataModel,name){for(var i=0,length=metadataModel.getMetadataCount();i<length;i++){if(name===metadataModel.get(i).getName()){return i}}return-1};morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS=["target","gene_target","moa"];morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS=new morpheus.Set;["pr_analyte_id","pr_gene_title","pr_gene_id","pr_analyte_num","pr_bset_id","pr_lua_id","pr_pool_id","pr_is_bing","pr_is_inf","pr_is_lmark","qc_slope","qc_f_logp","qc_iqr","bead_batch","bead_revision","bead_set","det_mode","det_plate","det_well","mfc_plate_dim","mfc_plate_id","mfc_plate_name","mfc_plate_quad","mfc_plate_well","pert_dose_unit","pert_id_vendor","pert_mfc_desc","pert_mfc_id","pert_time","pert_time_unit","pert_univ_id","pert_vehicle","pool_id","rna_plate","rna_well","count_mean","count_cv","provenance_code"].forEach(function(name){morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS.add(name)});morpheus.MetadataUtil.maybeConvertStrings=function(metadata,metadataStartIndex){for(var i=metadataStartIndex,count=metadata.getMetadataCount();i<count;i++){morpheus.VectorUtil.maybeConvertStringToNumber(metadata.get(i))}morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS.forEach(function(field){if(metadata.getByName(field)){morpheus.VectorUtil.maybeConvertToStringArray(metadata.getByName(field),",")}})};morpheus.MetadataUtil.copy=function(src,dest){if(src.getItemCount()!=dest.getItemCount()){throw"Item count not equal in source and destination. "+src.getItemCount()+" != "+dest.getItemCount()}var itemCount=src.getItemCount();var metadataColumns=src.getMetadataCount();for(var j=0;j<metadataColumns;j++){var srcVector=src.get(j);var destVector=dest.getByName(srcVector.getName());if(destVector==null){destVector=dest.add(srcVector.getName())}for(var i=0;i<itemCount;i++){destVector.setValue(i,srcVector.getValue(i))}}};morpheus.MetadataUtil.addVectorIfNotExists=function(metadataModel,name){var v=metadataModel.getByName(name);if(!v){v=metadataModel.add(name)}return v};morpheus.MetadataUtil.getMatchingIndices=function(metadataModel,tokens){var indices={};for(var itemIndex=0,nitems=metadataModel.getItemCount();itemIndex<nitems;itemIndex++){var matches=false;for(var metadataIndex=0,metadataCount=metadataModel.getMetadataCount();metadataIndex<metadataCount&&!matches;metadataIndex++){var vector=metadataModel.get(metadataModel.getColumnName(metadataIndex));var value=vector.getValue(itemIndex);for(var i=0,length=tokens.length;i<length;i++){if(tokens[i]==value){matches=true;break}}}if(matches){indices[itemIndex]=1}}return indices};morpheus.MolarConcentration=function(){};morpheus.MolarConcentration.getMicroMolarConcentration=function(text){text=text.toLowerCase();for(var i=0;i<morpheus.MolarConcentration.CONCENTRATIONS.length;i++){var pair=morpheus.MolarConcentration.CONCENTRATIONS[i];var key=pair[0];var factorToMolar=pair[1];var index=text.indexOf(key);if(index!=-1){var value=text.substring(0,index).trim();var factor=factorToMolar/1e7;var conc=parseFloat(value);return conc/factor}}};morpheus.MolarConcentration.CONCENTRATIONS=[["mm",1e4],["um",1e7],["µ"+"m",1e7],["nm",1e10],["pm",1e13],["fm",1e16],["am",1e19],["zm",1e22],["ym",1e25],["m",1]];morpheus.Positions=function(){this.spaces=undefined;this.defaultPositionFunction=function(index){return this.size*index};this.squishedPositionFunction=function(index){return this.positions[index]};this.positionFunction=this.defaultPositionFunction;this.squishedIndices={};this.isSquished=false};morpheus.Positions.getBottom=function(rect,rowPositions){var bottom=rowPositions.getLength();if(rect!=null){bottom=1+rowPositions.getIndex(rect.y+rect.height,false);bottom=Math.max(0,bottom);bottom=Math.min(rowPositions.getLength(),bottom)}return bottom};morpheus.Positions.getTop=function(rect,rowPositions){var top=0;if(rect!=null){top=rowPositions.getIndex(rect.y,false)-1;top=Math.max(0,top);top=Math.min(rowPositions.getLength(),top)}return top};morpheus.Positions.getLeft=function(rect,columnPositions){var left=0;if(rect!=null){left=columnPositions.getIndex(rect.x,false)-1;left=Math.max(0,left);left=Math.min(columnPositions.getLength(),left)}return left};morpheus.Positions.getRight=function(rect,columnPositions){var right=columnPositions.getLength();if(rect!=null){right=1+columnPositions.getIndex(rect.x+rect.width,false);right=Math.min(columnPositions.getLength(),right)}return right};morpheus.Positions.prototype={length:0,size:13,squishFactor:.1,compress:true,copy:function(){var copy=new morpheus.Positions;if(this.spaces){copy.spaces=this.spaces.slice()}copy.compress=this.compress;copy.squishFactor=this.squishFactor;copy.size=this.size;copy.length=this.length;if(this.isSquished){copy.positionFunction=copy.squishedPositionFunction;copy.squishedIndices=_.clone(this.squishedIndices);copy.isSquished=true}return copy},getIndex:function(position,exact){if(this.getLength()===0){return-1}if(exact){return this.binaryExactSearch(position)}else{return this.binaryInExactSearch(position)}},getLength:function(){return this.length},getPosition:function(index){return this.positionFunction(index)+(this.spaces!==undefined?this.spaces[index]:0)},getItemSize:function(index){return this.squishedIndices[index]===true?this.size*this.squishFactor:this.size},getSize:function(){return this.size},setSpaces:function(spaces){this.spaces=spaces},setLength:function(length){this.length=length;this.trigger("change",{source:this,value:"length"})},setSize:function(size){this.size=size;if(this.isSquished){this.setSquishedIndices(this.squishedIndices)}this.trigger("change",{source:this,value:"size"})},setSquishedIndices:function(squishedIndices){if(squishedIndices!=null){var compress=this.compress;this.squishedIndices=squishedIndices;var positions=[];var squishFactor=this.squishFactor;var size=this.size;var position=0;for(var i=0,length=this.getLength();i<length;i++){var itemSize;if(squishedIndices[i]===true){positions.push(position);itemSize=size*squishFactor;position+=itemSize}else{if(!compress){position=size*i}positions.push(position);position+=size}}this.isSquished=true;this.positions=positions;this.positionFunction=this.squishedPositionFunction}else{this.squishedIndices={};this.isSquished=false;this.positionFunction=this.defaultPositionFunction}this.trigger("change",{source:this,value:"squishedIndices"})},setSquishFactor:function(f){if(this.squishFactor!==f){this.squishFactor=f;if(this.isSquished){this.setSquishedIndices(this.squishedIndices)}this.trigger("change",{source:this,value:"squishFactor"})}},getSquishFactor:function(){return this.squishFactor},binaryExactSearch:function(position){var low=0;var high=this.length-1;while(low<=high){var mid=low+high>>1;var midVal=this.getPosition(mid);var size=this.getItemSize(mid);if(midVal<=position&&position<midVal+size){return mid}if(midVal<position){low=mid+1}else if(midVal>position){high=mid-1}else{return mid}}return-1},binaryInExactSearch:function(position){var low=0;var high=this.getLength()-1;var maxIndex=this.getLength()-1;if(position<=this.getPosition(0)){return 0}while(low<=high){var mid=low+high>>1;var midVal=this.getPosition(mid);var size=this.getItemSize(mid);var nextStart=maxIndex===mid?midVal+size:this.getPosition(mid+1);if(midVal<=position&&position<nextStart){return mid}if(midVal<position){low=mid+1}else if(midVal>position){high=mid-1}else{return mid}}return low-1}};morpheus.Util.extend(morpheus.Positions,morpheus.Events);morpheus.Project=function(dataset){this.originalDataset=dataset;this.rowIndexMapper=new morpheus.IndexMapper(this,true);this.columnIndexMapper=new morpheus.IndexMapper(this,false);this.groupRows=[];this.groupColumns=[];this.rowColorModel=new morpheus.VectorColorModel;this.columnColorModel=new morpheus.VectorColorModel;this.rowShapeModel=new morpheus.VectorShapeModel;this.columnShapeModel=new morpheus.VectorShapeModel;this.rowFontModel=new morpheus.VectorFontModel;this.columnFontModel=new morpheus.VectorFontModel;this.hoverColumnIndex=-1;this.hoverRowIndex=-1;this.columnSelectionModel=new morpheus.SelectionModel(this,true);this.rowSelectionModel=new morpheus.SelectionModel(this,false);this.elementSelectionModel=new morpheus.ElementSelectionModel(this);this.symmetricProjectListener=null;morpheus.Project._recomputeCalculatedColumnFields(this.originalDataset,morpheus.VectorKeys.RECOMPUTE_FUNCTION_NEW_HEAT_MAP);morpheus.Project._recomputeCalculatedColumnFields(new morpheus.TransposedDatasetView(this.originalDataset),morpheus.VectorKeys.RECOMPUTE_FUNCTION_NEW_HEAT_MAP)};morpheus.Project.Events={DATASET_CHANGED:"datasetChanged",ROW_GROUP_BY_CHANGED:"rowGroupByChanged",COLUMN_GROUP_BY_CHANGED:"columnGroupByChanged",ROW_FILTER_CHANGED:"rowFilterChanged",COLUMN_FILTER_CHANGED:"columnFilterChanged",ROW_SORT_ORDER_CHANGED:"rowSortOrderChanged",COLUMN_SORT_ORDER_CHANGED:"columnSortOrderChanged",ROW_TRACK_REMOVED:"rowTrackRemoved",COLUMN_TRACK_REMOVED:"columnTrackRemoved"};morpheus.Project._recomputeCalculatedColumnFields=function(dataset,key){var metadata=dataset.getColumnMetadata();var view=new morpheus.DatasetColumnView(dataset);var nfound=0;for(var metadataIndex=0,count=metadata.getMetadataCount();metadataIndex<count;metadataIndex++){var vector=metadata.get(metadataIndex);if(vector.getProperties().get(morpheus.VectorKeys.FUNCTION)!=null&&vector.getProperties().get(key)){var f=morpheus.VectorUtil.jsonToFunction(vector,morpheus.VectorKeys.FUNCTION);for(var j=0,size=vector.size();j<size;j++){view.setIndex(j);vector.setValue(j,f(view,dataset,j))}nfound++}}return nfound};morpheus.Project.prototype={isSymmetric:function(){return this.symmetricProjectListener!=null},setSymmetric:function(heatMap){if(heatMap!=null){if(this.symmetricProjectListener==null){this.symmetricProjectListener=new morpheus.SymmetricProjectListener(heatMap.getProject(),heatMap.vscroll,heatMap.hscroll)}}else{if(this.symmetricProjectListener!=null){this.symmetricProjectListener.dispose()}this.symmetricProjectListener=null}},getHoverColumnIndex:function(){return this.hoverColumnIndex},setHoverColumnIndex:function(index){this.hoverColumnIndex=index},getHoverRowIndex:function(){return this.hoverRowIndex},setHoverRowIndex:function(index){this.hoverRowIndex=index},getRowColorModel:function(){return this.rowColorModel},getRowShapeModel:function(){return this.rowShapeModel},getColumnShapeModel:function(){return this.columnShapeModel},getRowFontModel:function(){return this.rowFontModel},getColumnFontModel:function(){return this.columnFontModel},getGroupRows:function(){return this.groupRows},getGroupColumns:function(){return this.groupColumns},getFullDataset:function(){return this.originalDataset},getColumnSelectionModel:function(){return this.columnSelectionModel},getRowSelectionModel:function(){return this.rowSelectionModel},getFilteredSortedRowIndices:function(){return this.rowIndexMapper.convertToView()},getFilteredSortedColumnIndices:function(){return this.columnIndexMapper.convertToView()},getElementSelectionModel:function(){return this.elementSelectionModel},setFullDataset:function(dataset,notify){this.originalDataset=dataset;this.rowIndexMapper.setFilter(this.rowIndexMapper.getFilter());this.columnIndexMapper.setFilter(this.columnIndexMapper.getFilter());this.columnSelectionModel.clear();this.rowSelectionModel.clear();this.elementSelectionModel.clear();if(notify){this.trigger(morpheus.Project.Events.DATASET_CHANGED)}},setGroupRows:function(keys,notify){this.groupRows=keys;for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(false)}}if(notify){this.trigger(morpheus.Project.Events.ROW_GROUP_BY_CHANGED)}},setGroupColumns:function(keys,notify){this.groupColumns=keys;for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(true)}}if(notify){this.trigger(morpheus.Project.Events.COLUMN_GROUP_BY_CHANGED)}},setRowFilter:function(filter,notify){this._saveSelection(false);this.rowIndexMapper.setFilter(filter);this._restoreSelection(false);if(notify){this.trigger(morpheus.Project.Events.ROW_FILTER_CHANGED)}},getRowFilter:function(){return this.rowIndexMapper.getFilter()},getColumnFilter:function(){return this.columnIndexMapper.getFilter()},setColumnFilter:function(filter,notify){this._saveSelection(true);this.columnIndexMapper.setFilter(filter);this._restoreSelection(true);if(notify){this.trigger(morpheus.Project.Events.COLUMN_FILTER_CHANGED)}},getColumnColorModel:function(){return this.columnColorModel},getSortedFilteredDataset:function(){return morpheus.DatasetUtil.slicedView(this.getFullDataset(),this.rowIndexMapper.convertToView(),this.columnIndexMapper.convertToView())},getSelectedDataset:function(options){options=$.extend({},{selectedRows:true,selectedColumns:true,emptyToAll:true},options);var dataset=this.getSortedFilteredDataset();var rows=null;if(options.selectedRows){rows=this.rowSelectionModel.getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(rows.length===0&&options.emptyToAll){rows=null}}var columns=null;if(options.selectedColumns){columns=this.columnSelectionModel.getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(columns.length===0&&options.emptyToAll){columns=null}}return rows==null&&columns==null?dataset:new morpheus.SlicedDatasetView(dataset,rows,columns)},_saveSelection:function(isColumns){this.elementSelectionModel.save();if(isColumns){this.columnSelectionModel.save()}else{this.rowSelectionModel.save()}},_restoreSelection:function(isColumns){if(isColumns){this.columnSelectionModel.restore()}else{this.rowSelectionModel.restore()}this.elementSelectionModel.restore()},setRowSortKeys:function(keys,notify){this._saveSelection(false);for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(false)}}this.rowIndexMapper.setSortKeys(keys);this._restoreSelection(false);if(notify){this.trigger(morpheus.Project.Events.ROW_SORT_ORDER_CHANGED)}},setColumnSortKeys:function(keys,notify){this._saveSelection(true);for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(true)}}this.columnIndexMapper.setSortKeys(keys);this._restoreSelection(true);if(notify){this.trigger(morpheus.Project.Events.COLUMN_SORT_ORDER_CHANGED)}},getRowSortKeys:function(){return this.rowIndexMapper.sortKeys},getColumnSortKeys:function(){return this.columnIndexMapper.sortKeys},convertViewColumnIndexToModel:function(viewIndex){return this.columnIndexMapper.convertViewIndexToModel(viewIndex)},convertViewRowIndexToModel:function(viewIndex){return this.rowIndexMapper.convertViewIndexToModel(viewIndex)},convertModelRowIndexToView:function(modelIndex){return this.rowIndexMapper.convertModelIndexToView(modelIndex)},convertModelColumnIndexToView:function(modelIndex){return this.columnIndexMapper.convertModelIndexToView(modelIndex)},isColumnViewIndexSelected:function(index){return this.columnSelectionModel.isViewIndexSelected(index)},isRowViewIndexSelected:function(index){return this.rowSelectionModel.isViewIndexSelected(index)}};morpheus.Util.extend(morpheus.Project,morpheus.Events);morpheus.QNorm=function(){};morpheus.QNorm.execute=function(data){var rows=data.getRowCount();var cols=data.getColumnCount();var i,j,ind;var dimat;var row_mean=new Float32Array(rows);var ranks=new Float32Array(rows);dimat=morpheus.QNorm.get_di_matrix(data);for(j=0;j<cols;j++){dimat[j].sort(function(s1,s2){if(s1.data<s2.data){return-1}if(s1.data>s2.data){return 1}return 0})}for(i=0;i<rows;i++){var sum=0;var numNonMissing=0;for(j=0;j<cols;j++){var f=dimat[j][i].data;if(!isNaN(f)){sum+=f;numNonMissing++}}row_mean[i]=sum/numNonMissing}for(j=0;j<cols;j++){morpheus.QNorm.get_ranks(ranks,dimat[j],rows);for(i=0;i<rows;i++){ind=dimat[j][i].rank;if(ranks[i]-Math.floor(ranks[i])>.4){data.setValue(ind,j,.5*(row_mean[Math.floor(ranks[i])-1]+row_mean[Math.floor(ranks[i])]))}else{data.setValue(ind,j,row_mean[Math.floor(ranks[i])-1])}}}};morpheus.QNorm.get_di_matrix=function(data){var i,j;var rows=data.getRowCount();var cols=data.getColumnCount();var dimat=[];for(j=0;j<cols;j++){dimat.push([]);for(i=0;i<rows;i++){dimat[j][i]={};dimat[j][i].data=data.getValue(i,j);dimat[j][i].rank=i}}return dimat};morpheus.QNorm.get_ranks=function(rank,x,n){var i,j,k;i=0;while(i<n){j=i;while(j<n-1&&x[j].data==x[j+1].data){j++}if(i!=j){for(k=i;k<=j;k++){rank[k]=(i+j+2)/2}}else{rank[i]=i+1}i=j+1}};morpheus.SelectionModel=function(project,isColumns){this.viewIndices=new morpheus.Set;this.project=project;this.isColumns=isColumns};morpheus.SelectionModel.prototype={setViewIndices:function(indices,notify){this.viewIndices=indices;if(notify){this.trigger("selectionChanged")}},isViewIndexSelected:function(index){return this.viewIndices.has(index)},clear:function(){this.viewIndices=new morpheus.Set},getViewIndices:function(){return this.viewIndices},count:function(){return this.viewIndices.size()},toModelIndices:function(){var project=this.project;var f=this.isColumns?project.convertViewColumnIndexToModel:project.convertViewRowIndexToModel;f=_.bind(f,project);var modelIndices=[];this.viewIndices.forEach(function(index){var m=f(index);modelIndices.push(m)});return modelIndices},save:function(){this.modelIndices=this.toModelIndices()},restore:function(){var project=this.project;this.viewIndices=new morpheus.Set;var f=this.isColumns?project.convertModelColumnIndexToView:project.convertModelRowIndexToView;f=_.bind(f,project);for(var i=0,length=this.modelIndices.length;i<length;i++){var index=f(this.modelIndices[i]);if(index!==-1){this.viewIndices.add(index)}}}};morpheus.Util.extend(morpheus.SelectionModel,morpheus.Events);morpheus.SlicedDatasetView=function(dataset,rowIndices,columnIndices){morpheus.DatasetAdapter.call(this,dataset);if(rowIndices==null){rowIndices=null}if(columnIndices==null){columnIndices=null}this.rowIndices=rowIndices;this.columnIndices=columnIndices};morpheus.SlicedDatasetView.prototype={getRowCount:function(){return this.rowIndices!==null?this.rowIndices.length:this.dataset.getRowCount()},getColumnCount:function(){return this.columnIndices!==null?this.columnIndices.length:this.dataset.getColumnCount()},getValue:function(i,j,seriesIndex){return this.dataset.getValue(this.rowIndices!==null?this.rowIndices[i]:i,this.columnIndices!==null?this.columnIndices[j]:j,seriesIndex)},setValue:function(i,j,value,seriesIndex){this.dataset.setValue(this.rowIndices!==null?this.rowIndices[i]:i,this.columnIndices!==null?this.columnIndices[j]:j,value,seriesIndex)},getRowMetadata:function(){return this.rowIndices!==null?new morpheus.MetadataModelItemView(this.dataset.getRowMetadata(),this.rowIndices):this.dataset.getRowMetadata()},getColumnMetadata:function(){return this.columnIndices!==null?new morpheus.MetadataModelItemView(this.dataset.getColumnMetadata(),this.columnIndices):this.dataset.getColumnMetadata()},toString:function(){return this.getName()}};morpheus.Util.extend(morpheus.SlicedDatasetView,morpheus.DatasetAdapter);morpheus.SlicedVector=function(v,indices){morpheus.VectorAdapter.call(this,v);this.indices=indices};morpheus.SlicedVector.prototype={setValue:function(i,value){this.v.setValue(this.indices[i],value)},getValue:function(i){return this.v.getValue(this.indices[i])},size:function(){return this.indices.length}};morpheus.Util.extend(morpheus.SlicedVector,morpheus.VectorAdapter);morpheus.AbstractSortKey=function(name,columns){this.name=name;this.columns=columns};morpheus.AbstractSortKey.prototype={lockOrder:0,columns:true,preservesDendrogram:false,unlockable:true,isColumns:function(){return this.columns},setColumns:function(columns){this.columns=columns},isPreservesDendrogram:function(){return this.preservesDendrogram},setPreservesDendrogram:function(preservesDendrogram){this.preservesDendrogram=preservesDendrogram},getLockOrder:function(){return this.lockOrder},isUnlockable:function(){return this.unlockable},setUnlockable:function(unlockable){this.unlockable=unlockable},setLockOrder:function(lockOrder){this.lockOrder=lockOrder},setSortOrder:function(sortOrder){this.sortOrder=sortOrder},getSortOrder:function(){return this.sortOrder},init:function(){}};morpheus.MatchesOnTopSortKey=function(project,modelIndices,name,columns){morpheus.AbstractSortKey.call(this,name,columns);var highlightedModelIndices={};var p=project;var viewIndices=[];for(var i=0,j=modelIndices.length,length=modelIndices.length;i<length;i++,j--){highlightedModelIndices[modelIndices[i]]=-1;viewIndices.push(i)}this.comparator=function(i1,i2){var a=highlightedModelIndices[i1];if(a===undefined){a=0}var b=highlightedModelIndices[i2];if(b===undefined){b=0}return a===b?0:a<b?-1:1};this.indices=viewIndices};morpheus.MatchesOnTopSortKey.prototype={toString:function(){return this.name},getSortOrder:function(){return 2},getComparator:function(){return this.comparator},getValue:function(i){return i}};morpheus.Util.extend(morpheus.MatchesOnTopSortKey,morpheus.AbstractSortKey);morpheus.SortKey=function(field,sortOrder,columns){morpheus.AbstractSortKey.call(this,field,columns);if(typeof sortOrder==="string"){sortOrder=morpheus.SortKey.SortOrder[sortOrder.toUpperCase()];if(sortOrder===undefined){sortOrder=0}}this.v=null;this.c=null;this.setSortOrder(sortOrder)};morpheus.SortKey.prototype={toString:function(){return this.name},init:function(dataset,visibleModelIndices){this.v=dataset.getRowMetadata().getByName(this.name);if(!this.v){this.v={};this.v.getValue=function(){return 0};this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.ASCENDING_COMPARATOR:morpheus.SortKey.DESCENDING_COMPARATOR}else{var dataType=morpheus.VectorUtil.getDataType(this.v);if(dataType==="number"){this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR:morpheus.SortKey.NUMBER_DESCENDING_COMPARATOR}else if(dataType==="[number]"){var summary=this.v.getProperties().get(morpheus.VectorKeys.ARRAY_SUMMARY_FUNCTION)||morpheus.SortKey.ARRAY_MAX_SUMMARY_FUNCTION;this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.ARRAY_ASCENDING_COMPARATOR(summary):morpheus.SortKey.ARRAY_DESCENDING_COMPARATOR(summary)}else{this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.ASCENDING_COMPARATOR:morpheus.SortKey.DESCENDING_COMPARATOR}if(this.customComparator!=null){var oldC=this.c;var customComparator=this.customComparator;if(this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING){this.c=function(a,b){var val=customComparator(a,b);return val===0?oldC(a,b):val}}else{this.c=function(a,b){var val=customComparator(b,a);return val===0?oldC(a,b):val}}}}if(this.sortOrder===morpheus.SortKey.SortOrder.TOP_N){var pairs=[];var missingIndices=[];for(var i=0,nrows=visibleModelIndices.length;i<nrows;i++){var index=visibleModelIndices[i];var value=this.v.getValue(index);if(!isNaN(value)){pairs.push({index:index,value:value})}else{missingIndices.push(index)}}var c=this.c;this.c=morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR;pairs.sort(function(pair1,pair2){return c(pair1.value,pair2.value)});var modelIndexToValue=[];var nInGroup=Math.min(pairs.length,10);var counter=0;var topIndex=0;var half=Math.floor(pairs.length/2);var topPairs=pairs.slice(0,half);var bottomPairs=pairs.slice(half);var bottomIndex=bottomPairs.length-1;var ntop=topPairs.length;var npairs=pairs.length;while(counter<npairs){for(var i=0;i<nInGroup&&topIndex<ntop;i++,topIndex++,counter++){modelIndexToValue[topPairs[topIndex].index]=counter}var indexCounterPairs=[];for(var i=0;i<nInGroup&&bottomIndex>=0;i++,bottomIndex--,counter++){indexCounterPairs.push([bottomPairs[bottomIndex].index,counter])}for(var i=indexCounterPairs.length-1,j=0;i>=0;i--,j++){var item_i=indexCounterPairs[i];var item_j=indexCounterPairs[j];modelIndexToValue[item_i[0]]=item_j[1]}}for(var i=0,length=missingIndices.length;i<length;i++,counter++){modelIndexToValue[missingIndices[i]]=counter}this.modelIndexToValue=modelIndexToValue}else{delete this.modelIndexToValue}},getComparator:function(){return this.c},getValue:function(i){return this.modelIndexToValue?this.modelIndexToValue[i]:this.v.getValue(i)}};morpheus.Util.extend(morpheus.SortKey,morpheus.AbstractSortKey);morpheus.SortByValuesKey=function(modelIndices,sortOrder,isColumnSort){morpheus.AbstractSortKey.call(this,"values",isColumnSort);this.bothCount=10;this.modelIndices=modelIndices;this.sortOrder=sortOrder;this.setSortOrder(sortOrder)};morpheus.SortByValuesKey.prototype={toString:function(){return this.name},init:function(dataset,visibleModelIndices){this.dataset=morpheus.DatasetUtil.slicedView(dataset,null,this.modelIndices);this.rowView=new morpheus.DatasetRowView(this.dataset);this.summaryFunction=this.modelIndices.length>1?morpheus.Median:function(row){return row.getValue(0)};if(this.sortOrder===morpheus.SortKey.SortOrder.TOP_N){var pairs=[];var missingIndices=[];for(var i=0,nrows=visibleModelIndices.length;i<nrows;i++){var index=visibleModelIndices[i];var value=this.summaryFunction(this.rowView.setIndex(index));if(!isNaN(value)){pairs.push({index:index,value:value})}else{missingIndices.push(index)}}pairs.sort(function(a,b){return a.value<b.value?1:a.value===b.value?0:-1});var modelIndexToValue=[];var nInGroup=Math.min(pairs.length,this.bothCount);var counter=0;var topIndex=0;var half=Math.floor(pairs.length/2);var topPairs=pairs.slice(0,half);var bottomPairs=pairs.slice(half);var bottomIndex=bottomPairs.length-1;var ntop=topPairs.length;var npairs=pairs.length;while(counter<npairs){for(var i=0;i<nInGroup&&topIndex<ntop;i++,topIndex++,counter++){modelIndexToValue[topPairs[topIndex].index]=counter}var indexCounterPairs=[];for(var i=0;i<nInGroup&&bottomIndex>=0;i++,bottomIndex--,counter++){indexCounterPairs.push([bottomPairs[bottomIndex].index,counter])}for(var i=indexCounterPairs.length-1,j=0;i>=0;i--,j++){var item_i=indexCounterPairs[i];var item_j=indexCounterPairs[j];modelIndexToValue[item_i[0]]=item_j[1]}}for(var i=0,length=missingIndices.length;i<length;i++,counter++){modelIndexToValue[missingIndices[i]]=counter}this.modelIndexToValue=modelIndexToValue}else{delete this.modelIndexToValue}},getComparator:function(){return this.c},getValue:function(i){return this.modelIndexToValue?this.modelIndexToValue[i]:this.summaryFunction(this.rowView.setIndex(i))},setSortOrder:function(sortOrder){if(typeof sortOrder==="string"){sortOrder=morpheus.SortKey.SortOrder[sortOrder.toUpperCase()]}this.sortOrder=sortOrder;if(this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING){this.c=morpheus.SortKey.ELEMENT_ASCENDING_COMPARATOR}else if(this.sortOrder===morpheus.SortKey.SortOrder.DESCENDING){this.c=morpheus.SortKey.ELEMENT_DESCENDING_COMPARATOR}else{this.c=morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR}}};morpheus.Util.extend(morpheus.SortByValuesKey,morpheus.AbstractSortKey);morpheus.SpecifiedModelSortOrder=function(modelIndices,nvisible,name,columns){morpheus.AbstractSortKey.call(this,name,columns);this.nvisible=nvisible;var modelIndexToValue=[];for(var i=0,length=modelIndices.length;i<length;i++){modelIndexToValue[modelIndices[i]]=i}this.modelIndices=modelIndices;this.modelIndexToValue=modelIndexToValue;this.c=morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR};morpheus.SpecifiedModelSortOrder.prototype={toString:function(){return this.name},getComparator:function(a,b){return this.c},getValue:function(i){return this.modelIndexToValue[i]},setSortOrder:function(sortOrder){this.sortOrder=sortOrder;this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR:morpheus.SortKey.NUMBER_DESCENDING_COMPARATOR}};morpheus.Util.extend(morpheus.SpecifiedModelSortOrder,morpheus.AbstractSortKey);morpheus.SpecifiedGroupByKey=function(clusterIds,columns){morpheus.AbstractSortKey.call(this,"Dendrogram Cut",columns);this.clusterIds=clusterIds;this.c=function(a,b){return a===b?0:a<b?-1:1}};morpheus.SpecifiedGroupByKey.prototype={toString:function(){return this.name},getComparator:function(a,b){return this.c},getValue:function(i){return this.clusterIds[i]}};morpheus.Util.extend(morpheus.SpecifiedGroupByKey,morpheus.AbstractSortKey);morpheus.SortKey.SortOrder={ASCENDING:0,DESCENDING:1,UNSORTED:2,CUSTOM:3,TOP_N:4};morpheus.SortKey.ASCENDING_COMPARATOR=function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=(""+a).toLowerCase();b=(""+b).toLowerCase();return a===b?0:a<b?-1:1};morpheus.SortKey.DESCENDING_COMPARATOR=function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=(""+a).toLowerCase();b=(""+b).toLowerCase();return a===b?0:a<b?1:-1};morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR=function(a,b){var aNaN=a==null||isNaN(a);var bNaN=b==null||isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?-1:1};morpheus.SortKey.NUMBER_DESCENDING_COMPARATOR=function(a,b){var aNaN=a==null||isNaN(a);var bNaN=b==null||isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?1:-1};morpheus.SortKey.STRING_ASCENDING_COMPARATOR=function(a,b){a=a==null||a.toLowerCase===undefined?null:a.toLowerCase();b=b==null||b.toLowerCase===undefined?null:b.toLowerCase();return a===b?0:a<b?-1:1};morpheus.SortKey.STRING_DESCENDING_COMPARATOR=function(a,b){a=a==null||a.toLowerCase===undefined?null:a.toLowerCase();b=b==null||b.toLowerCase===undefined?null:b.toLowerCase();return a===b?0:a<b?1:-1};morpheus.SortKey.ELEMENT_ASCENDING_COMPARATOR=function(obj1,obj2){var a=+obj1;var b=+obj2;var aNaN=isNaN(a);var bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}if(a===b){if(obj1!=null&&obj1.toObject&&obj2!=null&&obj2.toObject){var a1=obj1.toObject();var b1=obj2.toObject();for(var name in a1){a=a1[name];b=b1[name];var c=a===b?0:a<b?-1:1;if(c!==0){return c}}}}return a===b?0:a<b?-1:1};morpheus.SortKey.ELEMENT_DESCENDING_COMPARATOR=function(obj1,obj2){var a=+obj1;var b=+obj2;var aNaN=isNaN(a);var bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}if(a===b){if(obj1!=null&&obj1.toObject&&obj2!=null&&obj2.toObject){var a1=obj1.toObject();var b1=obj2.toObject();for(var name in a1){a=a1[name];b=b1[name];var c=a===b?0:a<b?1:-1;if(c!==0){return c}}}}return a===b?0:a<b?1:-1};morpheus.SortKey.BOX_PLOT_SUMMARY_FUNCTION=function(array){var box=array.box;if(box==null){var v=morpheus.VectorUtil.arrayAsVector(array);box=morpheus.BoxPlotItem(this.indices!=null?new morpheus.SlicedVector(v,this.indices):v);array.box=box}return box.q3};morpheus.SortKey.ARRAY_MAX_SUMMARY_FUNCTION=function(array){var a=0;if(array!=null){var aPosMax=-Number.MAX_VALUE;var aNegMax=Number.MAX_VALUE;for(var i=0,length=array.length;i<length;i++){var value=array[i];if(!isNaN(value)){if(value>=0){aPosMax=value>aPosMax?value:aPosMax}else{aNegMax=value<aNegMax?value:aNegMax}}}if(aPosMax!==-Number.MAX_VALUE){a=aPosMax}if(aNegMax!==Number.MAX_VALUE){a=Math.abs(aNegMax)>a?aNegMax:a}}return a};morpheus.SortKey.ARRAY_ASCENDING_COMPARATOR=function(summary){return function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=summary(a);b=summary(b);aNaN=isNaN(a);bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?-1:1}};morpheus.SortKey.ARRAY_DESCENDING_COMPARATOR=function(summary){return function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=summary(a);b=summary(b);aNaN=isNaN(a);bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?1:-1}};morpheus.SortKey.reverseComparator=function(c){return function(a,b){return c(b,a)}};morpheus.SortKey.keepExistingSortKeys=function(newSortKeys,existingSortKeys){for(var i=0,length=existingSortKeys.length;i<length;i++){var key=existingSortKeys[i];if(key.getLockOrder()>0){var existingIndex=-1;for(var j=0;j<newSortKeys.length;j++){if(newSortKeys[j]===key){existingIndex=j;break}}if(existingIndex!==-1){newSortKeys.splice(existingIndex,1)}newSortKeys.splice(key.getLockOrder()===1?0:newSortKeys.length,0,key)}}return newSortKeys};morpheus.SortKey.fromJSON=function(project,json){var sortKeys=[];json.forEach(function(key){var sortKey=null;if(key.type==="annotation"){sortKey=new morpheus.SortKey(key.field,key.order,key.isColumns);if(key.customSortOrder!=null){var customSortOrderMap=new morpheus.Map;for(var i=0,size=key.customSortOrder.length;i<size;i++){customSortOrderMap.set(key.customSortOrder[i],i)}var comparator=function(a,b){var v1=customSortOrderMap.get(a);var v2=customSortOrderMap.get(b);if(v1===undefined&&v2===undefined){return 0}if(v1===undefined){v1=Infinity}if(v2===undefined){v2=Infinity}return v1<v2?-1:1};sortKey.customComparator=comparator;if(key.preservesDendrogram){sortKey.nvisible=key.customSortOrder.length}}}else if(key.type==="byValues"){sortKey=new morpheus.SortByValuesKey(key.modelIndices,key.order,key.isColumns)}else if(key.type==="specified"){sortKey=new morpheus.SpecifiedModelSortOrder(key.modelIndices,key.nvisible,key.name,key.isColumns)}else if(key.type==="matchesOnTop"){sortKey=new morpheus.MatchesOnTopSortKey(project,key.modelIndices,key.name,key.isColumns)}else{if(key.field!=null){sortKey=new morpheus.SortKey(key.field,key.order)}else{console.log("Unknown key: "+key)}}if(sortKey!=null){if(key.preservesDendrogram!=null){sortKey.setPreservesDendrogram(key.preservesDendrogram)}if(key.lockOrder!=null&&key.lockOrder!==0){sortKey.setLockOrder(key.lockOrder);sortKey.setUnlockable(key.unlockable)}sortKeys.push(sortKey)}});return sortKeys};morpheus.SortKey.toJSON=function(sortKeys){var json=[];sortKeys.forEach(function(key){var sortKey=null;if(key instanceof morpheus.SortKey){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"annotation",field:""+key}}else if(key instanceof morpheus.SortByValuesKey){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"byValues",modelIndices:key.modelIndices}}else if(key instanceof morpheus.SpecifiedModelSortOrder){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"specified",modelIndices:key.modelIndices,name:key.name,nvisible:key.nvisible}}else if(key instanceof morpheus.MatchesOnTopSortKey){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"matchesOnTop",modelIndices:key.modelIndices,name:key.name}}if(sortKey!=null){sortKey.preservesDendrogram=key.isPreservesDendrogram();if(key.getLockOrder&&key.getLockOrder()!==0){sortKey.lockOrder=key.getLockOrder();sortKey.unlockable=key.isUnlockable?key.isUnlockable():false}json.push(sortKey)}else{console.log("Unknown sort key type")}});return json};morpheus.SymmetricProjectListener=function(project,vscroll,hscroll){var ignoreEvent=false;var rowGroupBy;var columnGroupBy;var rowFilter;var columnFilter;var rowSortOrder;var columnSortOrder;var columnSelection;var rowSelection;var vscrollFunction;var hscrollFunction;project.on(morpheus.Project.Events.ROW_GROUP_BY_CHANGED,rowGroupBy=function(){if(ignoreEvent){return}ignoreEvent=true;project.setGroupColumns(project.getGroupRows(),true);ignoreEvent=false});project.on(morpheus.Project.Events.COLUMN_GROUP_BY_CHANGED,columnGroupBy=function(){if(ignoreEvent){return}ignoreEvent=true;project.setGroupRows(project.getGroupColumns(),true);ignoreEvent=false});project.on(morpheus.Project.Events.ROW_FILTER_CHANGED,rowFilter=function(){if(ignoreEvent){return}ignoreEvent=true;project.setColumnFilter(project.getRowFilter(),true);ignoreEvent=false});project.on(morpheus.Project.Events.COLUMN_FILTER_CHANGED,columnFilter=function(){if(ignoreEvent){return}ignoreEvent=true;project.setRowFilter(project.getColumnFilter(),true);ignoreEvent=false});project.on(morpheus.Project.Events.ROW_SORT_ORDER_CHANGED,rowSortOrder=function(){if(ignoreEvent){return}ignoreEvent=true;project.setColumnSortKeys(project.getRowSortKeys(),true);ignoreEvent=false});project.on(morpheus.Project.Events.COLUMN_SORT_ORDER_CHANGED,columnSortOrder=function(){if(ignoreEvent){return}ignoreEvent=true;project.setRowSortKeys(project.getColumnSortKeys(),true);ignoreEvent=false});project.getColumnSelectionModel().on("selectionChanged",columnSelection=function(){if(ignoreEvent){return}ignoreEvent=true;project.getRowSelectionModel().setViewIndices(project.getColumnSelectionModel().getViewIndices(),true);ignoreEvent=false});project.getRowSelectionModel().on("selectionChanged",rowSelection=function(){if(ignoreEvent){return}ignoreEvent=true;project.getColumnSelectionModel().setViewIndices(project.getRowSelectionModel().getViewIndices(),true);ignoreEvent=false});vscroll.on("scroll",vscrollFunction=function(){if(ignoreEvent){return}ignoreEvent=true;var f=vscroll.getMaxValue()===0?0:vscroll.getValue()/vscroll.getMaxValue();hscroll.setValue(f*hscroll.getMaxValue(),true);ignoreEvent=false});hscroll.on("scroll",hscrollFunction=function(){if(ignoreEvent){return}ignoreEvent=true;var f=hscroll.getMaxValue()===0?0:hscroll.getValue()/hscroll.getMaxValue();vscroll.setValue(f*vscroll.getMaxValue(),true);ignoreEvent=false});this.dispose=function(){project.off(morpheus.Project.Events.ROW_GROUP_BY_CHANGED,rowGroupBy);project.off(morpheus.Project.Events.COLUMN_GROUP_BY_CHANGED,columnGroupBy);project.off(morpheus.Project.Events.ROW_FILTER_CHANGED,rowFilter);project.off(morpheus.Project.Events.COLUMN_FILTER_CHANGED,columnFilter);project.off(morpheus.Project.Events.ROW_SORT_ORDER_CHANGED,rowSortOrder);project.off(morpheus.Project.Events.COLUMN_SORT_ORDER_CHANGED,columnSortOrder);project.getColumnSelectionModel().off("selectionChanged",columnSelection);project.getRowSelectionModel().off("selectionChanged",rowSelection);vscroll.off("scroll",vscrollFunction);hscroll.off("scroll",hscrollFunction)}};morpheus.TransposedDatasetView=function(dataset){morpheus.DatasetAdapter.call(this,dataset)};morpheus.TransposedDatasetView.prototype={getRowCount:function(){return this.dataset.getColumnCount()},getColumnCount:function(){return this.dataset.getRowCount()},getValue:function(i,j,seriesIndex){return this.dataset.getValue(j,i,seriesIndex)},setValue:function(i,j,value,seriesIndex){this.dataset.setValue(j,i,value,seriesIndex)},getRowMetadata:function(){return this.dataset.getColumnMetadata()},getColumnMetadata:function(){return this.dataset.getRowMetadata()}};morpheus.Util.extend(morpheus.TransposedDatasetView,morpheus.DatasetAdapter);morpheus.Percentile=function(vector,p,isSorted){return morpheus.ArrayPercentile(morpheus.RemoveNaN(vector),p,isSorted)};morpheus.Percentile.toString=function(){return"Percentile"};morpheus.RemoveNaN=function(values){var array=[];for(var i=0,size=values.size();i<size;i++){var value=values.getValue(i);if(!isNaN(value)){array.push(value)}}return array};morpheus.Median=function(vector){return morpheus.ArrayPercentile(morpheus.RemoveNaN(vector),50,false)};morpheus.Median.toString=function(){return"Median"};morpheus.ArrayPercentile=function(values,p,isSorted){if(!isSorted){values.sort(function(a,b){return a<b?-1:a===b?0:1})}return d3.quantile(values,p/100)};morpheus.MaxPercentiles=function(percentiles){var f=function(vector){var values=[];for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(!isNaN(value)){values.push(value)}}if(values.length===0){return NaN}values.sort(function(a,b){return a<b?-1:a===b?0:1});var max=0;for(var i=0;i<percentiles.length;i++){var p=morpheus.ArrayPercentile(values,percentiles[i],true);if(Math.abs(p)>Math.abs(max)){max=p}}return max};f.toString=function(){var s=["Maximum of "];for(var i=0,length=percentiles.length;i<length;i++){if(i>0&&length>2){s.push(", ")}if(i===length-1){s.push(length==2?" and ":"and ")}s.push(percentiles[i])}s.push(" percentiles");return s.join("")};return f};morpheus.CountIf=function(vector,criteria){if(!/[<>=!]/.test(criteria)){criteria='=="'+criteria+'"'}var matches=0;for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(eval(value+criteria)){matches++}}return matches};morpheus.Mean=function(vector){var sum=0;var count=0;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){sum+=val;count++}}return count===0?NaN:sum/count};morpheus.Mean.toString=function(){return"Mean"};morpheus.Sum=function(vector){var sum=0;var found=false;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){found=true;sum+=val}}return!found?NaN:sum};morpheus.Sum.toString=function(){return"Sum"};morpheus.CountNonNaN=function(vector){var count=0;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){count++}}return count};morpheus.CountNonNaN.toString=function(){return"Count non-NaN"};morpheus.Max=function(vector){var max=-Number.MAX_VALUE;var found=false;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){found=true;max=Math.max(max,val)}}return!found?NaN:max};morpheus.Max.toString=function(){return"Max"};morpheus.Min=function(vector){var min=Number.MAX_VALUE;var found=false;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){found=true;min=Math.min(min,val)}}return!found?NaN:min};morpheus.Min.toString=function(){return"Min"};morpheus.Variance=function(list,mean){if(mean==undefined){mean=morpheus.Mean(list)}var sum=0;var n=0;for(var j=0,size=list.size();j<size;j++){var x=list.getValue(j);if(!isNaN(x)){var diff=x-mean;diff=diff*diff;sum+=diff;n++}}if(n<=1){return NaN}n=n-1;if(n<1){n=1}var variance=sum/n;return variance};morpheus.Variance.toString=function(){return"Variance"};morpheus.StandardDeviation=function(list,mean){return Math.sqrt(morpheus.Variance(list,mean))};morpheus.StandardDeviation.toString=function(){return"Standard deviation"};var LOG_10=Math.log(10);morpheus.Log10=function(x){return x<=0?0:Math.log(x)/LOG_10};var LOG_2=Math.log(2);morpheus.Log2=function(x){return x<=0?0:Math.log(x)/LOG_2};morpheus.FDR_BH=function(nominalPValues){var size=nominalPValues.length;var fdr=[];var pValueIndices=morpheus.Util.indexSort(nominalPValues,true);var ranks=morpheus.Util.rankIndexArray(pValueIndices);for(var i=pValueIndices.length-1;i>0;i--){var bigPValue=nominalPValues[pValueIndices[i]];var smallPValue=nominalPValues[pValueIndices[i-1]];if(bigPValue==smallPValue){ranks[pValueIndices[i-1]]=ranks[pValueIndices[i]]}}for(var i=0;i<size;i++){var rank=ranks[i];var p=nominalPValues[i];fdr[i]=p*size/rank}var pIndices=morpheus.Util.indexSort(nominalPValues,false);for(var i=0;i<pIndices.length-1;i++){var highIndex=pIndices[i];var lowIndex=pIndices[i+1];fdr[lowIndex]=Math.min(fdr[lowIndex],fdr[highIndex])}for(var i=0;i<size;i++){fdr[i]=Math.min(fdr[i],1)}return fdr};morpheus.FDR_BH.tString=function(){return"FDR(BH)"};morpheus.MAD=function(list,median){if(median==null){median=morpheus.Percentile(list,50)}var temp=[];for(var j=0,size=list.size();j<size;j++){var value=list.getValue(j);if(!isNaN(value)){temp.push(Math.abs(value-median))}}var r=morpheus.Percentile(new morpheus.Vector("",temp.length).setArray(temp),50);return 1.4826*r};morpheus.MAD.toString=function(){return"Median absolute deviation"};morpheus.CV=function(list){var mean=morpheus.Mean(list);var stdev=Math.sqrt(morpheus.Variance(list,mean));return stdev/mean};morpheus.CV.toString=function(){return"Coefficient of variation"};morpheus.BoxPlotItem=function(list){var values=morpheus.RemoveNaN(list);values.sort(function(a,b){return a===b?0:a<b?-1:1});if(values.length===0){return{median:NaN,q1:NaN,q3:NaN,lowerAdjacentValue:NaN,upperAdjacentValue:NaN}}return morpheus.BoxPlotArrayItem(values)};morpheus.BoxPlotArrayItem=function(values){var median=morpheus.ArrayPercentile(values,50,true);var q1=morpheus.ArrayPercentile(values,25,true);var q3=morpheus.ArrayPercentile(values,75,true);var w=1.5;var upperAdjacentValue=-Number.MAX_VALUE;var lowerAdjacentValue=Number.MAX_VALUE;var upperOutlier=q3+w*(q3-q1);var lowerOutlier=q1-w*(q3-q1);var sum=0;for(var i=0,length=values.length;i<length;i++){var value=values[i];if(value<=upperOutlier){upperAdjacentValue=Math.max(upperAdjacentValue,value)}if(value>=lowerOutlier){lowerAdjacentValue=Math.min(lowerAdjacentValue,value)}sum+=value}var mean=sum/values.length;if(lowerAdjacentValue>q1){lowerAdjacentValue=q1}if(upperAdjacentValue<q3){upperAdjacentValue=q3}return{mean:mean,median:median,q1:q1,q3:q3,lowerAdjacentValue:lowerAdjacentValue,upperAdjacentValue:upperAdjacentValue}};morpheus.VectorColorModel=function(){this.vectorNameToColorMap=new morpheus.Map;this.vectorNameToColorScheme=new morpheus.Map;this.colors=morpheus.VectorColorModel.TWENTY_COLORS};morpheus.VectorColorModel.YES_COLOR="#d8b365";morpheus.VectorColorModel.FEMALE="#ff99ff";morpheus.VectorColorModel.MALE="#66ccff";morpheus.VectorColorModel.TWENTY_COLORS=["#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b","#c49c94","#e377c2","#f7b6d2","#7f7f7f","#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"];morpheus.VectorColorModel.CATEGORY_20A=morpheus.VectorColorModel.TWENTY_COLORS;morpheus.VectorColorModel.CATEGORY_20B=["#393b79","#5254a3","#6b6ecf","#9c9ede","#637939","#8ca252","#b5cf6b","#cedb9c","#8c6d31","#bd9e39","#e7ba52","#e7cb94","#843c39","#ad494a","#d6616b","#e7969c","#7b4173","#a55194","#ce6dbd","#de9ed6"];morpheus.VectorColorModel.CATEGORY_20C=["#3182bd","#6baed6","#9ecae1","#c6dbef","#e6550d","#fd8d3c","#fdae6b","#fdd0a2","#31a354","#74c476","#a1d99b","#c7e9c0","#756bb1","#9e9ac8","#bcbddc","#dadaeb","#636363","#969696","#bdbdbd","#d9d9d9"];morpheus.VectorColorModel.CATEGORY_ALL=[].concat(morpheus.VectorColorModel.CATEGORY_20A,morpheus.VectorColorModel.CATEGORY_20B,morpheus.VectorColorModel.CATEGORY_20C);morpheus.VectorColorModel.TABLEAU10=["#1f77b4","#ff7f0e","#2ca02c","#d62728","#9467bd","#8c564b","#e377c2","#7f7f7f","#bcbd22","#17becf"];morpheus.VectorColorModel.STANDARD_COLORS={na:"#c0c0c0",nan:"#c0c0c0","":"#ffffff",wt:"#ffffff",n:"#ffffff",0:"#ffffff",y:morpheus.VectorColorModel.YES_COLOR,1:morpheus.VectorColorModel.YES_COLOR,male:morpheus.VectorColorModel.MALE,m:morpheus.VectorColorModel.MALE,female:morpheus.VectorColorModel.FEMALE,f:morpheus.VectorColorModel.FEMALE,kd:"#C675A8",oe:"#56b4e9",cp:"#FF9933",pcl:"#003B4A","trt_sh.cgs":"#C675A8",trt_oe:"#56b4e9",trt_cp:"#FF9933",a375:"#1490C1",a549:"#AAC8E9",hcc515:"#1C9C2A",hepg2:"#94DC89",ht29:"#946DBE",mcf7:"#C5B2D5",pc3:"#38C697",asc:"#FF8000",cd34:"#FFBB75",ha1e:"#FB4124",neu:"#FF9A94",npc:"#E57AC6",cancer:"#1490C1","immortalized normal":"#FF8000"};morpheus.VectorColorModel.getStandardColor=function(value){if(value==null){return"#ffffff"}var stringValue=value.toString().toLowerCase();return morpheus.VectorColorModel.STANDARD_COLORS[stringValue]};morpheus.VectorColorModel.getColorMapForNumber=function(length){var colors;if(length<3){colors=colorbrewer.Set1[3]}else{colors=colorbrewer.Paired[length]}return colors?colors:morpheus.VectorColorModel.TWENTY_COLORS};morpheus.VectorColorModel.prototype={toJSON:function(tracks){var _this=this;var json={};tracks.forEach(function(track){if(track.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)){var colorMap=_this.vectorNameToColorMap.get(track.getName());if(colorMap!=null){json[track.getName()]=colorMap}}else{var colorScheme=_this.vectorNameToColorScheme.get(track.getName());if(colorScheme!=null){var colorSchemeJSON=morpheus.AbstractColorSupplier.toJSON(colorScheme.getCurrentColorSupplier());json[track.getName()]=colorSchemeJSON}}});return json},fromJSON:function(json){for(var name in json){var obj=json[name];if(obj.colors){obj.scalingMode="fixed";this.vectorNameToColorScheme.set(name,morpheus.AbstractColorSupplier.fromJSON(obj))}else{this.vectorNameToColorMap.set(name,morpheus.Map.fromJSON(obj))}}},clear:function(vector){this.vectorNameToColorMap.remove(vector.getName());this.vectorNameToColorScheme.remove(vector.getName())},copy:function(){var c=new morpheus.VectorColorModel;c.colors=this.colors.slice(0);this.vectorNameToColorMap.forEach(function(colorMap,name){var newColorMap=new morpheus.Map;newColorMap.setAll(colorMap);c.vectorNameToColorMap.set(name,newColorMap)});this.vectorNameToColorScheme.forEach(function(colorScheme,name){c.vectorNameToColorScheme.set(name,colorScheme.copy(new morpheus.Project(new morpheus.Dataset({name:"",rows:1,columns:1}))))});return c},clearAll:function(){this.vectorNameToColorMap=new morpheus.Map;this.vectorNameToColorScheme=new morpheus.Map},containsDiscreteColor:function(vector,value){var metadataValueToColorMap=this.vectorNameToColorMap.get(vector.getName());if(metadataValueToColorMap===undefined){return false}var c=metadataValueToColorMap.get(value);return c!=null},setDiscreteColorMap:function(colors){this.colors=colors},getContinuousColorScheme:function(vector){return this.vectorNameToColorScheme.get(vector.getName())},isContinuous:function(vector){return this.vectorNameToColorScheme.has(vector.getName())},getDiscreteColorScheme:function(vector){return this.vectorNameToColorMap.get(vector.getName())},createContinuousColorMap:function(vector){var minMax=morpheus.VectorUtil.getMinMax(vector);var min=minMax.min;var max=minMax.max;var cs=new morpheus.HeatMapColorScheme(new morpheus.Project(new morpheus.Dataset({name:"",rows:1,columns:1})),{type:"fixed",map:[{value:min,color:colorbrewer.Greens[3][0]},{value:max,color:colorbrewer.Greens[3][2]}]});this.vectorNameToColorScheme.set(vector.getName(),cs);return cs},_getColorForValue:function(value){var color=morpheus.VectorColorModel.getStandardColor(value);if(color==null){var existingMetadataValueToColorMap=this.vectorNameToColorMap.values();for(var i=0,length=existingMetadataValueToColorMap.length;i<length;i++){color=existingMetadataValueToColorMap[i].get(value);if(color!==undefined){return color}}}return color},getContinuousMappedValue:function(vector,value){var cs=this.vectorNameToColorScheme.get(vector.getName());if(cs===undefined){cs=this.createContinuousColorMap(vector)}return cs.getColor(0,0,value)},getMappedValue:function(vector,value){var metadataValueToColorMap=this.vectorNameToColorMap.get(vector.getName());if(metadataValueToColorMap===undefined){metadataValueToColorMap=new morpheus.Map;this.vectorNameToColorMap.set(vector.getName(),metadataValueToColorMap);var values=morpheus.VectorUtil.getValues(vector);var ncolors=0;var colors=null;if(values.length<3){colors=colorbrewer.Dark2[3]}else{colors=colorbrewer.Paired[values.length]}if(!colors){if(values.length<=20){colors=d3.scale.category20().range()}else{colors=morpheus.VectorColorModel.CATEGORY_ALL}}if(colors){var ncolors=colors.length;for(var i=0,nvalues=values.length;i<nvalues;i++){var color=this._getColorForValue(values[i]);if(color==null){color=colors[i%ncolors]}metadataValueToColorMap.set(values[i],color)}}else{var _this=this;_.each(values,function(val){_this.getMappedValue(vector,val)})}}var color=metadataValueToColorMap.get(value);if(color==null){color=this._getColorForValue(value);if(color==null){var index=metadataValueToColorMap.size();color=this.colors[index%this.colors.length]}metadataValueToColorMap.set(value,color)}return color},setMappedValue:function(vector,value,color){var metadataValueToColorMap=this.vectorNameToColorMap.get(vector.getName());if(metadataValueToColorMap===undefined){metadataValueToColorMap=new morpheus.Map;this.vectorNameToColorMap.set(vector.getName(),metadataValueToColorMap)}metadataValueToColorMap.set(value,color)}};morpheus.VectorFontModel=function(){this.vectorNameToMappedValue=new morpheus.Map;this.fonts=morpheus.VectorFontModel.FONTS};morpheus.VectorFontModel.FONTS=[{weight:400},{weight:700},{weight:900}];morpheus.VectorFontModel.prototype={toJSON:function(tracks){var _this=this;var json={};tracks.forEach(function(track){if(track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){var map=_this.vectorNameToMappedValue.get(track.getName());if(map!=null){json[track.getName()]=map}}});return json},fromJSON:function(json){for(var name in json){var obj=json[name];this.vectorNameToMappedValue.set(name,morpheus.Map.fromJSON(obj))}},clear:function(vector){this.vectorNameToMappedValue.remove(vector.getName())},copy:function(){var c=new morpheus.VectorFontModel;c.fonts=this.fonts.slice(0);this.vectorNameToMappedValue.forEach(function(fontMap,name){var newFontMap=new morpheus.Map;newFontMap.setAll(fontMap);c.vectorNameToMappedValue.set(name,newFontMap)});return c},clearAll:function(){this.vectorNameToMappedValue=new morpheus.Map},_getFontForValue:function(value){if(value==null){return morpheus.VectorFontModel.FONTS[0]}var existingMetadataValueToFontMap=this.vectorNameToMappedValue.values();for(var i=0,length=existingMetadataValueToFontMap.length;i<length;i++){var font=existingMetadataValueToFontMap[i].get(value);if(font!==undefined){return font}}},getMap:function(name){return this.vectorNameToMappedValue.get(name)},getMappedValue:function(vector,value){var metadataValueToFontMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToFontMap===undefined){metadataValueToFontMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToFontMap);var values=morpheus.VectorUtil.getValues(vector);for(var i=0,nvalues=values.length;i<nvalues;i++){var font=this._getFontForValue(values[i]);if(font==null){font=this.fonts[0]}metadataValueToFontMap.set(values[i],font)}}var font=metadataValueToFontMap.get(value);if(font==null){font=this._getFontForValue(value);if(font==null){font=this.fonts[0]}metadataValueToFontMap.set(value,font)}return font},setMappedValue:function(vector,value,font){var metadataValueToFontMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToFontMap===undefined){metadataValueToFontMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToFontMap)}metadataValueToFontMap.set(value,font)}};morpheus.VectorKeys={};morpheus.VectorKeys.FIELDS="morpheus.fields";morpheus.VectorKeys.VALUE_TO_INDICES="morpheus.valueToIndices";morpheus.VectorKeys.VISIBLE_FIELDS="morpheus.visibleFields";morpheus.VectorKeys.DATA_TYPE="morpheus.dataType";morpheus.VectorKeys.ARRAY_SUMMARY_FUNCTION="morpheus.arraySummaryFunct";morpheus.VectorKeys.HEADER_SUMMARY="morpheus.headerSummary";morpheus.VectorKeys.SHOW_HEADER_SUMMARY="morpheus.showHeaderSummary";morpheus.VectorKeys.TITLE="morpheus.title";morpheus.VectorKeys.FUNCTION="morpheus.funct";morpheus.VectorKeys.SELECTION="morpheus.selection";morpheus.VectorKeys.RECOMPUTE_FUNCTION_NEW_HEAT_MAP="morpheus.recompute.funct.new.heat.map";morpheus.VectorKeys.RECOMPUTE_FUNCTION_SELECTION="morpheus.recompute.funct.selection";morpheus.VectorKeys.FORMATTER="morpheus.formatter";morpheus.VectorKeys.IS_INDEX="morpheus.isIndex";morpheus.VectorKeys.DISCRETE="morpheus.discrete";morpheus.VectorKeys.COPY_IGNORE=new morpheus.Set;morpheus.VectorKeys.COPY_IGNORE.add(morpheus.VectorKeys.HEADER_SUMMARY);morpheus.VectorKeys.COPY_IGNORE.add(morpheus.VectorKeys.DATA_TYPE);morpheus.VectorKeys.COPY_IGNORE.add(morpheus.VectorKeys.VALUE_TO_INDICES);morpheus.VectorKeys.JSON_WHITELIST=new morpheus.Set;morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.FIELDS);morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.FORMATTER);morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.DATA_TYPE);morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.TITLE);morpheus.VectorShapeModel=function(){this.shapes=morpheus.VectorShapeModel.SHAPES;this.vectorNameToMappedValue=new morpheus.Map};morpheus.VectorShapeModel.SHAPES=["circle","square","plus","x","asterisk","diamond","triangle-up","triangle-down","triangle-left","triangle-right","circle-minus"];morpheus.VectorShapeModel.FILLED_SHAPES=["circle","square","diamond","triangle-up","triangle-down","triangle-left","triangle-right"];morpheus.VectorShapeModel.prototype={toJSON:function(tracks){var _this=this;var json={};tracks.forEach(function(track){if(track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){var map=_this.vectorNameToMappedValue.get(track.getName());if(map!=null){json[track.getName()]=map}}});return json},fromJSON:function(json){for(var name in json){var obj=json[name];this.vectorNameToMappedValue.set(name,morpheus.Map.fromJSON(obj))}},clear:function(vector){this.vectorNameToMappedValue.remove(vector.getName())},copy:function(){var c=new morpheus.VectorShapeModel;c.shapes=this.shapes.slice(0);this.vectorNameToMappedValue.forEach(function(shapeMap,name){var newShapeMap=new morpheus.Map;newShapeMap.setAll(shapeMap);c.vectorNameToMappedValue.set(name,newShapeMap)});return c},clearAll:function(){this.vectorNameToMappedValue=new morpheus.Map},_getShapeForValue:function(value){if(value==null){return"none"}var existingMetadataValueToShapeMap=this.vectorNameToMappedValue.values();for(var i=0,length=existingMetadataValueToShapeMap.length;i<length;i++){var shape=existingMetadataValueToShapeMap[i].get(value);if(shape!==undefined){return shape}}},getMap:function(name){return this.vectorNameToMappedValue.get(name)},getMappedValue:function(vector,value){var metadataValueToShapeMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToShapeMap===undefined){metadataValueToShapeMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToShapeMap);var values=morpheus.VectorUtil.getValues(vector);for(var i=0,nvalues=values.length;i<nvalues;i++){var shape=this._getShapeForValue(values[i]);if(shape==null){shape=this.shapes[i%this.shapes.length]}metadataValueToShapeMap.set(values[i],shape)}}var shape=metadataValueToShapeMap.get(value);if(shape==null){shape=this._getShapeForValue(value);if(shape==null){var index=metadataValueToShapeMap.size();shape=this.shapes[index%this.shapes.length]}metadataValueToShapeMap.set(value,shape)}return shape},setMappedValue:function(vector,value,shape){var metadataValueToShapeMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToShapeMap===undefined){metadataValueToShapeMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToShapeMap)}metadataValueToShapeMap.set(value,shape)}};morpheus.VectorUtil=function(){};morpheus.VectorUtil.jsonToFunction=function(vector,key){var f=vector.getProperties().get(key);if(typeof f==="object"){var binSize=f.binSize;var min=f.domain[0];var max=f.domain[1];var numberOfBins=Math.ceil((max-min)/binSize);var percent=f.percent;var cumulative=f.cumulative;var histogramFunction=function(view,selectedDataset,columnIndex){var total=0;var binNumberToOccurences=new Uint32Array(numberOfBins);for(var i=0,nrows=selectedDataset.getRowCount();i<nrows;i++){var value=selectedDataset.getValue(i,columnIndex);if(!isNaN(value)){if(value>=min&&value<=max){var bin=Math.floor((value-min)/binSize);if(bin<0){bin=0}else if(bin>=numberOfBins){bin=numberOfBins-1}binNumberToOccurences[bin]++}total++}}if(cumulative){for(var i=numberOfBins-2;i>=0;i--){binNumberToOccurences[i]+=binNumberToOccurences[i+1]}}if(percent){var percents=new Float32Array(numberOfBins);for(var i=0;i<numberOfBins;i++){percents[i]=100*(binNumberToOccurences[i]/total)}return percents}return binNumberToOccurences};vector.getProperties().set(key,histogramFunction);var jsonSpec=f;f=histogramFunction;f.toJSON=function(){return jsonSpec}}return f};morpheus.VectorUtil.createValueToIndexMap=function(vector,splitArrayValues){var map=new morpheus.Map;var isArray=splitArrayValues&&morpheus.VectorUtil.getDataType(vector)[0]==="[";for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(isArray){if(val!=null){for(var k=0;k<val.length;k++){map.set(val[k],j)}}}else{map.set(val,j)}}return map};morpheus.VectorUtil.createValueToIndicesMap=function(vector,splitArrayValues){if(!vector){throw"vector is null"}var isArray=splitArrayValues&&morpheus.VectorUtil.getDataType(vector)[0]==="[";var map=new morpheus.Map;for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(isArray){if(val!=null){for(var k=0;k<val.length;k++){var list=map.get(val[k]);if(list===undefined){list=[];map.set(val[k],list)}list.push(j)}}}else{var list=map.get(val);if(list===undefined){list=[];map.set(val,list)}list.push(j)}}return map};morpheus.VectorUtil.createValueToCountMap=function(vector){if(!vector){throw"vector is null"}var map=new morpheus.Map;var dataType=morpheus.VectorUtil.getDataType(vector);var isArray=dataType[0]==="[";for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(val!=null){if(isArray){for(var k=0;k<val.length;k++){var count=map.get(val[k])||0;map.set(val[k],count+1)}}else{var count=map.get(val)||0;map.set(val,count+1)}}}return map};morpheus.VectorUtil.createValuesToIndicesMap=function(vectors){var map=new morpheus.Map;var nvectors=vectors.length;if(vectors[0]==null){throw"no vectors found"}for(var i=0,nitems=vectors[0].size();i<nitems;i++){var array=[];for(var j=0;j<nvectors;j++){var vector=vectors[j];var val=vector.getValue(i);array.push(val)}var key=new morpheus.Identifier(array);var list=map.get(key);if(list===undefined){list=[];map.set(key,list)}list.push(i)}return map};morpheus.VectorUtil.createValuesToIndexMap=function(vectors){var map=new morpheus.Map;var nvectors=vectors.length;if(vectors[0]==null){throw"no vectors found"}for(var i=0,nitems=vectors[0].size();i<nitems;i++){var array=[];for(var j=0;j<nvectors;j++){var vector=vectors[j];var val=vector.getValue(i);array.push(val)}var key=new morpheus.Identifier(array);map.set(key,i)}return map};morpheus.VectorUtil.createValuesToCountMap=function(vectors){var map=new morpheus.Map;var nvectors=vectors.length;if(vectors[0]==null){throw"no vectors found"}for(var i=0,nitems=vectors[0].size();i<nitems;i++){var array=[];for(var j=0;j<nvectors;j++){var vector=vectors[j];var val=vector.getValue(i);array.push(val)}var key=new morpheus.Identifier(array);var count=map.get(key)||0;map.set(key,count+1)}return map};morpheus.VectorUtil.getValues=function(vector,excludeNull){var set=new morpheus.Set;for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(excludeNull&&val==null){continue}set.add(val)}var array=set.values();array.sort(morpheus.SortKey.ASCENDING_COMPARATOR);return array};morpheus.VectorUtil.getSet=function(vector,splitArrayValues){var set=new morpheus.Set;var isArray=splitArrayValues&&morpheus.VectorUtil.getDataType(vector)[0]==="[";for(var j=0,size=vector.size();j<size;j++){var value=vector.getValue(j);if(isArray){if(value!=null){for(var k=0,nvalues=value.length;k<nvalues;k++){set.add(value[k])}}}else{set.add(value)}}return set};morpheus.VectorUtil.maybeConvertToStringArray=function(vector,delim){var newValues=[];var regex=new RegExp(delim);var found=false;for(var i=0,nrows=vector.size();i<nrows;i++){var s=vector.getValue(i);if(s!=null){if(!s.split){return false}var tokens=s.split(regex);newValues.push(tokens);if(!found&&tokens.length>1){found=true}}}if(found){for(var i=0,nrows=newValues.length;i<nrows;i++){vector.setValue(i,newValues[i])}vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"[string]")}return found};morpheus.VectorUtil.maybeConvertStringToNumber=function(vector){var newValues=[];var found=false;for(var i=0,nrows=vector.size();i<nrows;i++){var s=vector.getValue(i);if(s!=null&&s!==""&&s!=="NA"&&s!=="NaN"){if(!$.isNumeric(s)){return false}else{found=true}}newValues.push(parseFloat(s))}if(!found){return false}for(var i=0,nrows=newValues.length;i<nrows;i++){vector.setValue(i,newValues[i])}vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"number");return true};morpheus.VectorUtil.containsMoreThanOneValue=function(vector){return morpheus.VectorUtil.containsMoreThanNValues(vector,1)};morpheus.VectorUtil.containsMoreThanNValues=function(vector,n){var s=new morpheus.Set;for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);s.add(val);if(s.size()>n){return true}}return false};morpheus.VectorUtil.createSpanMap=function(vector){var previous=vector.getValue(0);var startIndexToEndIndex=new morpheus.Map;var start=0;for(var i=1,nrows=vector.size();i<nrows;i++){var val=vector.getValue(i);if(previous!==val){previous=val;startIndexToEndIndex.set(start,i);start=i}}startIndexToEndIndex.set(start,vector.size());return startIndexToEndIndex};morpheus.VectorUtil.toArray=function(vector){var array=[];for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);array.push(val)}return array};morpheus.VectorUtil.arrayAsVector=function(array,name){var v=new morpheus.Vector(name,array.length);v.array=array;return v};morpheus.VectorUtil.toString=function(vector){var array=[];for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);array.push(val)}return array.join(", ")};morpheus.VectorUtil.getDataType=function(vector){var dataType=vector.getProperties().get(morpheus.VectorKeys.DATA_TYPE);if(dataType===undefined){var firstNonNull=morpheus.VectorUtil.getFirstNonNull(vector);dataType=morpheus.Util.getDataType(firstNonNull);vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,dataType)}return dataType};morpheus.VectorUtil.getMinMax=function(vector){var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;var fields=vector.getProperties().get(morpheus.VectorKeys.FIELDS);var isArray=morpheus.VectorUtil.getDataType(vector)[0]==="[";if(fields!=null){var nvalues=fields.length;for(var i=0,size=vector.size();i<size;i++){var array=vector.getValue(i);if(array){for(var j=0;j<nvalues;j++){var value=array[j];if(!isNaN(value)){min=value<min?value:min;max=value>max?value:max}}}}}else if(isArray){for(var i=0,size=vector.size();i<size;i++){var array=vector.getValue(i);if(array!=null){for(var j=0,nvalues=array.length;j<nvalues;j++){var value=array[j];if(!isNaN(value)){min=value<min?value:min;max=value>max?value:max}}}}}else{for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(!isNaN(value)){min=value<min?value:min;max=value>max?value:max}}}return{min:min,max:max}};morpheus.VectorUtil.getFirstNonNull=function(vector){for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(val!=null){return val}}return null};morpheus.VectorUtil.isNumber=function(vector){return morpheus.VectorUtil.getDataType(vector)==="number"};morpheus.Vector=function(name,size){this.array=[];morpheus.AbstractVector.call(this,name,size)};morpheus.Vector.fromArray=function(name,array){var v=new morpheus.Vector(name,array.length);v.array=array;return v};morpheus.Vector.prototype={push:function(value){this.array.push(value)},setValue:function(index,value){this.array[index]=value},getValue:function(index){return this.array[index]},setName:function(name){this.name=name},setArray:function(array){this.array=array;return this}};morpheus.Util.extend(morpheus.Vector,morpheus.AbstractVector);morpheus.LandingPage=function(pageOptions){pageOptions=$.extend({},{el:$("#vis")},pageOptions);this.pageOptions=pageOptions;var _this=this;var html=[];html.push('<div style="display:none;" class="container-fluid">');html.push('<div style="min-height:78vh" class="row">');html.push('<div class="col-xs-12 col-md-offset-1 col-md-7"><div'+' data-name="input"></div>');html.push('<div class="clearfix"></div>');html.push("</div>");html.push('<div data-name="desc" class="col-xs-12 col-md-3"><p><img'+' src="https://software.broadinstitute.org/morpheus/css/images/morpheus_landing_img.png" style="width:100%;"></p></div>');html.push("</div>");html.push('<div class="row"><div class="col-xs-12 morpheus-footer"></div></div>');html.push("</div>");var $el=$(html.join(""));(new morpheus.HelpMenu).$el.appendTo($el.find(".morpheus-footer"));this.$el=$el;var $description=$el.find("[data-name=desc]");morpheus.Util.createMorpheusHeader().appendTo($description);$("<p>Versatile matrix visualization and analysis software</p><p>View your dataset as a heat"+" map,"+" then explore"+" the"+' interactive tools in Morpheus. Cluster, create new annotations, search, filter, sort, display charts, and more.</p><p style="color:#586069;">30,000+ users <br />100,000+'+" matrices analyzed</p>").appendTo($description);var $input=$el.find("[data-name=input]");$('<svg width="32px" height="32px"><g><rect x="0" y="0" width="32" height="14" style="fill:#ca0020;stroke:none"/><rect x="0" y="18" width="32" height="14" style="fill:#0571b0;stroke:none"/></g></svg><h2 style="padding-left: 4px; display:inline-block;">Open</h2>').appendTo($input);$('<div style="margin-bottom:20px;"><small>All'+" data is"+" processed in the"+" browser and never sent to any server.</small></div>").appendTo($input);var filePicker=new morpheus.FilePicker({fileCallback:function(file){_this.openFile(file)},optionsCallback:function(opt){_this.open(opt)}});filePicker.$el.appendTo($input);if(pageOptions.tabManager){this.tabManager=pageOptions.tabManager}else{this.tabManager=new morpheus.TabManager({landingPage:this});this.tabManager.on("change rename add remove",function(e){var title=_this.tabManager.getTabText(_this.tabManager.getActiveTabId());if(title==null||title===""){title="Morpheus"}document.title=title});this.tabManager.$nav.appendTo($(this.pageOptions.el));this.tabManager.$tabContent.appendTo($(this.pageOptions.el))}};morpheus.LandingPage.prototype={open:function(openOptions){this.dispose();var optionsArray=_.isArray(openOptions)?openOptions:[openOptions];var _this=this;for(var i=0;i<optionsArray.length;i++){var options=optionsArray[i];options.tabManager=_this.tabManager;options.focus=i===0;options.standalone=true;options.landingPage=_this;new morpheus.HeatMap(options)}},dispose:function(){this.$el.hide()},show:function(){var _this=this;this.$el.show();$(window).on("beforeunload.morpheus",function(){if(_this.tabManager.getTabCount()>0){return"Are you sure you want to close Morpheus?"}})},openFile:function(value){var _this=this;var fileName=morpheus.Util.getFileName(value);if(fileName.toLowerCase().indexOf(".json")===fileName.length-5){morpheus.Util.getText(value).done(function(text){_this.open(JSON.parse(text))}).fail(function(err){morpheus.FormBuilder.showMessageModal({title:"Error",message:"Unable to load session"})})}else{var options={dataset:{file:value,options:{interactive:true}}};morpheus.OpenDatasetTool.fileExtensionPrompt(fileName,function(readOptions){if(readOptions){for(var key in readOptions){options.dataset.options[key]=readOptions[key]}}_this.open(options)})}}};morpheus.SampleDatasets=function(options){var _this=this;var $el=options.$el;this.callback=options.callback;$el.on("click","[name=ccle]",function(e){var $this=$(this);var obj={};$this.parents(".collapse").find("input:checked").each(function(i,c){obj[$(c).data("type")]=true});_this.openCCLE(obj);e.preventDefault()});$el.on("click","[name=tcgaLink]",function(e){e.preventDefault();var $this=$(this);var type=$this.data("disease-type");var obj={};$this.parents(".collapse").find("input:checked").each(function(i,c){obj[$(c).data("type")]=true});var disease;for(var i=0;i<_this.diseases.length;i++){if(_this.diseases[i].type===type){disease=_this.diseases[i];break}}obj.type=type;obj.name=disease.name;_this.openTcga(obj)});$el.on("click","[data-toggle=dataTypeToggle]",function(e){var $this=$(this);var $button=$this.parents(".collapse").find("button");var isDisabled=$this.parents(".collapse").find("input:checked").length===0;$button.prop("disabled",isDisabled)});fetch("https://software.broadinstitute.org/morpheus/preloaded-datasets/tcga/tcga_index.txt").then(function(response){if(response.ok){return response.text()}}).then(function(text){var exampleHtml=[];var id=_.uniqueId("morpheus");exampleHtml.push('<a data-toggle="collapse" href="#'+id+'" aria-expanded="false" aria-controls="'+id+'">Cancer Cell Line Encyclopedia (CCLE), Project Achilles</a>');exampleHtml.push('<div class="collapse" id="'+id+'">');exampleHtml.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align:'+' top;">');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;"'+' data-toggle="dataTypeToggle"'+' data-type="mrna">GENE EXPRESSION</label>');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle"'+' data-type="cn">COPY NUMBER BY GENE</label>');exampleHtml.push("</div>");exampleHtml.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align: top;">');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle"'+' data-type="sig_genes">MUTATIONS</label>');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle"'+' data-type="ach">GENE ESSENTIALITY</label>');exampleHtml.push("</div>");exampleHtml.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align: top;">');exampleHtml.push('<button disabled type="button" class="btn btn-default" name="ccle">Open</button>');exampleHtml.push("</div>");exampleHtml.push("</div>");exampleHtml.push("<hr>");exampleHtml.push('<div>TCGA data <a target="_blank" href="https://confluence.broadinstitute.org/display/GDAC/Dashboard-Stddata">(Broad GDAC 1/28/2016)</a></div><span>Please adhere to the'+' <a target="_blank"'+' href="http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines">TCGA'+" publication guidelines</a></u> when using TCGA data in your publications.</span>");exampleHtml.push("<br />");exampleHtml.push('<div data-name="tcga"></div>');$(exampleHtml.join("")).appendTo($el);if(options.show){$el.css("display","")}var lines=text.split("\n");var diseases=[];for(var i=0;i<lines.length;i++){var line=lines[i];if(line===""){continue}var tokens=line.split("\t");var type=tokens[0];var dataTypes=tokens[1].split(",");var name=morpheus.TcgaUtil.DISEASE_STUDIES[type];var disease={mrna:dataTypes.indexOf("mRNAseq_RSEM_normalized_log2.txt")!==-1,sig_genes:dataTypes.indexOf("sig_genes.txt")!==-1,gistic:dataTypes.indexOf("all_lesions.conf_99.txt")!==-1,sample_info:dataTypes.indexOf("All_CDEs.txt")!==-1,mutation:dataTypes.indexOf("mutations_merged.maf.txt")!==-1,rppa:dataTypes.indexOf("rppa.txt")!==-1,methylation:dataTypes.indexOf("meth.by_mean.data.txt")!==-1,name:name,type:type,dataTypes:dataTypes};if(disease.mrna||disease.gistic||disease.sig_genes||disease.rppa||disease.methylation){diseases.push(disease)}}diseases.sort(function(a,b){a=a.name.toLowerCase();b=b.name.toLowerCase();return a===b?0:a<b?-1:1});var tcga=[];_this.diseases=diseases;for(var i=0;i<diseases.length;i++){var id=_.uniqueId("morpheus");var disease=diseases[i];tcga.push("<div>");tcga.push('<a data-toggle="collapse" href="#'+id+'" aria-expanded="false"'+' aria-controls="'+id+'">'+disease.name+" ("+disease.type+")</a>");tcga.push('<div class="collapse" id="'+id+'">');for(var j=0;j<morpheus.SampleDatasets.TCGA_DISEASE_TYPES_INFO.length;j++){var info=morpheus.SampleDatasets.TCGA_DISEASE_TYPES_INFO[j];if(j%2===0){if(j>0){tcga.push("</div>")}tcga.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align:top;">')}tcga.push('<label><input type="checkbox" style="margin-left:4px;"'+' data-toggle="dataTypeToggle"'+' data-type="'+info.type+'"'+(!disease[info.id]?" disabled":"")+">"+info.name+"</label>")}tcga.push("</div>");tcga.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align:top;">');tcga.push('<button disabled type="button" class="btn btn-default" name="tcgaLink"'+' data-disease-type="'+disease.type+'">Open</button>');tcga.push("</div>");tcga.push("</div>");tcga.push("</div>")}$(tcga.join("")).appendTo($el.find("[data-name=tcga]"))}).catch(function(error){console.log(error)})};morpheus.SampleDatasets.getTcgaDataset=function(options){var baseUrl="https://software.broadinstitute.org/morpheus/preloaded-datasets/tcga/"+options.type+"/";var datasetOptions={};if(options.mrna){datasetOptions.mrna=baseUrl+"mRNAseq_RSEM_normalized_log2.txt"}if(options.methylation){datasetOptions.methylation=baseUrl+"meth.by_mean.data.txt"}if(options.sig_genes){datasetOptions.mutation=baseUrl+"mutations_merged.maf.txt";datasetOptions.sigGenes=baseUrl+"sig_genes.txt"}if(options.rppa){datasetOptions.rppa=baseUrl+"rppa.txt"}if(options.gistic){datasetOptions.gistic=baseUrl+"all_lesions.conf_99.txt"}if(options.gisticGene){datasetOptions.gisticGene=baseUrl+"all_data_by_genes.txt"}datasetOptions.mrnaClust=baseUrl+"bestclus.txt";datasetOptions.columnAnnotations=[{file:baseUrl+"All_CDEs.txt",datasetField:"participant_id",fileField:"patient_id",transposed:false}];return morpheus.TcgaUtil.getDataset(datasetOptions)};morpheus.SampleDatasets.getCCLEDataset=function(options){var datasets=[];if(options.sig_genes){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/ccle2maf_081117.maf.txt")}if(options.cn){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/CCLE_copynumber_byGene_2013-12-03.gct")}if(options.mrna){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/CCLE_expression_081117.rpkm.gct")}if(options.ach){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/Achilles_v2.20.2_GeneSolutions.gct")}var d=$.Deferred();var datasetPromise=morpheus.DatasetUtil.readDatasetArray(datasets);datasetPromise.done(function(dataset){var idVector=dataset.getColumnMetadata().get(0);var siteVector=dataset.getColumnMetadata().add("site");for(var j=0,ncols=siteVector.size();j<ncols;j++){var id=idVector.getValue(j);var index=id.indexOf("_");if(index!==-1){idVector.setValue(j,id.substring(0,index));siteVector.setValue(j,id.substring(index+1))}}d.resolve(dataset)}).fail(function(err){d.reject(err)});return d};morpheus.SampleDatasets.prototype={openTcga:function(options){this.callback({name:options.name,renderReady:function(heatMap){var whitelist=["age_at_initial_pathologic_diagnosis","breast_carcinoma_estrogen_receptor_status","breast_carcinoma_progesterone_receptor_status","lab_proc_her2_neu_immunohistochemistry_receptor_status","days_to_death","ethnicity","gender","histological_type","pathologic_stage"];var columnMetadata=heatMap.getProject().getFullDataset().getColumnMetadata();for(var i=0;i<whitelist.length;i++){if(columnMetadata.getByName(whitelist[i])){heatMap.addTrack(whitelist[i],true,"color")}}if(options.sig_genes){if(heatMap.getTrackIndex("q_value",false)===-1){heatMap.addTrack("q_value",false,"text")}}},columns:[{field:"participant_id",display:"text"},{field:"sample_type",display:"color"},{field:"mutation_summary",display:"stacked_bar"},{field:"mutation_summary_selection",display:"stacked_bar"},{field:"mRNAseq_cluster",display:"color, highlight"}],dataset:morpheus.SampleDatasets.getTcgaDataset(options)})},openCCLE:function(options){var name=[];if(options.sig_genes){name.push("Mut")}if(options.cn){name.push("CN")}if(options.mrna){name.push("Exp")}if(options.ach){name.push("Ach")}this.callback({rows:[{field:"id",display:"text"},{field:"Description",display:"text, tooltip"},{field:"mutation_summary",display:"stacked_bar"},{field:"Source",display:"color"}],columns:[{field:"id",display:"text,tooltip"},{field:"mutation_summary",display:"stacked_bar"},{field:"site",display:"color, highlight"}],dataset:morpheus.SampleDatasets.getCCLEDataset(options),name:"CCLE - "+name.join(", ")})}};morpheus.SampleDatasets.TCGA_DISEASE_TYPES_INFO=[{id:"mrna",name:"GENE EXPRESSION",type:"mrna"},{id:"gistic",name:"GISTIC COPY NUMBER",type:"gistic"},{id:"gistic",name:"COPY NUMBER BY GENE",type:"gisticGene"},{id:"sig_genes",name:"MUTATION",type:"sig_genes"},{id:"rppa",name:"PROTEOMICS",type:"rppa"},{id:"methylation",name:"METHYLATION",type:"methylation"}];morpheus.AdjustDataTool=function(){};morpheus.AdjustDataTool.prototype={toString:function(){return"Adjust"},init:function(project,form){var _this=this;form.$form.find("[name=scale_column_sum]").on("change",function(e){form.setVisible("column_sum",form.getValue("scale_column_sum"))});form.setVisible("column_sum",false)},gui:function(){return[{name:"scale_column_sum",type:"checkbox",help:"Whether to scale each column sum to a specified value"},{name:"column_sum",type:"text",style:"max-width:150px;"},{name:"log_2",type:"checkbox"},{name:"inverse_log_2",type:"checkbox"},{name:"quantile_normalize",type:"checkbox"},{name:"z-score",type:"checkbox",help:"Subtract mean, divide by standard deviation"},{name:"robust_z-score",type:"checkbox",help:"Subtract median, divide by median absolute deviation"},{name:"use_selected_rows_and_columns_only",type:"checkbox"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;if(options.input.log_2||options.input.inverse_log_2||options.input["z-score"]||options.input["robust_z-score"]||options.input.quantile_normalize||options.input.scale_column_sum){var sortedFilteredDataset=morpheus.DatasetUtil.copy(project.getSortedFilteredDataset());var rowIndices=project.getRowSelectionModel().getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(rowIndices.length===0){rowIndices=null}var columnIndices=project.getColumnSelectionModel().getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(columnIndices.length===0){columnIndices=null}var dataset=options.input.use_selected_rows_and_columns_only?new morpheus.Slice:sortedFilteredDataset;var rowView=new morpheus.DatasetRowView(dataset);var functions=[];if(options.input.scale_column_sum){var scaleToValue=parseFloat(options.input.column_sum);if(!isNaN(scaleToValue)){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var sum=0;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var value=dataset.getValue(i,j);if(!isNaN(value)){sum+=value}}var ratio=scaleToValue/sum;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var value=dataset.getValue(i,j);dataset.setValue(i,j,value*ratio)}}}}if(options.input.log_2){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){dataset.setValue(i,j,morpheus.Log2(dataset.getValue(i,j)))}}}if(options.input.inverse_log_2){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(value>=0){dataset.setValue(i,j,Math.pow(2,value))}}}}if(options.input.quantile_normalize){morpheus.QNorm.execute(dataset)}if(options.input["z-score"]){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){rowView.setIndex(i);var mean=morpheus.Mean(rowView);var stdev=Math.sqrt(morpheus.Variance(rowView));for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){dataset.setValue(i,j,(dataset.getValue(i,j)-mean)/stdev)}}}if(options.input["robust_z-score"]){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){rowView.setIndex(i);var median=morpheus.Median(rowView);var mad=morpheus.MAD(rowView,median);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){dataset.setValue(i,j,(dataset.getValue(i,j)-median)/mad)}}}return new morpheus.HeatMap({name:heatMap.getName(),dataset:dataset,parent:heatMap,symmetric:project.isSymmetric()&&dataset.getColumnCount()===dataset.getRowCount()})}}};morpheus.AnnotateDendrogramTool=function(isColumns){this._isColumns=isColumns};morpheus.AnnotateDendrogramTool.prototype={toString:function(){return"Annotate Dendrogram"},gui:function(){return[{name:"file",value:"",type:"file",required:true,help:"an xlsx file or a tab-delimitted text file"}]},execute:function(options){var fileOrUrl=options.input.file;var isColumns=this._isColumns;var heatMap=options.heatMap;var result=morpheus.Util.readLines(fileOrUrl);var fileName=morpheus.Util.getFileName(fileOrUrl);var dendrogram=isColumns?heatMap.columnDendrogram:heatMap.rowDendrogram;var nameToNode=new morpheus.Map;morpheus.DendrogramUtil.dfs(dendrogram.tree.rootNode,function(node){nameToNode.set(node.name,node);return true});var tab=/\t/;result.done(function(lines){var header=lines[0].split(tab);var promptTool={};promptTool.execute=function(options){var nodeIdField=options.input.node_id_field;var nodeIdIndex=_.indexOf(header,nodeIdField);var numberOfMatchingNodes=0;for(var i=1;i<lines.length;i++){var array=lines[i].split(tab);var nodeName=array[nodeIdIndex];var node=nameToNode.get(nodeName);if(node!==undefined){numberOfMatchingNodes++;var info=node.info||(node.info={});for(var j=0;j<array.length;j++){if(j===nodeIdIndex){continue}var vals=info[header[j]];if(vals===undefined){vals=[];info[header[j]]=vals}vals.push(array[j])}}}heatMap.trigger("dendrogramAnnotated",{isColumns:isColumns});dendrogram.setInvalid(true);dendrogram.repaint()};promptTool.toString=function(){return"Select Node Id Field"};promptTool.gui=function(){return[{name:"node_id_field",type:"select",options:_.map(header,function(item){return{name:item,value:item}}),required:true}]};morpheus.HeatMap.showTool(promptTool,heatMap)})}};morpheus.ChartTool=function(chartOptions){var _this=this;this.project=chartOptions.project;this.heatmap=chartOptions.heatmap;var project=this.project;this.$el=$('<div class="container-fluid">'+'<div class="row">'+'<div data-name="configPane" class="col-xs-2"></div>'+'<div class="col-xs-10"><div style="position:relative;" data-name="chartDiv"></div></div>'+"</div></div>");var formBuilder=new morpheus.FormBuilder({formStyle:"vertical"});this.formBuilder=formBuilder;formBuilder.append({name:"chart_type",type:"bootstrap-select",options:["boxplot","row profile","column profile","row scatter matrix","column scatter"+" matrix"]});var rowOptions=[];var columnOptions=[];var numericRowOptions=[];var numericColumnOptions=[];var options=[];var numericOptions=[];var updateOptions=function(){var dataset=project.getFullDataset();rowOptions=[{name:"(None)",value:""}];columnOptions=[{name:"(None)",value:""}];numericRowOptions=[{name:"(None)",value:""}];numericColumnOptions=[{name:"(None)",value:""}];options=[{name:"(None)",value:""}];numericOptions=[{name:"(None)",value:""}];morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata()).forEach(function(name){var dataType=morpheus.VectorUtil.getDataType(dataset.getRowMetadata().getByName(name));if(dataType==="number"||dataType==="[number]"){numericRowOptions.push({name:name+" (row)",value:name+"_r"})}rowOptions.push({name:name+" (row)",value:name+"_r"})});morpheus.MetadataUtil.getMetadataNames(dataset.getColumnMetadata()).forEach(function(name){var dataType=morpheus.VectorUtil.getDataType(dataset.getColumnMetadata().getByName(name));if(dataType==="number"||dataType==="[number]"){numericColumnOptions.push({name:name+" (column)",value:name+"_c"})}columnOptions.push({name:name+" (column)",value:name+"_c"})});options=options.concat(rowOptions.slice(1));options=options.concat(columnOptions.slice(1));numericOptions=numericOptions.concat(numericRowOptions.slice(1));numericOptions=numericOptions.concat(numericColumnOptions.slice(1))};updateOptions();formBuilder.append({name:"group_by",type:"bootstrap-select",options:options});formBuilder.append({name:"axis_label",type:"bootstrap-select",options:rowOptions});formBuilder.append({name:"show_outliers",type:"checkbox",value:true});formBuilder.append({name:"color",type:"bootstrap-select",options:options});formBuilder.append({name:"tooltip",type:"bootstrap-select",multiple:true,search:true,options:options.slice(1)});formBuilder.append({name:"chart_width",type:"range",value:400,min:60,max:800,step:10});formBuilder.append({name:"chart_height",type:"range",value:400,min:20,max:800,step:10});var chartTypeToParameter={"row profile":{axis_label:"columns",tooltip:"columns",color:"rows"},"column profile":{axis_label:"rows",tooltip:"rows",color:"columns"},"row scatter matrix":{axis_label:"rows",color:"columns",tooltip:"columns"},"column scatter matrix":{axis_label:"columns",color:"rows",tooltip:"rows"},boxplot:{group_by:true,show_outliers:true,tooltip:"both"}};function setVisibility(){var chartType=formBuilder.getValue("chart_type");var chartOptions=chartTypeToParameter[chartType];if(chartOptions.axis_label!=null){formBuilder.setOptions("axis_label",chartOptions.axis_label==="rows"?rowOptions:columnOptions,true)}formBuilder.setVisible("color",chartOptions.color!=null);formBuilder.setVisible("axis_label",chartOptions.axis_label!=null);formBuilder.setVisible("group_by",chartOptions.group_by);formBuilder.setVisible("show_outliers",chartOptions.show_outliers);formBuilder.setOptions("tooltip",chartOptions.tooltip==="rows"?rowOptions.slice(1):chartOptions.tooltip==="columns"?columnOptions.slice(1):options);formBuilder.setOptions("color",chartOptions.color==="rows"?rowOptions:chartOptions.color==="columns"?columnOptions:options)}this.tooltip=[];var draw=function(){_.debounce(_this.draw(),100)};formBuilder.$form.on("change","select,input[type=range]",function(e){if($(this).attr("name")==="tooltip"){var tooltipVal=_this.formBuilder.getValue("tooltip");_this.tooltip.length=0;if(tooltipVal!=null){tooltipVal.forEach(function(tip){_this.tooltip.push(morpheus.ChartTool.getVectorInfo(tip))})}}else{setVisibility();draw()}});formBuilder.$form.on("click","input[type=checkbox]",function(e){draw()});formBuilder.$form.on("keypress","input[type=text]",function(e){if(e.which===13){draw()}});setVisibility();var trackChanged=function(){updateOptions();setVisibility();formBuilder.setOptions("group_by",options,true)};project.getColumnSelectionModel().on("selectionChanged.chart",draw);project.getRowSelectionModel().on("selectionChanged.chart",draw);project.on("trackChanged.chart",trackChanged);this.$chart=this.$el.find("[data-name=chartDiv]");var $dialog=$('<div style="background:white;" title="Chart"></div>');var $configPane=this.$el.find("[data-name=configPane]");formBuilder.$form.appendTo($configPane);this.$el.appendTo($dialog);$dialog.dialog({dialogClass:"morpheus",close:function(event,ui){project.off("trackChanged.chart",trackChanged);project.getRowSelectionModel().off("selectionChanged.chart",draw);project.getColumnSelectionModel().off("selectionChanged.chart",draw);_this.$el.empty()},resizable:true,height:600,width:900});this.$dialog=$dialog;this.draw()};morpheus.ChartTool.getVectorInfo=function(value){var field=value.substring(0,value.length-2);var isColumns=value.substring(value.length-2)==="_c";return{field:field,isColumns:isColumns}};morpheus.ChartTool.prototype={_createScatter:function(options){var _this=this;var dataset=options.dataset;var colorByVector=options.colorByVector;var colorModel=options.colorModel;var heatmap=this.heatmap;var chartWidth=options.chartWidth;var chartHeight=options.chartHeight;var axisLabelVector=options.axisLabelVector;var transpose=options.transpose;var chart={animation:false,toolbox:{feature:{brush:{title:{rect:"Rectangle selection",polygon:"Polygon selection",clear:"Clear Selection",keep:"Keep previous selection"}}}},brush:{brushLink:"all",xAxisIndex:[],yAxisIndex:[],inBrush:{opacity:1}},tooltip:{trigger:"item"},grid:[],xAxis:[],yAxis:[],series:[]};var index=0;var GAP=20;var BASE_LEFT=40;var BASE_TOP=40;for(var rowIndexOne=1,nrows=dataset.getRowCount();rowIndexOne<nrows;rowIndexOne++){for(var rowIndexTwo=0;rowIndexTwo<rowIndexOne;rowIndexTwo++){(function(){var data=[];var color=[];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){data.push([dataset.getValue(rowIndexOne,j),dataset.getValue(rowIndexTwo,j),j])}if(colorByVector){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var colorByValue=colorByVector.getValue(j);color.push(colorModel.getMappedValue(colorByVector,colorByValue))}}chart.grid.push({left:GAP+(rowIndexOne-1)*(chartWidth+GAP),top:BASE_TOP+rowIndexTwo*(chartHeight+GAP),width:chartWidth,height:chartHeight});chart.brush.xAxisIndex&&chart.brush.xAxisIndex.push(index);chart.brush.yAxisIndex&&chart.brush.yAxisIndex.push(index);chart.xAxis.push({splitNumber:3,position:"top",name:axisLabelVector!=null&&rowIndexTwo===0?axisLabelVector.getValue(rowIndexOne):"",nameGap:25,nameLocation:"middle",axisLine:{show:false,onZero:false},axisTick:{show:rowIndexTwo===0,inside:true},axisLabel:{show:rowIndexTwo===0},type:"value",gridIndex:index,scale:true});chart.yAxis.push({splitNumber:3,nameGap:50,name:axisLabelVector!=null&&rowIndexOne===nrows-1?axisLabelVector.getValue(rowIndexTwo):"",nameLocation:"middle",position:"right",axisLine:{show:false,onZero:false},axisTick:{show:rowIndexOne===nrows-1,inside:true},axisLabel:{show:rowIndexOne===nrows-1},type:"value",gridIndex:index,scale:true});chart.series.push({symbolSize:4,tooltip:{formatter:function(obj){var value=obj.value;var s=[];s.push("x: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[0]));s.push("<br>");s.push("y "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[1]));if(transpose){morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:new morpheus.TransposedDatasetView(dataset),rowIndex:value[2],columnIndex:-1})}else{morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:dataset,rowIndex:-1,columnIndex:value[2]})}return s.join("")}},itemStyle:{normal:{color:function(param){return color.length===0?"#1f78b4":color[param.dataIndex]}}},type:"scatter",xAxisIndex:index,yAxisIndex:index,data:data});index++})()}}var myChart=echarts.init(options.el);myChart.setOption(chart)},_createProfile:function(options){var _this=this;var dataset=options.dataset;var colorByVector=options.colorByVector;var colorModel=options.colorModel;var heatmap=this.heatmap;var chartWidth=options.chartWidth;var chartHeight=options.chartHeight;var axisLabelVector=options.axisLabelVector;var transpose=options.transpose;var axisLabel=[];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){axisLabel.push(axisLabelVector!=null?axisLabelVector.getValue(j):""+j)}var series=[];var colorMap=morpheus.VectorColorModel.getColorMapForNumber(dataset.getRowCount());for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var colorByValue=colorByVector!=null?colorByVector.getValue(i):""+i;var color=colorByVector!=null?colorModel.getMappedValue(colorByVector,colorByValue):colorMap[i%colorMap.length];var data=[];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){data.push([j,dataset.getValue(i,j),i])}series.push({name:colorByValue,type:"line",data:data,tooltip:{formatter:function(obj){var value=obj.value;var s=[];s.push(_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[1]));morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:dataset,rowIndex:value[2],columnIndex:value[0]});return s.join("")}}})}var chart={legend:{orient:"vertical",left:"right",top:2,itemWidth:14,height:dataset.getRowCount()*20,data:series.map(function(s){return s.name})},animation:false,tooltip:{trigger:"item"},xAxis:{type:"category",data:axisLabel},yAxis:{axisLine:{show:true,onZero:false},type:"value",name:""},grid:{right:120},series:series};var myChart=echarts.init(options.el);myChart.setOption(chart)},_createBoxPlot:function(options){var _this=this;var showPoints=options.showPoints;var datasets=options.datasets;var ids=options.ids;var heatmap=this.heatmap;var size=6;var boxData=[];var outliers=[];for(var k=0,ndatasets=datasets.length;k<ndatasets;k++){var dataset=datasets[k];var id=ids[k];var values=new Float32Array(dataset.getRowCount()*dataset.getColumnCount());var counter=0;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(!isNaN(value)){values[counter]=value;counter++}}}if(counter!==values.length){values=values.slice(0,counter)}values.sort();var item=morpheus.BoxPlotArrayItem(values);boxData.push([item.lowerAdjacentValue,item.q1,item.median,item.q3,item.upperAdjacentValue]);if(options.showOutliers){var w=1.5;var upperOutlier=item.q3+w*(item.q3-item.q1);var lowerOutlier=item.q1-w*(item.q3-item.q1);for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(value>upperOutlier||value<lowerOutlier){outliers.push([id,value,i,j])}}}}}var chart={animation:false,tooltip:{trigger:"item"},xAxis:{type:"category",data:ids},yAxis:{axisLine:{show:true,onZero:false},type:"value",name:""},series:[{animationDuration:0,hoverAnimation:false,name:"boxplot",type:"boxplot",data:boxData,tooltip:{formatter:function(param){var text=[];if(param.name!==""){text.push(param.name)}text=text.concat(["upper: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[4]),"Q3: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[3]),"median: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[2]),"Q1: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[1]),"lower: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[0])]);return text.join("<br/>")}}},{name:"outlier",type:"scatter",data:outliers,symbolSize:5,itemStyle:{normal:{borderWidth:1,borderColor:"black",opacity:.8}},tooltip:{formatter:function(obj){var value=obj.value;var s=[];if(value[0]!==""){s.push(value[0]);s.push("<br>")}s.push(_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[1]));morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:dataset,rowIndex:value[2],columnIndex:value[3]});return s.join("")}}}]};var myChart=echarts.init(options.el);myChart.setOption(chart)},draw:function(){var _this=this;this.$chart.empty();var gridWidth=parseInt(this.formBuilder.getValue("chart_width"));var gridHeight=parseInt(this.formBuilder.getValue("chart_height"));var showOutliers=this.formBuilder.getValue("show_outliers");var groupBy=this.formBuilder.getValue("group_by");var axisLabel=this.formBuilder.getValue("axis_label");var chartType=this.formBuilder.getValue("chart_type");var dataset=this.project.getSelectedDataset({emptyToAll:false});this.dataset=dataset;if(dataset.getRowCount()===0&&dataset.getColumnCount()===0){$("<h4>Please select rows and columns in the heat map.</h4>").appendTo(this.$chart);return}else if(dataset.getRowCount()===0){$("<h4>Please select rows in the heat map.</h4>").appendTo(this.$chart);return}if(dataset.getColumnCount()===0){$("<h4>Please select columns in the heat map.</h4>").appendTo(this.$chart);return}var heatmap=this.heatmap;var axisLabelInfo=morpheus.ChartTool.getVectorInfo(axisLabel);var axisLabelVector=axisLabelInfo.isColumns?dataset.getColumnMetadata().getByName(axisLabelInfo.field):dataset.getRowMetadata().getByName(axisLabelInfo.field);var rowIds=[undefined];var columnIds=[undefined];var colorBy=this.formBuilder.getValue("color");var colorByVector=null;var colorModel=null;if(colorBy!=null){var colorByInfo=morpheus.ChartTool.getVectorInfo(colorBy);colorModel=!colorByInfo.isColumns?this.project.getRowColorModel():this.project.getColumnColorModel();colorByVector=colorByInfo.isColumns?dataset.getColumnMetadata().getByName(colorByInfo.field):dataset.getRowMetadata().getByName(colorByInfo.field)}if(chartType==="row profile"||chartType==="column profile"){var transpose=chartType==="column profile";if(transpose){dataset=new morpheus.TransposedDatasetView(dataset)}if(dataset.getRowCount()>100){$("<h4>Maximum chart size exceeded.</h4>").appendTo(this.$chart);return}var $chart=$('<div style="width: '+(gridWidth+120)+"px;height:"+gridHeight+'px;"></div>');$chart.appendTo(this.$chart);this._createProfile({width:gridWidth,el:$chart[0],dataset:dataset,chartWidth:gridWidth,chartHeight:gridHeight,transpose:transpose,colorModel:colorModel,colorByVector:colorByVector,axisLabelVector:axisLabelVector})}else if(chartType==="row scatter matrix"||chartType==="column scatter matrix"){var transpose=chartType==="column scatter matrix";if(transpose){dataset=new morpheus.TransposedDatasetView(dataset)}if(dataset.getRowCount()>20){$("<h4>Maximum chart size exceeded.</h4>").appendTo(this.$chart);return}var $chart=$('<div style="width:'+(80+(dataset.getRowCount()-1)*(gridWidth+20))+"px;height:"+(80+dataset.getRowCount()*(gridHeight+20))+'px;"></div>');$chart.appendTo(this.$chart);this._createScatter({el:$chart[0],dataset:dataset,chartWidth:gridWidth,chartHeight:gridHeight,transpose:transpose,colorModel:colorModel,colorByVector:colorByVector,axisLabelVector:axisLabelVector})}else if(chartType==="boxplot"){var datasets=[];var ids=[];if(groupBy){var groupByInfo=morpheus.ChartTool.getVectorInfo(groupBy);var vector=groupByInfo.isColumns?dataset.getColumnMetadata().getByName(groupByInfo.field):dataset.getRowMetadata().getByName(groupByInfo.field);var isArray=morpheus.VectorUtil.getDataType(vector)[0]==="[";var valueToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector,true);valueToIndices.forEach(function(indices,value){datasets.push(new morpheus.SlicedDatasetView(dataset,groupByInfo.isColumns?null:indices,groupByInfo.isColumns?indices:null));ids.push(value)})}else{datasets.push(dataset);ids.push("")}var $chartEl=$('<div style="width: '+gridWidth+"px;height:"+gridHeight+'px;"></div>');$chartEl.appendTo(this.$chart);this._createBoxPlot({showOutliers:showOutliers,el:$chartEl[0],datasets:datasets,ids:ids})}}};morpheus.ChartTool.getTooltip=function(options){for(var tipIndex=0;tipIndex<options.tooltip.length;tipIndex++){var tip=options.tooltip[tipIndex];var metadata;var index;if(tip.isColumns){metadata=options.dataset.getColumnMetadata();index=options.columnIndex}else{metadata=options.dataset.getRowMetadata();index=options.rowIndex}if(index!==-1){var v=metadata.getByName(tip.field);morpheus.HeatMapTooltipProvider.vectorToString(v,index,options.text,"<br>")}}};morpheus.CollapseDatasetTool=function(){};morpheus.CollapseDatasetTool.Functions=[morpheus.Mean,morpheus.Median,new morpheus.MaxPercentiles([25,75]),morpheus.Min,morpheus.Max,morpheus.Percentile,morpheus.Sum];morpheus.CollapseDatasetTool.Functions.fromString=function(s){for(var i=0;i<morpheus.CollapseDatasetTool.Functions.length;i++){if(morpheus.CollapseDatasetTool.Functions[i].toString()===s){return morpheus.CollapseDatasetTool.Functions[i]}}throw new Error(s+" not found")};morpheus.CollapseDatasetTool.prototype={toString:function(){return"Collapse"},init:function(project,form){var setValue=function(val){var isRows=val==="Rows";var names=morpheus.MetadataUtil.getMetadataNames(isRows?project.getFullDataset().getRowMetadata():project.getFullDataset().getColumnMetadata());form.setOptions("collapse_to_fields",names)};form.$form.find("[name=collapse]").on("change",function(e){setValue($(this).val())});form.setVisible("percentile",false);form.$form.find("[name=collapse_method]").on("change",function(e){form.setVisible("percentile",$(this).val()===morpheus.Percentile.toString())});setValue("Rows")},gui:function(){return[{name:"collapse_method",options:morpheus.CollapseDatasetTool.Functions,value:morpheus.CollapseDatasetTool.Functions[1].toString(),type:"select"},{name:"percentile",value:75,type:"text"},{name:"collapse",options:["Columns","Rows"],value:"Rows",type:"radio"},{name:"collapse_to_fields",options:[],type:"select",multiple:true}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var f=morpheus.CollapseDatasetTool.Functions.fromString(options.input.collapse_method);if(f.toString()===morpheus.Percentile.toString()){var p=parseFloat(options.input.percentile);f=function(vector){return morpheus.Percentile(vector,p)}}var collapseToFields=options.input.collapse_to_fields;if(collapseToFields.length===0){throw new Error("Please select one or more fields to collapse to")}var dataset=project.getFullDataset();var rows=options.input.collapse=="Rows";if(!rows){dataset=new morpheus.TransposedDatasetView(dataset)}var allFields=morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata());dataset=morpheus.CollapseDataset(dataset,collapseToFields,f,true);if(!rows){dataset=new morpheus.TransposedDatasetView(dataset)}var set=new morpheus.Map;_.each(allFields,function(field){set.set(field,true)});_.each(collapseToFields,function(field){set.remove(field)});set.forEach(function(val,name){heatMap.setTrackVisible(name,false,!rows)});return new morpheus.HeatMap({name:heatMap.getName(),dataset:dataset,parent:heatMap,symmetric:false})}};morpheus.CreateAnnotation=function(){};morpheus.CreateAnnotation.prototype={toString:function(){return"Create Calculated Annotation"},gui:function(){return[{name:"annotate",options:["Columns","Rows"],value:"Rows",type:"radio"},{name:"annotation_name",value:"",type:"text",required:true,autocomplete:"off"},{name:"formula",value:"",type:"textarea",placeholder:"e.g MAD()",required:true,help:"JavaScript formula. Built-in functions (case-sensitive): COUNTIF(expression),"+" MAD(), MAX(),"+" MEAN(), MEDIAN(), MIN(), PERCENTILE(p), SUM(), VARIANCE(). Refer to a field using FIELD(name)"},{name:"use_selected_rows_and_columns_only",type:"checkbox"}]},execute:function(options){var __project=options.project;var isColumns=options.input.annotate=="Columns";var __formula=options.input.formula;var __dataset=options.input.use_selected_rows_and_columns_only?__project.getSelectedDataset():__project.getSortedFilteredDataset();if(isColumns){__dataset=morpheus.DatasetUtil.transposedView(__dataset)}var __rowView=new morpheus.DatasetRowView(__dataset);var __vector=__dataset.getRowMetadata().add(options.input.annotation_name);var COUNTIF=function(val){return morpheus.CountIf(__rowView,val)};var MAD=function(){return morpheus.MAD(__rowView)};var MAX=function(){return morpheus.Max(__rowView)};var MEAN=function(){return morpheus.Mean(__rowView)};var MEDIAN=function(p){return morpheus.Percentile(__rowView,50)};var MIN=function(){return morpheus.Min(__rowView)};var PERCENTILE=function(p){return morpheus.Percentile(__rowView,p)};var SUM=function(){return morpheus.Sum(__rowView)};var VARIANCE=function(){return morpheus.Variance(__rowView)};var __index=0;var FIELD=function(field){var vector=__dataset.getRowMetadata().getByName(field);return vector?vector.getValue(__index):undefined};for(var size=__dataset.getRowCount();__index<size;__index++){__rowView.setIndex(__index);var __val=eval(__formula);if(typeof __val==="function"){__val=""}__vector.setValue(__index,__val)}morpheus.VectorUtil.maybeConvertStringToNumber(__vector);__project.trigger("trackChanged",{vectors:[__vector],display:["text"],columns:isColumns})}};morpheus.DendrogramEnrichmentTool=function(isColumns){this.isColumns=isColumns};morpheus.DendrogramEnrichmentTool.prototype={toString:function(){return"Dendrogram Enrichment"},gui:function(project){var dataset=project.getSortedFilteredDataset();var fields=morpheus.MetadataUtil.getMetadataNames(this.isColumns?dataset.getColumnMetadata():dataset.getRowMetadata());return[{name:"field",options:fields,type:"bootstrap-select",multiple:false},{name:"min_p-value_for_enrichment",type:"text",value:"0.05"},{name:"minimum_number_of_total_members_in_group",type:"text",value:"5"},{name:"minimum_number_of_members_in_group",type:"text",value:"3"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var pValue=options.input["min_p-value_for_enrichment"];var minTotalGroupSize=options.input.minimum_number_of_total_members_in_group;var minGroupSize=options.input.minimum_number_of_members_in_group;var dataset=project.getSortedFilteredDataset();var dendrogram=this.isColumns?heatMap.columnDendrogram:heatMap.rowDendrogram;var vector=this.isColumns?dataset.getColumnMetadata().getByName(options.input.field):dataset.getRowMetadata().getByName(options.input.field);var valueToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector);var valueToGlobalCount=new morpheus.Map;var values=[];valueToIndices.forEach(function(indices,value){valueToGlobalCount.set(value,indices.length);values.push(value)});var nvalues=values.length;var N=vector.size();morpheus.DendrogramUtil.dfs(dendrogram.tree.rootNode,function(node){delete node.info;var valueToCount=new morpheus.Map;for(var i=0;i<nvalues;i++){valueToCount.set(values[i],0)}var min=node.minIndex;var max=node.maxIndex;var n=max-min+1;if(n>1&&n>=minTotalGroupSize){for(var i=min;i<=max;i++){var value=vector.getValue(i);valueToCount.set(value,valueToCount.get(value)+1)}for(var i=0;i<nvalues;i++){var K=valueToGlobalCount.get(values[i]);var k=valueToCount.get(values[i]);if(k>=minGroupSize){var a=k;var b=K-k;var c=n-k;var d=N+k-n-K;var p=morpheus.FisherExact.fisherTest(a,b,c,d);if(p<=pValue){if(!node.info){node.info={}}node.info[values[i]]=p}}}}return true});dendrogram.setInvalid(true);dendrogram.repaint()}};morpheus.DevAPI=function(){};morpheus.DevAPI.prototype={toString:function(){return"API"},gui:function(){return[{name:"code",value:"",type:"textarea",required:true,help:"Enter your code"}]},execute:function(options){var heatMap=options.heatMap;var code=options.input.code;eval(code);heatMap.getProject().setFullDataset(heatMap.getProject().getFullDataset(),true)}};morpheus.HClusterTool=function(){};morpheus.HClusterTool.PRECOMPUTED_DIST="Matrix values (for a precomputed distance matrix)";morpheus.HClusterTool.PRECOMPUTED_SIM="Matrix values (for a precomputed similarity matrix)";morpheus.HClusterTool.Functions=[morpheus.Euclidean,morpheus.Jaccard,new morpheus.OneMinusFunction(morpheus.Cosine),new morpheus.OneMinusFunction(morpheus.KendallsCorrelation),new morpheus.OneMinusFunction(morpheus.Pearson),new morpheus.OneMinusFunction(morpheus.Spearman),morpheus.HClusterTool.PRECOMPUTED_DIST,morpheus.HClusterTool.PRECOMPUTED_SIM];morpheus.HClusterTool.Functions.fromString=function(s){for(var i=0;i<morpheus.HClusterTool.Functions.length;i++){if(morpheus.HClusterTool.Functions[i].toString()===s){return morpheus.HClusterTool.Functions[i]}}throw new Error(s+" not found")};morpheus.HClusterTool.createLinkageMethod=function(linkageString){var linkageMethod;if(linkageString==="Average"){linkageMethod=morpheus.AverageLinkage}else if(linkageString==="Complete"){linkageMethod=morpheus.CompleteLinkage}else if(linkageString==="Single"){linkageMethod=morpheus.SingleLinkage}else{throw new Error("Unknown linkage method "+linkageString)}return linkageMethod};morpheus.HClusterTool.execute=function(dataset,input){var linkageMethod=morpheus.HClusterTool.createLinkageMethod(input.linkage_method);var f=morpheus.HClusterTool.Functions.fromString(input.metric);if(f===morpheus.HClusterTool.PRECOMPUTED_DIST){f=0}else if(f===morpheus.HClusterTool.PRECOMPUTED_SIM){f=1}var rows=input.cluster=="Rows"||input.cluster=="Rows and columns";var columns=input.cluster=="Columns"||input.cluster=="Rows and columns";var doCluster=function(d,groupByFields){return groupByFields&&groupByFields.length>0?new morpheus.HClusterGroupBy(d,groupByFields,f,linkageMethod):new morpheus.HCluster(morpheus.HCluster.computeDistanceMatrix(d,f),linkageMethod)};var rowsHcl;var columnsHcl;if(rows){rowsHcl=doCluster(input.selectedColumnsToUseForClusteringRows?new morpheus.SlicedDatasetView(dataset,null,input.selectedColumnsToUseForClusteringRows):dataset,input.group_rows_by)}if(columns){columnsHcl=doCluster(morpheus.DatasetUtil.transposedView(input.selectedRowsToUseForClusteringColumns?new morpheus.SlicedDatasetView(dataset,input.selectedRowsToUseForClusteringColumns,null):dataset),input.group_columns_by)}return{rowsHcl:rowsHcl,columnsHcl:columnsHcl}};morpheus.HClusterTool.prototype={toString:function(){return"Hierarchical Clustering"},init:function(project,form){form.setOptions("group_rows_by",morpheus.MetadataUtil.getMetadataNames(project.getFullDataset().getRowMetadata()));form.setOptions("group_columns_by",morpheus.MetadataUtil.getMetadataNames(project.getFullDataset().getColumnMetadata()));form.setVisible("group_rows_by",false);form.setVisible("cluster_rows_in_space_of_selected_columns_only",false);form.$form.find("[name=cluster]").on("change",function(e){var val=$(this).val();var showGroupColumns=false;var showGroupRows=false;if(val==="Columns"){showGroupColumns=true}else if(val==="Rows"){showGroupRows=true}else{showGroupColumns=true;showGroupRows=true}form.setVisible("group_columns_by",showGroupColumns);form.setVisible("group_rows_by",showGroupRows);form.setVisible("cluster_columns_in_space_of_selected_rows_only",showGroupColumns);form.setVisible("cluster_rows_in_space_of_selected_columns_only",showGroupRows)})},gui:function(){return[{name:"metric",options:morpheus.HClusterTool.Functions,value:morpheus.HClusterTool.Functions[4].toString(),type:"select"},{name:"linkage_method",options:["Average","Complete","Single"],value:"Average",type:"select"},{name:"cluster",options:["Columns","Rows","Rows and columns"],value:"Columns",type:"select"},{name:"group_columns_by",options:[],type:"bootstrap-select",multiple:true},{name:"group_rows_by",options:[],type:"bootstrap-select",multiple:true},{name:"cluster_columns_in_space_of_selected_rows_only",type:"checkbox"},{name:"cluster_rows_in_space_of_selected_columns_only",type:"checkbox"}]},execute:function(options){var project=options.project;var heatmap=options.heatMap;var selectedRowsToUseForClusteringColumns=options.input.cluster_columns_in_space_of_selected_rows_only?project.getRowSelectionModel().getViewIndices().values():null;if(selectedRowsToUseForClusteringColumns!=null&&selectedRowsToUseForClusteringColumns.length===0){selectedRowsToUseForClusteringColumns=null}var selectedColumnsToUseForClusteringRows=options.input.cluster_rows_in_space_of_selected_columns_only?project.getColumnSelectionModel().getViewIndices().values():null;if(selectedColumnsToUseForClusteringRows!=null&&selectedColumnsToUseForClusteringRows.length===0){selectedColumnsToUseForClusteringRows=null}var rows=options.input.cluster=="Rows"||options.input.cluster=="Rows and columns";var columns=options.input.cluster=="Columns"||options.input.cluster=="Rows and columns";options.input.selectedRowsToUseForClusteringColumns=selectedRowsToUseForClusteringColumns;options.input.selectedColumnsToUseForClusteringRows=selectedColumnsToUseForClusteringRows;var dataset=project.getSortedFilteredDataset();if(options.input.background===undefined){options.input.background=true}options.input.background=options.input.background&&typeof Worker!=="undefined";var rowModelOrder;var columnModelOrder;if(rows){rowModelOrder=[];for(var i=0;i<dataset.getRowCount();i++){rowModelOrder[i]=project.convertViewRowIndexToModel(i)}}if(columns){columnModelOrder=[];for(var i=0;i<dataset.getColumnCount();i++){columnModelOrder[i]=project.convertViewColumnIndexToModel(i)}}if(options.input.background===false){var result=morpheus.HClusterTool.execute(dataset,options.input);if(result.rowsHcl){var modelOrder=[];for(var i=0;i<result.rowsHcl.reorderedIndices.length;i++){modelOrder[i]=rowModelOrder[result.rowsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.rowsHcl.tree,false,modelOrder)}if(result.columnsHcl){var modelOrder=[];for(var i=0;i<result.columnsHcl.reorderedIndices.length;i++){modelOrder[i]=columnModelOrder[result.columnsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.columnsHcl.tree,true,modelOrder)}}else{var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.HClusterTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:options.input.group_columns_by||[],rowFields:options.input.group_rows_by||[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){var result=e.data;if(result.rowsHcl){var modelOrder=[];for(var i=0;i<result.rowsHcl.reorderedIndices.length;i++){modelOrder[i]=rowModelOrder[result.rowsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.rowsHcl.tree,false,modelOrder)}if(result.columnsHcl){var modelOrder=[];for(var i=0;i<result.columnsHcl.reorderedIndices.length;i++){modelOrder[i]=columnModelOrder[result.columnsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.columnsHcl.tree,true,modelOrder)}worker.terminate();window.URL.revokeObjectURL(url)};return worker}}};morpheus.KMeansTool=function(){};morpheus.KMeansTool.execute=function(dataset,input){var f=morpheus.HClusterTool.Functions.fromString(input.metric);if(f===morpheus.HClusterTool.PRECOMPUTED_DIST){f=0}else if(f===morpheus.HClusterTool.PRECOMPUTED_SIM){f=1}var rows=input.cluster=="Rows"||input.cluster=="Rows and columns";var columns=input.cluster=="Columns"||input.cluster=="Rows and columns";var doCluster=function(d){var kmeans=new morpheus.KMeansPlusPlusClusterer(input.number_of_clusters,input.maximum_iterations,f);var vectors=[];for(var i=0;i<d.getRowCount();i++){vectors.push(new morpheus.DatasetRowView(d).setIndex(i))}var clusters=kmeans.execute(vectors);var assignments=[];for(var i=0;i<clusters.length;i++){clusters[i].getPoints().forEach(function(p){assignments[p.i]=i+1})}return assignments};var rowAssignments;var columnAssignments;if(rows){rowAssignments=doCluster(input.selectedColumnsToUseForClusteringRows?new morpheus.SlicedDatasetView(dataset,null,input.selectedColumnsToUseForClusteringRows):dataset)}if(columns){columnAssignments=doCluster(morpheus.DatasetUtil.transposedView(input.selectedRowsToUseForClusteringColumns?new morpheus.SlicedDatasetView(dataset,input.selectedRowsToUseForClusteringColumns,null):dataset))}return{rowAssignments:rowAssignments,columnAssignments:columnAssignments}};morpheus.KMeansTool.prototype={toString:function(){return"KMeans Clustering"},init:function(project,form){form.setVisible("cluster_rows_in_space_of_selected_columns_only",false);form.$form.find("[name=cluster]").on("change",function(e){var val=$(this).val();var val=$(this).val();var showGroupColumns=false;var showGroupRows=false;if(val==="Columns"){showGroupColumns=true}else if(val==="Rows"){showGroupRows=true}else{showGroupColumns=true;showGroupRows=true}form.setVisible("cluster_columns_in_space_of_selected_rows_only",showGroupColumns);form.setVisible("cluster_rows_in_space_of_selected_columns_only",showGroupRows)})},gui:function(){return[{name:"metric",options:morpheus.HClusterTool.Functions,value:morpheus.HClusterTool.Functions[4].toString(),type:"select"},{name:"cluster",options:["Columns","Rows","Rows and columns"],value:"Columns",type:"select"},{name:"number_of_clusters",value:"2",type:"text"},{name:"cluster_columns_in_space_of_selected_rows_only",type:"checkbox"},{name:"cluster_rows_in_space_of_selected_columns_only",type:"checkbox"},{name:"maximum_iterations",value:"1000",type:"text"}]},execute:function(options){var project=options.project;var heatmap=options.heatMap;options.input.number_of_clusters=parseInt(options.input.number_of_clusters);options.input.maximum_iterations=parseInt(options.input.maximum_iterations);var selectedRowsToUseForClusteringColumns=options.input.cluster_columns_in_space_of_selected_rows_only?project.getRowSelectionModel().getViewIndices().values():null;if(selectedRowsToUseForClusteringColumns!=null&&selectedRowsToUseForClusteringColumns.length===0){selectedRowsToUseForClusteringColumns=null}var selectedColumnsToUseForClusteringRows=options.input.cluster_rows_in_space_of_selected_columns_only?project.getColumnSelectionModel().getViewIndices().values():null;if(selectedColumnsToUseForClusteringRows!=null&&selectedColumnsToUseForClusteringRows.length===0){selectedColumnsToUseForClusteringRows=null}var rows=options.input.cluster=="Rows"||options.input.cluster=="Rows and columns";var columns=options.input.cluster=="Columns"||options.input.cluster=="Rows and columns";options.input.selectedRowsToUseForClusteringColumns=selectedRowsToUseForClusteringColumns;options.input.selectedColumnsToUseForClusteringRows=selectedColumnsToUseForClusteringRows;var dataset=project.getSortedFilteredDataset();options.input.background=options.input.background&&typeof Worker!=="undefined";function addAssignments(d,assignments,k){var v=d.getColumnMetadata().add("k_means_"+k);for(var i=0;i<assignments.length;i++){v.setValue(i,assignments[i])}}if(options.input.background===false){var result=morpheus.KMeansTool.execute(dataset,options.input);if(result.columnAssignments){addAssignments(dataset,result.columnAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,true,{highlightMatchingValues:true,discreteAutoDetermined:true,display:["color"]})}if(result.rowAssignments){addAssignments(new morpheus.TransposedDatasetView(dataset),result.rowAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,false,{highlightMatchingValues:true,discreteAutoDetermined:true,display:["color"]})}heatmap.revalidate()}else{var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.KMeansTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){var result=e.data;if(result.columnAssignments){addAssignments(dataset,result.columnAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,true,{highlightMatchingValues:true,discrete:true,display:["color"]})}if(result.rowAssignments){addAssignments(new morpheus.TransposedDatasetView(dataset),result.rowAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,false,{highlightMatchingValues:true,discrete:true,display:["color"]})}heatmap.revalidate();worker.terminate();window.URL.revokeObjectURL(url)};return worker}}};morpheus.MarkerSelection=function(){};morpheus.MarkerSelection.Functions=[morpheus.FisherExact,morpheus.FoldChange,morpheus.MeanDifference,morpheus.SignalToNoise,morpheus.createSignalToNoiseAdjust(),morpheus.TTest];morpheus.MarkerSelection.Functions.fromString=function(s){for(var i=0;i<morpheus.MarkerSelection.Functions.length;i++){if(morpheus.MarkerSelection.Functions[i].toString()===s){return morpheus.MarkerSelection.Functions[i]}}throw s+" not found"};morpheus.MarkerSelection.execute=function(dataset,input){var aIndices=[];var bIndices=[];for(var i=0;i<input.numClassA;i++){aIndices[i]=i}for(var i=input.numClassA;i<dataset.getColumnCount();i++){bIndices[i]=i}var f=morpheus.MarkerSelection.Functions.fromString(input.metric);var permutations=new morpheus.PermutationPValues(dataset,aIndices,bIndices,input.npermutations,f);return{rowSpecificPValues:permutations.rowSpecificPValues,k:permutations.k,fdr:permutations.fdr,scores:permutations.scores}};morpheus.MarkerSelection.prototype={toString:function(){return"Marker Selection"},init:function(project,form){var _this=this;var updateAB=function(fieldNames){var ids=[];if(fieldNames!=null){var vectors=morpheus.MetadataUtil.getVectors(project.getFullDataset().getColumnMetadata(),fieldNames);var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);idToIndices.forEach(function(indices,id){ids.push(id)})}ids.sort();form.setOptions("class_a",ids);form.setOptions("class_b",ids)};var $field=form.$form.find("[name=field]");$field.on("change",function(e){updateAB($(this).val())});if($field[0].options.length>0){$field.val($field[0].options[0].value)}updateAB($field.val());var $metric=form.$form.find("[name=metric]");$metric.on("change",function(e){var isFishy=$(this).val()==="Fisher Exact Test";form.setVisible("grouping_value",isFishy);form.setVisible("permutations",!isFishy);form.setVisible("number_of_markers",!isFishy)});form.setVisible("grouping_value",false)},gui:function(project){var dataset=project.getSortedFilteredDataset();var fields=morpheus.MetadataUtil.getMetadataNames(dataset.getColumnMetadata());return[{name:"metric",options:morpheus.MarkerSelection.Functions,value:morpheus.SignalToNoise.toString(),type:"select",help:""},{name:"grouping_value",value:"1",help:"Class values are categorized into two groups based on whether dataset values are greater than or equal to this value"},{name:"field",options:fields,type:"select",multiple:true},{name:"class_a",title:"Class A",options:[],value:"",type:"checkbox-list",multiple:true},{name:"class_b",title:"Class B",options:[],value:"",type:"checkbox-list",multiple:true},{name:"number_of_markers",value:"100",type:"text",help:"The initial number of markers to show in each direction."},{name:"permutations",value:"0",type:"text"}]},execute:function(options){var project=options.project;var classA=options.input.class_a;var classB=options.input.class_b;if(classA.length===0&&classB.length===0){throw"No samples in class A and class B"}if(classA.length===0){throw"No samples in class A"}if(classB.length===0){throw"No samples in class B"}for(var i=0;i<classA.length;i++){var val=classA[i];if(!(val instanceof morpheus.Identifier)){classA[i]=new morpheus.Identifier(morpheus.Util.isArray(val)?val:[val])}}for(var i=0;i<classB.length;i++){var val=classB[i];if(!(val instanceof morpheus.Identifier)){classB[i]=new morpheus.Identifier(morpheus.Util.isArray(val)?val:[val])}}var npermutations=parseInt(options.input.permutations);var dataset=project.getSortedFilteredDataset();var fieldNames=options.input.field;if(!morpheus.Util.isArray(fieldNames)){fieldNames=[fieldNames]}var vectors=morpheus.MetadataUtil.getVectors(dataset.getColumnMetadata(),fieldNames);var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);var aIndices=[];var bIndices=[];classA.forEach(function(id){var indices=idToIndices.get(id);if(indices===undefined){throw new Error(id+" not found in "+idToIndices.keys())}aIndices=aIndices.concat(indices)});classB.forEach(function(id){var indices=idToIndices.get(id);if(indices===undefined){throw new Error(id+" not found in "+idToIndices.keys())}bIndices=bIndices.concat(indices)});var f=morpheus.MarkerSelection.Functions.fromString(options.input.metric);var classASet={};for(var i=0;i<aIndices.length;i++){classASet[aIndices[i]]=true}for(var i=0;i<bIndices.length;i++){if(classASet[bIndices[i]]){throw"The sample was found in class A and class B"}}var isFishy=f.toString()===morpheus.FisherExact.toString();if((aIndices.length===1||bIndices.length===1)&&!isFishy&&f.toString()!==morpheus.MeanDifference.toString()){f=morpheus.FoldChange}var list1=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,aIndices));var list2=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,bIndices));var markerSelectionFields=morpheus.MarkerSelection.Functions.map(function(f){return f.toString()}).concat(["odds_ratio","FDR(BH)","p_value"]);markerSelectionFields.forEach(function(name){var index=morpheus.MetadataUtil.indexOf(dataset.getRowMetadata(),name);if(index!==-1){dataset.getRowMetadata().remove(index);options.heatMap.removeTrack(name,false)}});var v=dataset.getRowMetadata().add(f.toString());var vectors=[v];var comparisonVector=dataset.getColumnMetadata().add("Comparison");for(var i=0;i<aIndices.length;i++){comparisonVector.setValue(aIndices[i],"A")}for(var i=0;i<bIndices.length;i++){comparisonVector.setValue(bIndices[i],"B")}function done(result){if(result){var pvalueVector=dataset.getRowMetadata().add("p_value");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var kVector=dataset.getRowMetadata().add("k");for(var i=0,size=pvalueVector.size();i<size;i++){pvalueVector.setValue(i,result.rowSpecificPValues[i]);fdrVector.setValue(i,result.fdr[i]);kVector.setValue(i,result.k[i]);v.setValue(i,result.scores[i])}kVector.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});vectors.push(pvalueVector);vectors.push(fdrVector);vectors.push(kVector)}if(project.getRowFilter().getFilters().length>0){project.getRowFilter().setAnd(true,true)}var rowFilters=project.getRowFilter().getFilters();for(var i=0;i<rowFilters.length;i++){if(rowFilters[i]instanceof morpheus.TopNFilter){project.getRowFilter().remove(i,true);i--}}if(!isFishy){project.getRowFilter().add(new morpheus.TopNFilter(parseInt(options.input.number_of_markers),morpheus.TopNFilter.TOP_BOTTOM,vectors[0].getName()),true)}project.setRowFilter(project.getRowFilter(),true);project.setRowSortKeys([new morpheus.SortKey(vectors[0].getName(),isFishy?morpheus.SortKey.SortOrder.ASCENDING:morpheus.SortKey.SortOrder.DESCENDING)],true);var selectedColumnIndices=new morpheus.Set;aIndices.forEach(function(index){selectedColumnIndices.add(index)});bIndices.forEach(function(index){selectedColumnIndices.add(index)});project.getColumnSelectionModel().setViewIndices(selectedColumnIndices,true);project.setColumnSortKeys([new morpheus.SortKey(comparisonVector.getName(),morpheus.SortKey.SortOrder.ASCENDING)],true);project.trigger("trackChanged",{vectors:vectors,display:vectors.map(function(){return"text"}),columns:false});project.trigger("trackChanged",{vectors:[comparisonVector],display:["color"],columns:true})}if(isFishy){var groupingValue=parseFloat(options.input.grouping_value);var oddsRatioVector=dataset.getRowMetadata().add("odds_ratio");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var contingencyTableVector=dataset.getRowMetadata().add("contingency_table");var pvalues=[];for(var i=0,size=dataset.getRowCount();i<size;i++){var abcd=morpheus.createContingencyTable(list1.setIndex(i),list2.setIndex(i),groupingValue);contingencyTableVector.setValue(i,"[["+abcd[0]+", "+abcd[1]+"], ["+abcd[2]+", "+abcd[3]+"]]");var ratio=abcd[0]*abcd[3]/(abcd[1]*abcd[2]);if(isNaN(ratio)||ratio===Number.POSITIVE_INFINITY){ratio=0}oddsRatioVector.setValue(i,ratio);v.setValue(i,morpheus.FisherExact.fisherTest(abcd[0],abcd[1],abcd[2],abcd[3]));pvalues.push(v.getValue(i))}var fdr=morpheus.FDR_BH(pvalues);for(var i=0,size=dataset.getRowCount();i<size;i++){fdrVector.setValue(i,fdr[i])}vectors.push(oddsRatioVector);vectors.push(fdrVector);vectors.push(contingencyTableVector);done()}else{if(npermutations>0){var subset=new morpheus.SlicedDatasetView(dataset,null,aIndices.concat(bIndices));options.input.background=options.input.background&&typeof Worker!=="undefined";options.input.numClassA=aIndices.length;options.input.npermutations=npermutations;if(options.input.background){var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.MarkerSelection.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(subset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){done(e.data);worker.terminate();window.URL.revokeObjectURL(url)};return worker}else{done(morpheus.MarkerSelection.execute(subset,options.input))}}else{for(var i=0,size=dataset.getRowCount();i<size;i++){v.setValue(i,f(list1.setIndex(i),list2.setIndex(i)))}if(f.toString()===morpheus.TTest.toString()&&typeof jStat!=="undefined"){var pvalueVector=dataset.getRowMetadata().add("p_value");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var rowSpecificPValues=new Float32Array(dataset.getRowCount());for(var i=0,size=dataset.getRowCount();i<size;i++){list1.setIndex(i);list2.setIndex(i);var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var v1=morpheus.Variance(list1,m1);var v2=morpheus.Variance(list2,m2);var n1=morpheus.CountNonNaN(list1);var n2=morpheus.CountNonNaN(list2);var df=morpheus.DegreesOfFreedom(v1,v2,n1,n2);var t=v.getValue(i);var p=2*(1-jStat.studentt.cdf(Math.abs(t),df));rowSpecificPValues[i]=p;pvalueVector.setValue(i,p)}vectors.push(pvalueVector);var fdr=morpheus.FDR_BH(rowSpecificPValues);for(var i=0,size=dataset.getRowCount();i<size;i++){fdrVector.setValue(i,fdr[i])}vectors.push(fdrVector)}done()}}}};morpheus.NearestNeighbors=function(){};morpheus.NearestNeighbors.Functions=[morpheus.Cosine,morpheus.Euclidean,morpheus.Jaccard,morpheus.KendallsCorrelation,morpheus.Pearson,morpheus.Spearman,morpheus.WeightedMean];morpheus.NearestNeighbors.Functions.fromString=function(s){for(var i=0;i<morpheus.NearestNeighbors.Functions.length;i++){if(morpheus.NearestNeighbors.Functions[i].toString()===s){return morpheus.NearestNeighbors.Functions[i]}}throw new Error(s+" not found")};morpheus.NearestNeighbors.execute=function(dataset,input){var f=morpheus.NearestNeighbors.Functions.fromString(input.metric);var permutations=new morpheus.PermutationPValues(dataset,null,null,input.npermutations,f,morpheus.Vector.fromArray("",input.listValues));return{rowSpecificPValues:permutations.rowSpecificPValues,k:permutations.k,fdr:permutations.fdr,scores:permutations.scores}};morpheus.NearestNeighbors.prototype={toString:function(){return"Nearest Neighbors"},init:function(project,form){var $selectedOnly=form.$form.find("[name=use_selected_only]").parent();form.$form.find("[name=compute_nearest_neighbors_of]").on("change",function(e){var val=$(this).val();if(val==="selected rows"||val==="column annotation"){$($selectedOnly.contents()[1]).replaceWith(document.createTextNode(" Use selected columns only"))}else{$($selectedOnly.contents()[1]).replaceWith(document.createTextNode(" Use selected rows only"))}form.setVisible("annotation",false);if(val==="column annotation"||val==="row annotation"){var metadata=val==="column annotation"?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata();var names=[];for(var i=0;i<metadata.getMetadataCount();i++){var v=metadata.get(i);if(morpheus.VectorUtil.getDataType(v)==="number"){names.push(v.getName())}}names.sort(function(a,b){a=a.toLowerCase();b=b.toLowerCase();return a<b?-1:a===b?0:1});form.setOptions("annotation",names);form.setVisible("annotation",true)}});$($selectedOnly.contents()[1]).replaceWith(document.createTextNode(" Use selected columns only"));form.setVisible("annotation",false)},gui:function(){return[{name:"metric",options:morpheus.NearestNeighbors.Functions,value:morpheus.Pearson.toString(),type:"select"},{name:"compute_nearest_neighbors_of",options:["selected rows","selected columns","column annotation","row annotation"],value:"selected rows",type:"radio"},{name:"use_selected_only",type:"checkbox"},{name:"annotation",type:"bootstrap-select"},{name:"permutations",value:"0",type:"text"}]},execute:function(options){var project=options.project;var isColumns=options.input.compute_nearest_neighbors_of=="selected columns"||options.input.compute_nearest_neighbors_of=="row annotation";var isAnnotation=options.input.compute_nearest_neighbors_of=="column annotation"||options.input.compute_nearest_neighbors_of=="row annotation";var heatMap=options.heatMap;var f=morpheus.NearestNeighbors.Functions.fromString(options.input.metric);var dataset=project.getSortedFilteredDataset();if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var selectedIndices=(isColumns?project.getColumnSelectionModel():project.getRowSelectionModel()).getViewIndices().values();if(!isAnnotation&&selectedIndices.length===0){throw new Error("No "+(isColumns?"columns":"rows")+" selected")}var spaceIndices=null;if(options.input.use_selected_only){spaceIndices=(!isColumns?project.getColumnSelectionModel():project.getRowSelectionModel()).getViewIndices().values();dataset=morpheus.DatasetUtil.slicedView(dataset,null,spaceIndices)}var d1=morpheus.DatasetUtil.slicedView(dataset,selectedIndices,null);var nearestNeighborsList;if(isAnnotation){nearestNeighborsList=dataset.getColumnMetadata().getByName(options.input.annotation);if(!nearestNeighborsList){throw new Error("No annotation selected.")}}else{if(d1.getRowCount()>1){var columnView=new morpheus.DatasetColumnView(d1);var newDataset=new morpheus.Dataset({name:"",rows:1,columns:d1.getColumnCount()});for(var j=0,ncols=d1.getColumnCount();j<ncols;j++){var v=morpheus.Percentile(columnView.setIndex(j),50);newDataset.setValue(0,j,v)}d1=newDataset}nearestNeighborsList=new morpheus.DatasetRowView(d1)}var npermutations=parseInt(options.input.permutations);var scoreVector=dataset.getRowMetadata().add(f.toString());if(npermutations>0){if(options.input.background===undefined){options.input.background=true}options.input.background=options.input.background&&typeof Worker!=="undefined";options.input.npermutations=npermutations;var done=function(result){var pvalueVector=dataset.getRowMetadata().add("p_value");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var kVector=dataset.getRowMetadata().add("k");for(var i=0,size=pvalueVector.size();i<size;i++){pvalueVector.setValue(i,result.rowSpecificPValues[i]);fdrVector.setValue(i,result.fdr[i]);kVector.setValue(i,result.k[i]);scoreVector.setValue(i,result.scores[i])}kVector.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});var vectors=[pvalueVector,fdrVector,kVector,scoreVector];project.trigger("trackChanged",{vectors:vectors,display:["text"],columns:isColumns})};var listValues=new Float32Array(nearestNeighborsList.size());for(var i=0,size=listValues.length;i<size;i++){listValues[i]=nearestNeighborsList.getValue(i)}options.input.listValues=listValues;if(options.input.background){var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.NearestNeighbors.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){done(e.data);worker.terminate();window.URL.revokeObjectURL(url)};return worker}else{done(morpheus.NearestNeighbors.execute(dataset,options.input))}}else{var datasetRowView=new morpheus.DatasetRowView(dataset);for(var i=0,size=dataset.getRowCount();i<size;i++){scoreVector.setValue(i,f(nearestNeighborsList,datasetRowView.setIndex(i)))}if(!isColumns){project.setRowSortKeys([new morpheus.SortKey(f.toString(),morpheus.SortKey.SortOrder.DESCENDING)],true)}else{project.setColumnSortKeys([new morpheus.SortKey(f.toString(),morpheus.SortKey.SortOrder.DESCENDING)],true)}project.trigger("trackChanged",{vectors:[scoreVector],display:["text"],columns:isColumns})}}};morpheus.NewHeatMapTool=function(){};morpheus.NewHeatMapTool.prototype={toString:function(){return"New Heat Map"},execute:function(options){var project=options.project;var heatMap=options.heatMap;var dataset=project.getSelectedDataset({selectedRows:true,selectedColumns:true});morpheus.DatasetUtil.shallowCopy(dataset);var heatmap=new morpheus.HeatMap({name:heatMap.getName(),dataset:dataset,parent:heatMap,symmetric:project.isSymmetric()&&dataset.getColumnCount()===dataset.getRowCount()})}};morpheus.OpenDatasetTool=function(){};morpheus.OpenDatasetTool.prototype={toString:function(){return"Open Dataset"},_read:function(options,deferred){var _this=this;var project=options.project;var heatMap=options.heatMap;var file=options.input.file;var action=options.input.open_file_action;var dataset=project.getSortedFilteredDataset();deferred.fail(function(err){var message=["Error opening "+morpheus.Util.getFileName(file)+"."];if(err.message){message.push("<br />Cause: ");message.push(err.message)}morpheus.FormBuilder.showInModal({title:"Error",html:message.join(""),focus:document.activeElement})});deferred.done(function(newDataset){var extension=morpheus.Util.getExtension(morpheus.Util.getFileName(file));var filename=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(file));if(action==="append"||action==="append columns"){var appendRows=action==="append";_.each(heatMap.options.rows,function(item){if(item.renameTo){var v=newDataset.getRowMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}});_.each(heatMap.options.columns,function(item){if(item.renameTo){var v=newDataset.getColumnMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}});if(heatMap.options.datasetReady){heatMap.options.datasetReady(newDataset)}var currentDatasetMetadataNames=morpheus.MetadataUtil.getMetadataNames(!appendRows?dataset.getRowMetadata():dataset.getColumnMetadata());var newDatasetMetadataNames=morpheus.MetadataUtil.getMetadataNames(!appendRows?newDataset.getRowMetadata():newDataset.getColumnMetadata());if(currentDatasetMetadataNames.length>1||newDatasetMetadataNames.length>1){_this._matchAppend(newDatasetMetadataNames,currentDatasetMetadataNames,heatMap,function(appendOptions){heatMap.getProject().setFullDataset(appendRows?new morpheus.JoinedDataset(dataset,newDataset,appendOptions.current_dataset_annotation_name,appendOptions.new_dataset_annotation_name):new morpheus.TransposedDatasetView(new morpheus.JoinedDataset(new morpheus.TransposedDatasetView(dataset),new morpheus.TransposedDatasetView(newDataset),appendOptions.current_dataset_annotation_name,appendOptions.new_dataset_annotation_name)),true);if(heatMap.options.renderReady){heatMap.options.renderReady(heatMap);heatMap.updateDataset()}if(appendRows){heatMap.getHeatMapElementComponent().getColorScheme().setSeparateColorSchemeForRowMetadataField("Source");var sourcesSet=morpheus.VectorUtil.getSet(heatMap.getProject().getFullDataset().getRowMetadata().getByName("Source"));sourcesSet.forEach(function(source){heatMap.autoDisplay({extension:morpheus.Util.getExtension(source),filename:source})})}heatMap.tabManager.setTabTitle(heatMap.tabId,heatMap.getProject().getFullDataset().getRowCount()+" row"+morpheus.Util.s(heatMap.getProject().getFullDataset().getRowCount())+" x "+heatMap.getProject().getFullDataset().getColumnCount()+" column"+morpheus.Util.s(heatMap.getProject().getFullDataset().getColumnCount()));heatMap.revalidate()})}else{heatMap.getProject().setFullDataset(appendRows?new morpheus.JoinedDataset(dataset,newDataset,currentDatasetMetadataNames[0],newDatasetMetadataNames[0]):new morpheus.TransposedDatasetView(new morpheus.JoinedDataset(new morpheus.TransposedDatasetView(dataset),new morpheus.TransposedDatasetView(newDataset),currentDatasetMetadataNames[0],newDatasetMetadataNames[0])),true);if(heatMap.options.renderReady){heatMap.options.renderReady(heatMap);heatMap.updateDataset()}if(appendRows){heatMap.getHeatMapElementComponent().getColorScheme().setSeparateColorSchemeForRowMetadataField("Source");var sourcesSet=morpheus.VectorUtil.getSet(heatMap.getProject().getFullDataset().getRowMetadata().getByName("Source"));sourcesSet.forEach(function(source){heatMap.autoDisplay({extension:morpheus.Util.getExtension(source),filename:source})})}heatMap.tabManager.setTabTitle(heatMap.tabId,heatMap.getProject().getFullDataset().getRowCount()+" row"+morpheus.Util.s(heatMap.getProject().getFullDataset().getRowCount())+" x "+heatMap.getProject().getFullDataset().getColumnCount()+" column"+morpheus.Util.s(heatMap.getProject().getFullDataset().getColumnCount()));heatMap.revalidate()}}else if(action==="overlay"){_this._matchOverlay(morpheus.MetadataUtil.getMetadataNames(newDataset.getColumnMetadata()),morpheus.MetadataUtil.getMetadataNames(dataset.getColumnMetadata()),morpheus.MetadataUtil.getMetadataNames(newDataset.getRowMetadata()),morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata()),heatMap,function(appendOptions){morpheus.DatasetUtil.overlay({dataset:dataset,newDataset:newDataset,rowAnnotationName:appendOptions.current_dataset_row_annotation_name,newRowAnnotationName:appendOptions.new_dataset_row_annotation_name,columnAnnotationName:appendOptions.current_dataset_column_annotation_name,newColumnAnnotationName:appendOptions.new_dataset_column_annotation_name})})}else if(action==="open"){console.log("open");new morpheus.HeatMap({dataset:newDataset,parent:heatMap,inheritFromParent:false})}else{console.log("Unknown action: "+action)}if(action!=="open"){heatMap.revalidate()}})},execute:function(options){var file=options.input.file;var _this=this;var d=$.Deferred();morpheus.OpenDatasetTool.fileExtensionPrompt(file,function(readOptions){if(!readOptions){readOptions={}}readOptions.interactive=true;var deferred=morpheus.DatasetUtil.read(file,readOptions);deferred.always(function(){d.resolve()});_this._read(options,deferred)});return d},_matchAppend:function(newDatasetMetadataNames,currentDatasetMetadataNames,heatMap,callback){var tool={};tool.execute=function(options){return options.input};tool.toString=function(){return"Select Fields"};tool.gui=function(){var items=[{name:"current_dataset_annotation_name",options:currentDatasetMetadataNames,type:"select",value:"id",required:true}];items.push({name:"new_dataset_annotation_name",type:"select",value:"id",options:newDatasetMetadataNames,required:true});return items};morpheus.HeatMap.showTool(tool,heatMap,callback)},_matchOverlay:function(newDatasetColumnMetadataNames,currentDatasetColumnMetadataNames,newDatasetRowMetadataNames,currentDatasetRowMetadataNames,heatMap,callback){var tool={};tool.execute=function(options){return options.input};tool.toString=function(){return"Select Fields"};tool.gui=function(){var items=[];items.push({name:"current_dataset_column_annotation_name",options:currentDatasetColumnMetadataNames,type:"select",value:"id",required:true});items.push({name:"new_dataset_column_annotation_name",type:"select",value:"id",options:newDatasetColumnMetadataNames,required:true});items.push({name:"current_dataset_row_annotation_name",options:currentDatasetRowMetadataNames,type:"select",value:"id",required:true});items.push({name:"new_dataset_row_annotation_name",type:"select",value:"id",options:newDatasetRowMetadataNames,required:true});return items};morpheus.HeatMap.showTool(tool,heatMap,callback)}};morpheus.OpenDatasetTool.fileExtensionPrompt=function(file,callback){var ext=morpheus.Util.getExtension(morpheus.Util.getFileName(file));var deferred;if(ext==="seg"||ext==="segtab"){this._promptSegtab(function(regions){callback(regions)})}else{callback(null)}};morpheus.OpenDatasetTool._promptMaf=function(promptCallback){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"MAF_gene_symbols",value:"",type:"textarea",required:true,help:"Enter one gene symbol per line to filter genes. Leave blank to show all genes."});morpheus.FormBuilder.showInModal({title:"Gene Symbols",html:formBuilder.$form,close:"OK",onClose:function(){var text=formBuilder.getValue("MAF_gene_symbols");var lines=morpheus.Util.splitOnNewLine(text);var mafGeneFilter=new morpheus.Map;for(var i=0,nlines=lines.length,counter=0;i<nlines;i++){var line=lines[i];if(line!==""){mafGeneFilter.set(line,counter++)}}var readOptions=mafGeneFilter.size()>0?{mafGeneFilter:mafGeneFilter}:null;promptCallback(readOptions)}})};morpheus.OpenDatasetTool._promptSegtab=function(promptCallback){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"regions",value:"",type:"textarea",required:true,help:"Define the regions over which you want to define the CNAs. Enter one region per line. Each line should contain region_id, chromosome, start, and end separated by a tab. Leave blank to use all unique segments in the segtab file as regions."});morpheus.FormBuilder.showInModal({title:"Regions",html:formBuilder.$form,close:"OK",onClose:function(){var text=formBuilder.getValue("regions");var lines=morpheus.Util.splitOnNewLine(text);var regions=[];var tab=/\t/;for(var i=0,nlines=lines.length,counter=0;i<nlines;i++){var line=lines[i];if(line!==""){var tokens=line.split(tab);if(tokens.length>=4){regions.push({id:tokens[0],chromosome:tokens[1],start:parseInt(tokens[2]),end:parseInt(tokens[3])})}}}var readOptions=regions.length>0?{regions:regions}:null;promptCallback(readOptions)}})};morpheus.OpenDendrogramTool=function(file){this._file=file};morpheus.OpenDendrogramTool.prototype={toString:function(){return"Open Dendrogram"},init:function(project,form){var setValue=function(val){var isRows=val==="Rows";var names=morpheus.MetadataUtil.getMetadataNames(isRows?project.getFullDataset().getRowMetadata():project.getFullDataset().getColumnMetadata());names.unshift("Newick file does not contain node ids");form.setOptions("match_leaf_node_ids_to",names)};form.$form.find("[name=orientation]").on("change",function(e){setValue($(this).val())});setValue("Columns")},gui:function(){return[{name:"orientation",options:["Columns","Rows"],value:"Columns",type:"radio"},{name:"match_leaf_node_ids_to",options:[],type:"select"}]},execute:function(options){var fileOrUrl=this._file;var isColumns=options.input.orientation==="Columns";var dendrogramField=options.input.match_leaf_node_ids_to;if(dendrogramField==""||dendrogramField==="Newick file does not contain node ids"){dendrogramField=null}var heatMap=options.heatMap;var dendrogramDeferred=morpheus.Util.getText(fileOrUrl);dendrogramDeferred.done(function(text){var dataset=options.project.getSortedFilteredDataset();if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var tree=morpheus.DendrogramUtil.parseNewick(text);if(tree.leafNodes.length!==dataset.getRowCount()){throw new Error("# leaf nodes in dendrogram "+tree.leafNodes.length+" != "+dataset.getRowCount())}var modelIndices=[];if(dendrogramField!=null){var vector=dataset.getRowMetadata().getByName(dendrogramField);var valueToIndex=morpheus.VectorUtil.createValueToIndexMap(vector);for(var i=0,length=tree.leafNodes.length;i<length;i++){var newickId=tree.leafNodes[i].name;var index=valueToIndex.get(newickId);if(index===undefined){throw new Error("Unable to find dendrogram id "+tree.leafNodes[i].name+" in annotations")}modelIndices.push(index)}}else{for(var i=0,length=tree.leafNodes.length;i<length;i++){var newickId=tree.leafNodes[i].name;newickId=parseInt(newickId);if(!isNaN(newickId)){modelIndices.push(newickId)}else{break}}if(modelIndices.length!==tree.leafNodes.length){modelIndices=[];for(var i=0,length=tree.leafNodes.length;i<length;i++){modelIndices.push(i)}}}heatMap.setDendrogram(tree,isColumns,modelIndices)})}};morpheus.OpenFileTool=function(options){this.options=options||{}};morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS=[{name:"Open session",value:"Open session"},{name:"Open dataset in new tab",value:"open"},{name:"Append rows to current dataset",value:"append"},{name:"Append columns to current dataset",value:"append columns"},{name:"Overlay onto current dataset",value:"overlay"},{divider:true},{name:"Annotate columns",value:"Annotate Columns"},{name:"Annotate rows",value:"Annotate Rows"},{divider:true},{name:"Open dendrogram",value:"Open dendrogram"}];morpheus.OpenFileTool.prototype={toString:function(){return"Open"+(this.options.file!=null?" - "+this.options.file.name:"")},gui:function(){var params=[{name:"open_file_action",value:"open",type:"bootstrap-select",options:morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS}];if(this.options.file==null){params.options={size:"modal-lg",cancel:false,ok:false}}else{var extension=morpheus.Util.getExtension(morpheus.Util.getFileName(this.options.file));if(extension==="json"){params[0].options=params[0].options.filter(function(opt){return opt.value!=null&&(opt.value==="Open session"||opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)})}else if(extension==="gct"){params[0].options=params[0].options.filter(function(opt){return opt.value!=null&&(opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)})}}return params},init:function(project,form,initOptions){var _this=this;if(this.options.file==null){form.setVisible("open_file_action",false);var $div=$("<div></div>");var $ok=$('<div style="display:none;padding:15px;text-align:right;"><button name="action-selected" type="button" class="btn'+' btn-default">OK</button></div>');$ok.find("[name=action-selected]").on("click",function(){_this.ok()});var filePicker=new morpheus.FilePicker({fileCallback:function(fileOrUrl){$div.hide();$ok.show();_this.options.file=fileOrUrl;var extension=morpheus.Util.getExtension(morpheus.Util.getFileName(_this.options.file));if(extension==="json"){form.setOptions("open_file_action",morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS.filter(function(opt){return opt.value!=null&&(opt.value==="Open session"||opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)}))}else if(extension==="gct"){form.setOptions("open_file_action",morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS.filter(function(opt){return opt.value!=null&&(opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)}))}form.setVisible("open_file_action",true)},optionsCallback:function(heatMapOptions){$div.hide();$ok.show();_this.options.file=heatMapOptions.dataset;form.setVisible("open_file_action",true);form.setOptions("open_file_action",morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS.filter(function(opt){return opt.value!=null&&(opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)}))}});filePicker.$el.appendTo($div);$ok.appendTo(form.$form);$div.appendTo(form.$form)}},execute:function(options){var _this=this;var isInteractive=this.options.file==null;var heatMap=options.heatMap;if(!isInteractive){options.input.file=this.options.file}var project=options.project;if(options.input.open_file_action==="Open session"){return morpheus.Util.getText(options.input.file).done(function(text){var options=JSON.parse(text);options.tabManager=heatMap.getTabManager();options.focus=true;options.inheritFromParent=false;options.landingPage=heatMap.options.landingPage;new morpheus.HeatMap(options)}).fail(function(err){morpheus.FormBuilder.showMessageModal({title:"Error",message:"Unable to load session",focus:document.activeElement})})}else if(options.input.open_file_action==="append columns"||options.input.open_file_action==="append"||options.input.open_file_action==="open"||options.input.open_file_action==="overlay"){return(new morpheus.OpenDatasetTool).execute(options)}else if(options.input.open_file_action==="Open dendrogram"){morpheus.HeatMap.showTool(new morpheus.OpenDendrogramTool(options.input.file),options.heatMap)}else{var d=$.Deferred();var isAnnotateColumns=options.input.open_file_action=="Annotate Columns";var fileOrUrl=options.input.file;var dataset=project.getFullDataset();var fileName=morpheus.Util.getFileName(fileOrUrl);if(morpheus.Util.endsWith(fileName,".cls")){var result=morpheus.Util.readLines(fileOrUrl);result.always(function(){d.resolve()});result.done(function(lines){_this.annotateCls(heatMap,dataset,fileName,isAnnotateColumns,lines)})}else if(morpheus.Util.endsWith(fileName,".gmt")){morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,buf){d.resolve();if(err){throw new Error("Unable to read "+fileOrUrl)}var sets=(new morpheus.GmtReader).read(new morpheus.ArrayBufferReader(new Uint8Array(buf)));_this.promptSets(dataset,heatMap,isAnnotateColumns,sets,morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl)))})}else{var result=morpheus.Util.readLines(fileOrUrl);result.done(function(lines){_this.prompt(lines,dataset,heatMap,isAnnotateColumns)}).always(function(){d.resolve()});return d}}},annotateCls:function(heatMap,dataset,fileName,isColumns,lines){if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var assignments=(new morpheus.ClsReader).read(lines);if(assignments.length!==dataset.getRowCount()){throw new Error("Number of samples in cls file does not match dataset.")}var vector=dataset.getRowMetadata().add(morpheus.Util.getBaseFileName(fileName));for(var i=0;i<assignments.length;i++){vector.setValue(i,assignments[i])}if(heatMap){heatMap.getProject().trigger("trackChanged",{vectors:[vector],display:["color"],columns:isColumns})}},annotateSets:function(dataset,isColumns,sets,datasetMetadataName,setSourceFileName){if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var vector=dataset.getRowMetadata().getByName(datasetMetadataName);var idToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector);var setVector=dataset.getRowMetadata().add(setSourceFileName);sets.forEach(function(set){var name=set.name;var members=set.ids;members.forEach(function(id){var indices=idToIndices.get(id);if(indices!==undefined){for(var i=0,nIndices=indices.length;i<nIndices;i++){var array=setVector.getValue(indices[i]);if(array===undefined){array=[]}array.push(name);setVector.setValue(indices[i],array)}}})});return setVector},annotate:function(lines,dataset,isColumns,sets,metadataName,fileColumnName,fileColumnNamesToInclude,transposed){if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var vector=dataset.getRowMetadata().getByName(metadataName);if(!vector){throw new Error("vector "+metadataName+" not found.")}var fileColumnNamesToIncludeSet=null;if(fileColumnNamesToInclude){fileColumnNamesToIncludeSet=new morpheus.Set;fileColumnNamesToInclude.forEach(function(name){fileColumnNamesToIncludeSet.add(name)})}var vectors=[];var idToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector);if(!lines){_.each(sets,function(set){var name=set.name;var members=set.ids;var v=dataset.getRowMetadata().add(name);vectors.push(v);_.each(members,function(id){var indices=idToIndices.get(id);if(indices!==undefined){for(var i=0,nIndices=indices.length;i<nIndices;i++){v.setValue(indices[i],name)}}})})}else{var tab=/\t/;if(!transposed){var header=lines[0].split(tab);var fileMatchOnColumnIndex=_.indexOf(header,fileColumnName);if(fileMatchOnColumnIndex===-1){throw new Error(fileColumnName+" not found in header:"+header)}var columnIndices=[];var nheaders=header.length;for(var j=0;j<nheaders;j++){var name=header[j];if(j===fileMatchOnColumnIndex){continue}if(fileColumnNamesToIncludeSet&&!fileColumnNamesToIncludeSet.has(name)){continue}var v=dataset.getRowMetadata().getByName(name);if(!v){v=dataset.getRowMetadata().add(name)}columnIndices.push(j);vectors.push(v)}var nheaders=columnIndices.length;for(var i=1,nrows=lines.length;i<nrows;i++){var line=lines[i].split(tab);var id=line[fileMatchOnColumnIndex];var indices=idToIndices.get(id);if(indices!==undefined){var nIndices=indices.length;for(var j=0;j<nheaders;j++){var token=line[columnIndices[j]];var v=vectors[j];for(var r=0;r<nIndices;r++){v.setValue(indices[r],token)}}}}}else{var splitLines=[];var matchOnLine;for(var i=0,nrows=lines.length;i<nrows;i++){var line=lines[i].split(tab);var name=line[0];if(fileColumnName===name){matchOnLine=line}else{if(fileColumnNamesToIncludeSet&&!fileColumnNamesToIncludeSet.has(name)){continue}splitLines.push(line);var v=dataset.getRowMetadata().getByName(name);if(!v){v=dataset.getRowMetadata().add(name)}vectors.push(v)}}if(matchOnLine==null){throw new Error(fileColumnName+" not found in header.")}for(var fileColumnIndex=1,ncols=matchOnLine.length;fileColumnIndex<ncols;fileColumnIndex++){var id=matchOnLine[fileColumnIndex];var indices=idToIndices.get(id);if(indices!==undefined){var nIndices=indices.length;for(var j=0;j<splitLines.length;j++){var token=splitLines[j][fileColumnIndex];var v=vectors[j];for(var r=0;r<nIndices;r++){v.setValue(indices[r],token)}}}}}}for(var i=0;i<vectors.length;i++){morpheus.VectorUtil.maybeConvertStringToNumber(vectors[i])}return vectors},promptSets:function(dataset,heatMap,isColumns,sets,setSourceFileName){var promptTool={};var _this=this;promptTool.execute=function(options){var metadataName=options.input.dataset_field_name;var vector=_this.annotateSets(dataset,isColumns,sets,metadataName,setSourceFileName);heatMap.getProject().trigger("trackChanged",{vectors:[vector],display:["text"],columns:isColumns})};promptTool.toString=function(){return"Select Fields To Match On"};promptTool.gui=function(){return[{name:"dataset_field_name",options:morpheus.MetadataUtil.getMetadataNames(isColumns?dataset.getColumnMetadata():dataset.getRowMetadata()),type:"select",value:"id",required:true}]};morpheus.HeatMap.showTool(promptTool,heatMap)},prompt:function(lines,dataset,heatMap,isColumns){var promptTool={};var _this=this;var header=lines!=null?lines[0].split("\t"):null;promptTool.execute=function(options){var metadataName=options.input.dataset_field_name;var fileColumnName=options.input.file_field_name;var vectors=_this.annotate(lines,dataset,isColumns,null,metadataName,fileColumnName);var nameToIndex=new morpheus.Map;var display=[];for(var i=0;i<vectors.length;i++){display.push(isColumns?"color":"text");nameToIndex.set(vectors[i].getName(),i)}if(lines.colors){var colorModel=isColumns?heatMap.getProject().getColumnColorModel():heatMap.getProject().getRowColorModel();lines.colors.forEach(function(item){var index=nameToIndex.get(item.header);var vector=vectors[index];display[index]="color";colorModel.setMappedValue(vector,item.value,item.color)})}heatMap.getProject().trigger("trackChanged",{vectors:vectors,display:display,columns:isColumns})};promptTool.toString=function(){return"Select Fields To Match On"};promptTool.gui=function(){var items=[{name:"dataset_field_name",options:morpheus.MetadataUtil.getMetadataNames(isColumns?dataset.getColumnMetadata():dataset.getRowMetadata()),type:"select",required:true}];if(lines){items.push({name:"file_field_name",type:"select",options:_.map(header,function(item){return{name:item,value:item}}),required:true})}return items};morpheus.HeatMap.showTool(promptTool,heatMap)}};morpheus.SaveDatasetTool=function(){};morpheus.SaveDatasetTool.prototype={toString:function(){return"Save Dataset"},init:function(project,form){form.find("file_name").prop("autofocus",true).focus();var seriesNames=[];var dataset=project.getFullDataset();for(var i=0,nseries=dataset.getSeriesCount();i<nseries;i++){seriesNames.push(dataset.getName(i))}form.setOptions("series",seriesNames.length>1?seriesNames:null);form.setVisible("series",seriesNames.length>1)},gui:function(){return[{name:"file_name",type:"text",help:'<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>'+' or <a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a> file name',required:true},{name:"file_format",type:"radio",options:[{name:"GCT version 1.2",value:"1.2"},{name:"GCT version 1.3",value:"1.3"}],value:"1.3"},{name:"series",type:"select",options:[],required:true},{name:"save_selection_only",type:"checkbox",required:true}]},execute:function(options){var project=options.project;var format=options.input.file_format;var fileName=options.input.file_name;if(fileName===""){fileName="dataset"}var series=options.input.series;var heatMap=options.heatMap;var dataset=options.input.save_selection_only?project.getSelectedDataset():project.getSortedFilteredDataset();var writer;if(format==="1.2"){writer=new morpheus.GctWriter12}else if(format==="1.3"){writer=new morpheus.GctWriter}if(series!=null){var seriesIndex=morpheus.DatasetUtil.getSeriesIndex(dataset,series);if(seriesIndex===-1){seriesIndex=0}dataset=seriesIndex===0?dataset:new morpheus.DatasetSeriesView(dataset,[seriesIndex])}var ext=writer.getExtension?writer.getExtension():"";if(ext!==""&&!morpheus.Util.endsWith(fileName.toLowerCase(),"."+ext)){fileName+="."+ext}writer.setNumberFormat(heatMap.getHeatMapElementComponent().getDrawValuesFormat());var blobs=[];var textArray=[];var proxy={push:function(text){textArray.push(text);if(textArray.length===1e4){var blob=new Blob([textArray.join("")],{type:"text/plain;charset=charset=utf-8"});textArray=[];blobs.push(blob)}},join:function(){if(textArray.length>0){var blob=new Blob([textArray.join("")],{type:"text/plain;charset=charset=utf-8"});blobs.push(blob);textArray=[]}var blob=new Blob(blobs,{type:"text/plain;charset=charset=utf-8"});saveAs(blob,fileName,true)}};writer.write(dataset,proxy)}};morpheus.SaveImageTool=function(){};morpheus.SaveImageTool.prototype={toString:function(){return"Save Image"},init:function(project,form){form.find("file_name").prop("autofocus",true).focus()},gui:function(){return[{name:"file_name",type:"text",required:true},{name:"format",type:"radio",options:["PDF","PNG","SVG"],value:"PNG",required:true}]},execute:function(options){var fileName=options.input.file_name;if(fileName===""){fileName="image"}var format=options.input.format.toLowerCase();if(!morpheus.Util.endsWith(fileName.toLowerCase(),"."+format)){fileName+="."+format}var heatMap=options.heatMap;heatMap.saveImage(fileName,format)}};morpheus.SaveSessionTool=function(){};morpheus.SaveSessionTool.prototype={toString:function(){return"Save Session"},init:function(project,form){form.find("file_name").prop("autofocus",true).focus()},gui:function(){return[{name:"file_name",type:"text",required:true}]},execute:function(options){var fileName=options.input.file_name;if(fileName===""){fileName="session.json"}if(!morpheus.Util.endsWith(fileName.toLowerCase(),".json")){fileName+=".json"}var heatMap=options.heatMap;var options={dataset:true};var json=heatMap.toJSON(options);var nativeArrayToArray=Array.from||function(typedArray){var normalArray=Array.prototype.slice.call(typedArray);normalArray.length===typedArray.length;normalArray.constructor===Array};var blob=new Blob([JSON.stringify(json,function(key,value){if(morpheus.Util.isArray(value)){return value instanceof Array?value:nativeArrayToArray(value)}return value})],{type:"application/json;charset=charset=utf-8"});saveAs(blob,fileName,true)}};morpheus.SimilarityMatrixTool=function(){};morpheus.SimilarityMatrixTool.Functions=[morpheus.Euclidean,morpheus.Jaccard,morpheus.Cosine,morpheus.KendallsCorrelation,morpheus.Pearson,morpheus.Spearman];morpheus.SimilarityMatrixTool.Functions.fromString=function(s){for(var i=0;i<morpheus.SimilarityMatrixTool.Functions.length;i++){if(morpheus.SimilarityMatrixTool.Functions[i].toString()===s){return morpheus.SimilarityMatrixTool.Functions[i]}}throw new Error(s+" not found")};morpheus.SimilarityMatrixTool.execute=function(dataset,input){var isColumnMatrix=input.compute_matrix_for=="Columns";var f=morpheus.SimilarityMatrixTool.Functions.fromString(input.metric);return morpheus.HCluster.computeDistanceMatrix(isColumnMatrix?new morpheus.TransposedDatasetView(dataset):dataset,f)};morpheus.SimilarityMatrixTool.prototype={toString:function(){return"Similarity Matrix"},init:function(project,form){},gui:function(){return[{name:"metric",options:morpheus.SimilarityMatrixTool.Functions,value:morpheus.SimilarityMatrixTool.Functions[4].toString(),type:"select"},{name:"compute_matrix_for",options:["Columns","Rows"],value:"Columns",type:"radio"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var isColumnMatrix=options.input.compute_matrix_for=="Columns";var f=morpheus.SimilarityMatrixTool.Functions.fromString(options.input.metric);var dataset=project.getSortedFilteredDataset();var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.SimilarityMatrixTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){var name=heatMap.getName();var matrix=e.data;var n=isColumnMatrix?dataset.getColumnCount():dataset.getRowCount();var d=new morpheus.Dataset({name:name,rows:n,columns:n});var isDistance=f.toString()===morpheus.Euclidean.toString()||f.toString()===morpheus.Jaccard.toString();for(var i=1;i<n;i++){for(var j=0;j<i;j++){var value=matrix[i][j];d.setValue(i,j,value);d.setValue(j,i,value)}}if(!isDistance){for(var i=0;i<n;i++){d.setValue(i,i,1)}}var metadata=isColumnMatrix?dataset.getColumnMetadata():dataset.getRowMetadata();d.rowMetadataModel=morpheus.MetadataUtil.shallowCopy(metadata);d.columnMetadataModel=morpheus.MetadataUtil.shallowCopy(metadata);var colorScheme;if(!isDistance){colorScheme={type:"fixed",map:[{value:-1,color:"blue"},{value:0,color:"white"},{value:1,color:"red"}]}}else{colorScheme={type:"fixed",map:[{value:0,color:"white"},{value:morpheus.DatasetUtil.max(d),color:"red"}]}}new morpheus.HeatMap({colorScheme:colorScheme,name:name,dataset:d,parent:heatMap,inheritFromParentOptions:{rows:!isColumnMatrix,columns:isColumnMatrix}});worker.terminate();window.URL.revokeObjectURL(url)};return worker}};morpheus.TransposeTool=function(){};morpheus.TransposeTool.prototype={toString:function(){return"Transpose"},execute:function(options){var project=options.project;var heatMap=options.heatMap;var dataset=new morpheus.TransposedDatasetView(project.getSortedFilteredDataset());var rowMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getRowMetadata());var columnMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata());dataset.getRowMetadata=function(){return rowMetadataModel};dataset.getColumnMetadata=function(){return columnMetadataModel};var name=options.input.name||heatMap.getName();new morpheus.HeatMap({name:name,dataset:dataset,inheritFromParentOptions:{transpose:true},parent:heatMap})}};morpheus.TsneTool=function(){};morpheus.TsneTool.execute=function(dataset,input){var matrix=[];var rows=input.project=="Rows";if(!rows){dataset=new morpheus.TransposedDatasetView(dataset)}var N=dataset.getRowCount();var f=morpheus.HClusterTool.Functions.fromString(input.metric);if(f===morpheus.TsneTool.PRECOMPUTED_DIST){for(var i=0;i<N;i++){matrix.push([]);for(var j=i+1;j<N;j++){matrix[i][j]=dataset.getValue(i,j)}}}else if(f===morpheus.TsneTool.PRECOMPUTED_SIM){var max=morpheus.DatasetUtil.max(dataset);for(var i=0;i<N;i++){matrix.push([]);for(var j=i+1;j<N;j++){matrix[i][j]=max-dataset.getValue(i,j)}}}else{var list1=new morpheus.DatasetRowView(dataset);var list2=new morpheus.DatasetRowView(dataset);for(var i=0;i<N;i++){matrix.push([]);list1.setIndex(i);for(var j=i+1;j<N;j++){var d=f(list1,list2.setIndex(j));matrix[i][j]=d}}}var opt={};opt.epsilon=input.epsilon;opt.perplexity=input.perplexity;opt.dim=2;var tsne=new tsnejs.tSNE(opt);tsne.initDataDist(matrix);for(var k=0;k<1e3;k++){tsne.step()}var Y=tsne.getSolution();return{solution:Y}};morpheus.TsneTool.prototype={toString:function(){return"t-SNE"},init:function(project,form){},gui:function(){return[{name:"metric",options:morpheus.HClusterTool.Functions,value:morpheus.HClusterTool.Functions[3].toString(),type:"select"},{name:"project",options:["Columns","Rows"],value:"Columns",type:"select"},{name:"epsilon",value:"10",type:"text",help:"learning rate"},{name:"perplexity",value:"30",type:"text",help:"number of effective nearest neighbors"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var rows=options.input.project=="Rows";var dataset=project.getSortedFilteredDataset();options.input.epsilon=parseInt(options.input.epsilon);options.input.perplexity=parseInt(options.input.perplexity);var blob=new Blob(["self.onmessage = function(e) {"+"e.data.scripts.forEach(function (s) { importScripts(s); });"+"self.postMessage(morpheus.TsneTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:[morpheus.Util.getScriptPath()],dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){if(rows){dataset=new morpheus.TransposedDatasetView(dataset)}var result=e.data.solution;var newDataset=new morpheus.Dataset({name:"t-SNE",rows:dataset.getColumnCount(),columns:2});for(var i=0;i<result.length;i++){newDataset.setValue(i,0,result[i][0]);newDataset.setValue(i,1,result[i][1])}var idVector=newDataset.getColumnMetadata().add("id");idVector.setValue(0,"P1");idVector.setValue(1,"P2");newDataset.setRowMetadata(morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata()));var min=morpheus.DatasetUtil.min(newDataset);var max=morpheus.DatasetUtil.max(newDataset);new morpheus.HeatMap({inheritFromParentOptions:{transpose:!rows},name:"t-SNE",dataset:newDataset,parent:heatMap,columns:[{field:"id",display:"text"}],colorScheme:{type:"fixed",map:[{value:min,color:colorbrewer.Greens[3][0]},{value:max,color:colorbrewer.Greens[3][2]}]}});worker.terminate();window.URL.revokeObjectURL(url)};return worker}};morpheus.AbstractCanvas=function(offscreen){this.canvas=morpheus.CanvasUtil.createCanvas();this.lastClip=null;if(offscreen){this.offscreenCanvas=morpheus.CanvasUtil.createCanvas()}this.offset={x:0,y:0}};morpheus.AbstractCanvas.prototype={visible:true,invalid:true,scrollX:0,scrollY:0,prefWidth:undefined,prefHeight:undefined,getCanvas:function(){return this.canvas},scrollTop:function(pos){if(pos===undefined){return this.offset.y}this.offset.y=pos},appendTo:function($el){$(this.canvas).appendTo($el)},scrollLeft:function(pos){if(pos===undefined){return this.offset.x}this.offset.x=pos},dispose:function(){$(this.canvas).remove();this.offscreenCanvas=undefined},getPrefWidth:function(){return this.prefWidth},setInvalid:function(invalid){this.invalid=invalid},setBounds:function(bounds){var backingScale=morpheus.CanvasUtil.BACKING_SCALE;var canvases=[this.canvas];if(this.offscreenCanvas){canvases.push(this.offscreenCanvas)}if(bounds.height!=null){_.each(canvases,function(canvas){canvas.height=bounds.height*backingScale;canvas.style.height=bounds.height+"px"})}if(bounds.width!=null){_.each(canvases,function(canvas){canvas.width=bounds.width*backingScale;canvas.style.width=bounds.width+"px"})}if(bounds.left!=null){_.each(canvases,function(canvas){canvas.style.left=bounds.left+"px"})}if(bounds.top!=null){_.each(canvases,function(canvas){canvas.style.top=bounds.top+"px"})}},paint:function(clip){var canvas=this.canvas;var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();context.clearRect(0,0,width,height);if(this.prePaint){morpheus.CanvasUtil.resetTransform(context);context.translate(this.offset.x,this.offset.y);this.prePaint(clip,context)}morpheus.CanvasUtil.resetTransform(context);if(this.offscreenCanvas){if(this.invalid){var oc=this.offscreenCanvas.getContext("2d");morpheus.CanvasUtil.resetTransform(oc);context.translate(this.offset.x,this.offset.y);oc.clearRect(0,0,width,height);this.draw(clip,oc)}context.drawImage(this.offscreenCanvas,0,0,width,height)}else{this.draw(clip,context)}if(this.postPaint){morpheus.CanvasUtil.resetTransform(context);context.translate(this.offset.x,this.offset.y);this.postPaint(clip,context)}this.lastClip=clip;this.invalid=false},repaint:function(){if(!this.lastClip){this.lastClip={x:0,y:0,width:this.getUnscaledWidth(),height:this.getUnscaledHeight()}}this.paint(this.lastClip)},draw:function(clip,context){console.log("Not implemented")},getPrefHeight:function(){return this.prefHeight},setPrefWidth:function(prefWidth){this.prefWidth=prefWidth},setPrefHeight:function(prefHeight){this.prefHeight=prefHeight},isVisible:function(){return this.visible},setVisible:function(visible){if(this.visible!==visible){this.visible=visible;this.canvas.style.display=visible?"":"none"}},getUnscaledWidth:function(){return this.canvas.width/morpheus.CanvasUtil.BACKING_SCALE},getUnscaledHeight:function(){return this.canvas.height/morpheus.CanvasUtil.BACKING_SCALE},getWidth:function(){return this.canvas.width},getHeight:function(){return this.canvas.height}};morpheus.AbstractColorSupplier=function(){this.fractions=[0,.5,1];this.colors=["#0000ff","#ffffff","#ff0000"];this.names=null;this.min=0;this.max=1;this.missingColor="#c0c0c0";this.scalingMode=morpheus.HeatMapColorScheme.ScalingMode.RELATIVE;this.stepped=false;this.sizer=new morpheus.HeatMapSizer;this.conditions=new morpheus.HeatMapConditions;this.transformValues=0};morpheus.AbstractColorSupplier.Z_SCORE=1;morpheus.AbstractColorSupplier.ROBUST_Z_SCORE=2;morpheus.AbstractColorSupplier.toJSON=function(cs){var json={fractions:cs.fractions,colors:cs.colors,min:cs.min,max:cs.max,missingColor:cs.missingColor,scalingMode:cs.scalingMode,stepped:cs.stepped,transformValues:cs.transformValues};if(cs.names){json.names=cs.names}if(cs.conditions&&cs.conditions.array.length>0){json.conditions=cs.conditions.array}if(cs.sizer&&cs.sizer.seriesName!=null){json.size={seriesName:cs.sizer.seriesName,min:cs.sizer.min,max:cs.sizer.max}}return json};morpheus.AbstractColorSupplier.fromJSON=function(json){var cs=json.stepped?new morpheus.SteppedColorSupplier:new morpheus.GradientColorSupplier;if(json.scalingMode==null&&json.type!=null){json.scalingMode=json.type}if(json.scalingMode==="relative"||json.scalingMode===0){json.scalingMode=0}else if(json.scalingMode==="fixed"||json.scalingMode===1){json.scalingMode=1}else{json.scalingMode=0}cs.setScalingMode(json.scalingMode);if(json.min!=null){cs.setMin(json.min)}if(json.max!=null){cs.setMax(json.max)}if(json.missingColor!=null){cs.setMissingColor(json.missingColor)}if(morpheus.HeatMapColorScheme.ScalingMode.RELATIVE!==json.scalingMode){cs.setTransformValues(json.transformValues)}if(json.map){json.values=json.map.map(function(item){return item.value});json.colors=json.map.map(function(item){return item.color})}var fractions=json.fractions;if(json.values){fractions=[];var values=json.values;var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;for(var i=0;i<values.length;i++){var value=values[i];min=Math.min(min,value);max=Math.max(max,value)}var valueToFraction=d3.scale.linear().domain([min,max]).range([0,1]).clamp(true);for(var i=0;i<values.length;i++){fractions.push(valueToFraction(values[i]))}if(json.min==null){cs.setMin(min)}if(json.max==null){cs.setMax(max)}}if(json.colors!=null&&json.colors.length>0){cs.setFractions({colors:json.colors,fractions:fractions,names:json.names})}if(json.size){cs.getSizer().setSeriesName(json.size.seriesName);cs.getSizer().setMin(json.size.min);cs.getSizer().setMax(json.size.max)}if(json.conditions&&_.isArray(json.conditions)){json.conditions.forEach(function(condition){var gtf=function(){return true};var ltf=function(){return true};if(condition.seriesName==null){condition.seriesName=condition.series}if(condition.v1!=null&&!isNaN(condition.v1)){gtf=condition.v1Op==="gt"?function(val){return val>condition.v1}:function(val){return val>=condition.v1}}if(condition.v2!=null&&!isNaN(condition.v2)){ltf=condition.v2Op==="lt"?function(val){return val<condition.v2}:function(val){return val<=condition.v2}}condition.accept=function(val){return gtf(val)&&ltf(val)}});cs.conditions.array=json.conditions}return cs};morpheus.AbstractColorSupplier.prototype={getTransformValues:function(){return this.transformValues},setTransformValues:function(transformValues){this.transformValues=transformValues},getSizer:function(){return this.sizer},getConditions:function(){return this.conditions},createInstance:function(){throw"not implemented"},copy:function(){var c=this.createInstance();c.stepped=this.stepped;c.setFractions({fractions:this.fractions.slice(0),colors:this.colors.slice(0)});if(this.names!=null){c.names=this.names.slice(0)}if(this.sizer){c.sizer=this.sizer.copy()}if(this.conditions){c.conditions=this.conditions.copy()}c.scalingMode=this.scalingMode;c.min=this.min;c.max=this.max;c.missingColor=this.missingColor;if(this.scalingMode!==morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){c.transformValues=this.transformValues}return c},setMissingColor:function(missingColor){this.missingColor=missingColor},getMissingColor:function(){return this.missingColor},getScalingMode:function(){return this.scalingMode},setScalingMode:function(scalingMode){if(scalingMode!==this.scalingMode){if(scalingMode===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){this.min=0;this.max=1}this.scalingMode=scalingMode}},isStepped:function(){return false},getColor:function(row,column,value){throw"not implemented"},getColors:function(){return this.colors},getNames:function(){return this.names},getFractions:function(){return this.fractions},getMin:function(){return this.min},getMax:function(){return this.max},setMin:function(min){this.min=min},setMax:function(max){this.max=max},setFractions:function(options){var index=morpheus.Util.indexSort(options.fractions,true);this.fractions=morpheus.Util.reorderArray(options.fractions,index);this.colors=morpheus.Util.reorderArray(options.colors,index);this.names=options.names?morpheus.Util.reorderArray(options.names,index):null}};morpheus.AbstractComponent=function(){this.lastClip=null;var c=document.createElement("div");c.setAttribute("tabindex","0");c.style.outline=0;c.style.overflow="hidden";c.style.position="absolute";this.el=c;this.$el=$(c)};morpheus.AbstractComponent.prototype={visible:true,invalid:true,prefWidth:undefined,prefHeight:undefined,appendTo:function($el){$(this.el).appendTo($el)},dispose:function(){$(this.el).remove()},getPrefWidth:function(){return this.prefWidth},setInvalid:function(invalid){this.invalid=invalid},setBounds:function(bounds){if(bounds.left!=null){this.$el.css("left",bounds.left+"px")}if(bounds.top!=null){this.$el.css("top",bounds.top+"px")}},paint:function(clip){var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();this.draw(clip);this.lastClip=clip;this.invalid=false},repaint:function(){if(!this.lastClip){this.lastClip={x:0,y:0,width:this.getUnscaledWidth(),height:this.getUnscaledHeight()}}this.paint(this.lastClip)},draw:function(clip){},getPrefHeight:function(){return this.prefHeight},setPrefWidth:function(prefWidth){this.prefWidth=prefWidth},setPrefHeight:function(prefHeight){this.prefHeight=prefHeight},isVisible:function(){return this.visible},setVisible:function(visible){if(this.visible!==visible){this.visible=visible;this.el.style.display=visible?"":"none"}},getUnscaledWidth:function(){return this.$el.width()},getUnscaledHeight:function(){return this.$el.height()},getWidth:function(){return this.$el.width()},getHeight:function(){return this.$el.height()}};morpheus.AbstractDendrogram=function(heatMap,tree,positions,project,type){morpheus.AbstractCanvas.call(this,true);this._overviewHighlightColor="#d8b365";this._searchHighlightColor="#e41a1c";this._selectedNodeColor=type===morpheus.AbstractDendrogram.Type.COLUMN?"#377eb8":"#984ea3";this.tree=tree;this.type=type;this.squishEnabled=false;this.heatMap=heatMap;this.positions=positions;this.project=project;var $label=$("<span></span>");$label.addClass("label label-info");$label.css("position","absolute");this.$label=$label;var $squishedLabel=$("<span></span>");$squishedLabel.addClass("label label-default");$squishedLabel.css("position","absolute").css("top",18);this.$squishedLabel=$squishedLabel;this.$label=$label;this.cutHeight=this.tree.maxHeight;this.drawLeafNodes=true;this.lineWidth=.7;this.selectedNodeIds={};this.selectedRootNodeIdToNode={};this.nodeIdToHighlightedPathsToRoot={};var _this=this;this.defaultStroke="rgb(0,0,0)";this.mouseMoveNodes=null;var mouseMove=function(event){if(!morpheus.CanvasUtil.dragging){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.lastClip.x,_this.lastClip.y);if(_this.isDragHotSpot(position)){_this.canvas.style.cursor=_this.getResizeCursor()}else{var nodes;if(_this.getNodes){nodes=_this.getNodes(position)}else{var node=_this.getNode(position);if(node){nodes=[node]}}_this.mouseMoveNodes=nodes;if(nodes!=null){nodes.sort(function(a,b){return a.name<b.name});var tipOptions={event:event};tipOptions[type===morpheus.AbstractDendrogram.Type.COLUMN?"columnNodes":"rowNodes"]=nodes;_this.heatMap.setToolTip(-1,-1,tipOptions);_this.canvas.style.cursor="pointer"}else{_this.heatMap.setToolTip(-1,-1);_this.canvas.style.cursor="default"}}}};var mouseExit=function(e){if(!morpheus.CanvasUtil.dragging){_this.mouseMoveNodes=null;_this.canvas.style.cursor="default"}};if(type!==morpheus.AbstractDendrogram.Type.RADIAL){$(this.canvas).on("contextmenu",function(e){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();var position=morpheus.CanvasUtil.getMousePosWithScroll(e.target,e,_this.lastClip.x,_this.lastClip.y);var selectedNode=_this.getNode(position);morpheus.Popup.showPopup([{name:"Flip",disabled:selectedNode==null},{name:"Branch Color",disabled:selectedNode==null},{separator:true},{name:"Annotate..."},{name:"Save"},{separator:true},{name:"Enrichment..."},{separator:true},{name:"Squish Singleton Clusters",checked:_this.squishEnabled},{separator:true},{name:"Delete"}],{x:e.pageX,y:e.pageY},e.target,function(menuItem,item){if(item==="Save"){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"file_name",type:"text",required:true});formBuilder.append({name:"leaf_node_id_field",type:"bootstrap-select",required:true,options:morpheus.MetadataUtil.getMetadataNames(type===morpheus.AbstractDendrogram.Type.COLUMN?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata())});morpheus.FormBuilder.showOkCancel({title:"Save Dendrogram",content:formBuilder.$form,focus:document.activeElement,okCallback:function(){var fileName=formBuilder.getValue("file_name");if(fileName===""){fileName="dendrogram.txt"}var leafNodeIdField=formBuilder.getValue("leaf_node_id_field");var out=[];var vector=type===morpheus.AbstractDendrogram.Type.COLUMN?project.getFullDataset().getColumnMetadata().getByName(leafNodeIdField):project.getFullDataset().getRowMetadata().getByName(leafNodeIdField);var leafNodeToString=function(n){return vector.getValue(n.index)};morpheus.DendrogramUtil.writeNewick(tree.rootNode,out,leafNodeToString);var blob=new Blob([out.join("")],{type:"text/plain;charset=charset=utf-8"});saveAs(blob,fileName,true)}})}else if(item==="Flip"){if(selectedNode!=null){var isColumns=morpheus.AbstractDendrogram.Type.COLUMN===_this.type;var min=selectedNode.minIndex;var max=selectedNode.maxIndex;var leafNodes=tree.leafNodes;for(var i=min,index=max;i<=max;i++,index--){var n=leafNodes[i];n.index=index;n.maxIndex=index;n.minIndex=index}leafNodes.sort(function(a,b){return a.index<b.index?-1:1});var setIndex=function(n){if(n.children!=null&&n.children.length>0){for(var i=0;i<n.children.length;i++){setIndex(n.children[i])}var sum=0;for(var i=0;i<n.children.length;i++){sum+=n.children[i].index}n.index=sum/n.children.length;var maxIndex=-Number.MAX_VALUE;var minIndex=Number.MAX_VALUE;for(var i=0;i<n.children.length;i++){maxIndex=Math.max(maxIndex,n.children[i].maxIndex);minIndex=Math.min(minIndex,n.children[i].minIndex)}n.minIndex=minIndex;n.maxIndex=maxIndex}};setIndex(selectedNode);var currentOrder=[];var count=isColumns?heatMap.getProject().getSortedFilteredDataset().getColumnCount():heatMap.getProject().getSortedFilteredDataset().getRowCount();for(var i=0;i<count;i++){currentOrder.push(isColumns?project.convertViewColumnIndexToModel(i):project.convertViewRowIndexToModel(i))}for(var i=min,j=max;i<j;i++,j--){var tmp=currentOrder[j];currentOrder[j]=currentOrder[i];currentOrder[i]=tmp}var key=new morpheus.SpecifiedModelSortOrder(currentOrder,currentOrder.length,"dendrogram",isColumns);key.setPreservesDendrogram(true);key.setLockOrder(2);key.setUnlockable(false);if(isColumns){heatMap.getProject().setColumnSortKeys([key],true)}else{heatMap.getProject().setRowSortKeys([key],true)}heatMap.revalidate()}}else if(item==="Branch Color"){if(selectedNode!=null){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"color",type:"color",value:selectedNode.color,required:true,style:"max-width:50px;"});formBuilder.find("color").on("change",function(){var color=$(this).val();morpheus.DendrogramUtil.dfs(selectedNode,function(n){n.color=color;return true});_this.setSelectedNode(null)});morpheus.FormBuilder.showInModal({title:"Color",close:"Close",html:formBuilder.$form,focus:document.activeElement})}}else if(item==="Annotate..."){morpheus.HeatMap.showTool(new morpheus.AnnotateDendrogramTool(type===morpheus.AbstractDendrogram.Type.COLUMN),_this.heatMap)}else if(item==="Enrichment..."){morpheus.HeatMap.showTool(new morpheus.DendrogramEnrichmentTool(type===morpheus.AbstractDendrogram.Type.COLUMN),_this.heatMap)}else if(item==="Squish Singleton Clusters"){_this.squishEnabled=!_this.squishEnabled;if(!_this.squishEnabled){_this.positions.setSquishedIndices(null)}}else if(item==="Delete"){_this.resetCutHeight();_this.heatMap.setDendrogram(null,type===morpheus.AbstractDendrogram.Type.COLUMN)}});return false});$(this.canvas).on("mousemove",_.throttle(mouseMove,100)).on("mouseout",_.throttle(mouseExit,100)).on("mouseenter",_.throttle(mouseMove,100))}var dragStartScaledCutHeight=0;this.cutTreeHotSpot=false;if(type!==morpheus.AbstractDendrogram.Type.RADIAL){this.hammer=morpheus.Util.hammer(this.canvas,["pan","tap"]).on("tap",this.tap=function(event){if(!morpheus.CanvasUtil.dragging){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.lastClip.x,_this.lastClip.y);_this.cutTreeHotSpot=_this.isDragHotSpot(position);if(_this.cutTreeHotSpot){return}var node=_this.getNode(position);if(node!=null&&node.parent===undefined){node=null}var commandKey=morpheus.Util.IS_MAC?event.srcEvent.metaKey:event.srcEvent.ctrlKey;_this.setSelectedNode(node,event.srcEvent.shiftKey||commandKey)}}).on("panend",this.panend=function(event){morpheus.CanvasUtil.dragging=false;_this.canvas.style.cursor="default";_this.cutTreeHotSpot=true}).on("panstart",this.panstart=function(event){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.lastClip.x,_this.lastClip.y,true);_this.cutTreeHotSpot=_this.isDragHotSpot(position);if(_this.cutTreeHotSpot){morpheus.CanvasUtil.dragging=true;_this.canvas.style.cursor=_this.getResizeCursor();dragStartScaledCutHeight=_this.scale(_this.cutHeight)}}).on("panmove",this.panmove=function(event){if(_this.cutTreeHotSpot){var cutHeight;if(_this.type===morpheus.AbstractDendrogram.Type.COLUMN){var delta=event.deltaY;cutHeight=Math.max(0,Math.min(_this.tree.maxHeight,_this.scale.invert(dragStartScaledCutHeight+delta)))}else if(_this.type===morpheus.AbstractDendrogram.Type.ROW){var delta=event.deltaX;cutHeight=Math.max(0,Math.min(_this.tree.maxHeight,_this.scale.invert(dragStartScaledCutHeight+delta)))}else{var point=morpheus.CanvasUtil.getMousePos(event.target,event);point.x=_this.radius-point.x;point.y=_this.radius-point.y;var radius=Math.sqrt(point.x*point.x+point.y*point.y);if(radius<=4){cutHeight=_this.tree.maxHeight}else{cutHeight=Math.max(0,Math.min(_this.tree.maxHeight,_this.scale.invert(radius)))}}if(cutHeight>=_this.tree.maxHeight){_this.resetCutHeight()}else{_this.setCutHeight(cutHeight)}event.preventDefault()}})}};morpheus.AbstractDendrogram.Type={COLUMN:0,ROW:1,RADIAL:2};morpheus.AbstractDendrogram.prototype={setSelectedNode:function(node,add){var _this=this;var viewIndices;var selectionModel=this.type===morpheus.AbstractDendrogram.Type.COLUMN?this.project.getColumnSelectionModel():this.project.getRowSelectionModel();if(node==null){_this.selectedNodeIds={};_this.selectedRootNodeIdToNode={};viewIndices=new morpheus.Set}else{if(add){viewIndices=selectionModel.getViewIndices()}else{viewIndices=new morpheus.Set;_this.selectedNodeIds={};_this.selectedRootNodeIdToNode={}}if(node!=null){if(node.children===undefined){var contains=_this.nodeIdToHighlightedPathsToRoot[node.id];if(!add){_this.nodeIdToHighlightedPathsToRoot={}}if(contains){delete _this.nodeIdToHighlightedPathsToRoot[node.id]}else{_this.nodeIdToHighlightedPathsToRoot[node.id]=node}}else{_this.selectedRootNodeIdToNode[node.id]=node;morpheus.DendrogramUtil.dfs(node,function(d){_this.selectedNodeIds[d.id]=true;return true})}for(var i=node.minIndex;i<=node.maxIndex;i++){viewIndices.add(i)}}}_this.trigger("nodeSelectionChanged",_this.selectedRootNodeIdToNode);selectionModel.setViewIndices(viewIndices,true);_this.repaint()},getPathStroke:function(node){if(this.selectedNodeIds[node.id]){return this._selectedNodeColor}if(node.color!==undefined){return node.color}return this.defaultStroke},getNodeFill:function(node){if(this.selectedRootNodeIdToNode[node.id]){return this._selectedNodeColor}if(node.search){return this._searchHighlightColor}if(node.info!==undefined){return this._overviewHighlightColor}},resetCutHeight:function(){this.positions.setSquishedIndices(null);if(this.type===morpheus.AbstractDendrogram.Type.COLUMN){this.project.setGroupColumns([],true)}else{this.project.setGroupRows([],true)}this.$label.text("");this.$squishedLabel.text("");var dataset=this.project.getSortedFilteredDataset();var clusterIdVector=this.type===morpheus.AbstractDendrogram.Type.COLUMN?dataset.getColumnMetadata().getByName("dendrogram_cut"):dataset.getRowMetadata().getByName("dendrogram_cut");if(clusterIdVector){for(var i=0,size=clusterIdVector.size();i<size;i++){clusterIdVector.setValue(i,NaN)}}},setCutHeight:function(height){this.cutHeight=height;var squishedIndices={};var clusterNumber=0;var nsquished=0;var squishEnabled=this.squishEnabled;var roots=morpheus.DendrogramUtil.cutAtHeight(this.tree.rootNode,this.cutHeight);var dataset=this.project.getSortedFilteredDataset();var clusterIdVector=this.type===morpheus.AbstractDendrogram.Type.COLUMN?dataset.getColumnMetadata().add("dendrogram_cut"):dataset.getRowMetadata().add("dendrogram_cut");for(var i=0,nroots=roots.length;i<nroots;i++){var root=roots[i];var minChild=morpheus.DendrogramUtil.getDeepestChild(root,true);var maxChild=morpheus.DendrogramUtil.getDeepestChild(root,false);var clusterId;if(squishEnabled&&minChild.index===maxChild.index){squishedIndices[minChild.index]=true;clusterId=-2;nsquished++}else{clusterNumber++;clusterId=clusterNumber}for(var j=minChild.index;j<=maxChild.index;j++){clusterIdVector.setValue(j,clusterId)}}this.$label.text(clusterNumber+" cluster"+morpheus.Util.s(clusterNumber));if(nsquished>0){this.$squishedLabel.text(nsquished+" squished")}else{this.$squishedLabel.text("")}if(squishEnabled){this.positions.setSquishedIndices(squishedIndices)}if(this.heatMap.getTrackIndex(clusterIdVector.getName(),this.type===morpheus.AbstractDendrogram.Type.COLUMN)===-1){var settings={discrete:true,discreteAutoDetermined:true,display:["color"]};this.heatMap.addTrack(clusterIdVector.getName(),this.type===morpheus.AbstractDendrogram.Type.COLUMN,settings)}if(this.type===morpheus.AbstractDendrogram.Type.COLUMN){this.project.setGroupColumns([new morpheus.SortKey(clusterIdVector.getName(),morpheus.SortKey.SortOrder.UNSORTED)],true)}else{this.project.setGroupRows([new morpheus.SortKey(clusterIdVector.getName(),morpheus.SortKey.SortOrder.UNSORTED)],true)}},dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.$label.remove();this.$squishedLabel.remove();this.hammer.off("panend",this.panend).off("panstart",this.panstart).off("panmove",this.panmove).off("tap",this.tap);this.hammer.destroy();this.$label=null;this.$squishedLabel=null},isCut:function(){return this.cutHeight<this.tree.maxHeight},getMinIndex:function(){return 0},getMaxIndex:function(){return this.positions.getLength()-1},getNode:function(p){var _this=this;if(this.lastNode){var xy=_this.toPix(this.lastNode);if(Math.abs(xy[0]-p.x)<4&&Math.abs(xy[1]-p.y)<4){return this.lastNode}}this.lastNode=this._getNode(p);return this.lastNode},_getNode:function(p){var _this=this;var hit=null;try{morpheus.DendrogramUtil.dfs(this.tree.rootNode,function(node){var xy=_this.toPix(node);if(Math.abs(xy[0]-p.x)<4&&Math.abs(xy[1]-p.y)<4){hit=node;throw"break"}return hit===null})}catch(x){}return hit},getResizeCursor:function(){if(this.type===morpheus.AbstractDendrogram.Type.COLUMN){return"ns-resize"}else if(this.type===morpheus.AbstractDendrogram.Type.ROW){return"ew-resize"}return"nesw-resize"},isDragHotSpot:function(p){return false},preDraw:function(context,clip){},postDraw:function(context,clip){},prePaint:function(clip,context){this.scale=this.createScale();var min=this.getMinIndex(clip);var max=this.getMaxIndex(clip);if(min!==this.lastMinIndex||max!==this.lastMinIndex){this.lastMinIndex=min;this.lastMaxIndex=max}this.invalid=true},draw:function(clip,context){context.translate(-clip.x,-clip.y);context.strokeStyle="black";context.fillStyle="black";this.scale=this.createScale();var min=this.lastMinIndex;var max=this.lastMaxIndex;context.lineWidth=this.lineWidth;this.preDraw(context,clip);context.strokeStyle=this.defaultStroke;context.fillStyle="rgba(166,206,227,0.5)";this.drawDFS(context,this.tree.rootNode,min,max,0);context.strokeStyle="black";context.fillStyle="black";this.postDraw(context,clip)},drawCutSlider:function(){throw new Error},postPaint:function(clip,context){context.strokeStyle="black";this.paintMouseOver(clip,context);this.drawCutSlider(clip,context)},getNodeRadius:function(node){return 4},drawNode:function(context,node){},drawDFS:function(context,node,minIndex,maxIndex){if(this.type!==morpheus.AbstractDendrogram.Type.RADIAL){if(node.maxIndex<minIndex||node.minIndex>maxIndex){return}}var nodeFill=this.getNodeFill(node);if(nodeFill!==undefined){context.fillStyle=nodeFill;this.drawNode(context,node)}context.strokeStyle=this.getPathStroke(node);var children=node.children;if(children!==undefined){this.drawNodePath(context,node,minIndex,maxIndex);for(var i=0,nchildren=children.length;i<nchildren;i++){this.drawDFS(context,children[i],minIndex,maxIndex)}}}};morpheus.Util.extend(morpheus.AbstractDendrogram,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.AbstractDendrogram,morpheus.Events);morpheus.ActionManager=function(){this.actionNameToAction=new morpheus.Map;this.actions=[];this.add({ellipsis:true,name:"Sort/Group",cb:function(options){new morpheus.SortDialog(options.heatMap.getProject())},icon:"fa fa-sort-alpha-asc"});var $filterModal=null;this.add({name:"Filter",ellipsis:true,cb:function(options){if($filterModal==null){var filterModal=[];var filterLabelId=_.uniqueId("morpheus");filterModal.push('<div class="modal" tabindex="1" role="dialog" aria-labelledby="'+filterLabelId+'">');filterModal.push('<div class="modal-dialog" role="document">');filterModal.push('<div class="modal-content">');filterModal.push('<div class="modal-header">');filterModal.push('<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>');filterModal.push('<h4 class="modal-title" id="'+filterLabelId+'">Filter</h4>');filterModal.push("</div>");filterModal.push('<div class="modal-body"></div>');filterModal.push('<div class="modal-footer"><button type="button" class="btn btn-default" data-dismiss="modal">Close</button></div>');filterModal.push("</div>");filterModal.push("</div>");filterModal.push("</div>");$filterModal=$(filterModal.join(""));$filterModal.on("mousewheel",function(e){e.stopPropagation()});var $filter=$('<div style="padding-bottom:30px;"></div>');$filter.appendTo($filterModal.find(".modal-body"));var filterHtml=[];filterHtml.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="rows" checked>Rows</label></div> ');filterHtml.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="columns">Columns</label></div>');var $filterChooser=$(filterHtml.join(""));$filterChooser.appendTo($filter);var columnFilterUI=new morpheus.FilterUI(options.heatMap.getProject(),true);var rowFilterUI=new morpheus.FilterUI(options.heatMap.getProject(),false);rowFilterUI.$div.appendTo($filter);columnFilterUI.$div.appendTo($filter);columnFilterUI.$div.css("display","none");var $filterRadio=$filterChooser.find("[name=rowsOrColumns]");$filterRadio.on("change",function(e){var val=$filterRadio.filter(":checked").val();if(val==="columns"){columnFilterUI.$div.show();rowFilterUI.$div.hide()}else{columnFilterUI.$div.hide();rowFilterUI.$div.show()}e.preventDefault()});$filterModal.appendTo(options.heatMap.$content);$filterModal.on("hidden.bs.modal",function(){options.heatMap.focus()})}$filterModal.modal("show")},icon:"fa fa-filter"});this.add({name:"Options",ellipsis:true,cb:function(options){options.heatMap.showOptions()},icon:"fa fa-cog"});this.add({which:[191],commandKey:true,global:true,name:"Toggle Search",cb:function(options){options.heatMap.getToolbar().toggleSearch()}});this.add({name:"Copy Image",icon:"fa fa-clipboard",cb:function(options){var bounds=options.heatMap.getTotalSize();var height=bounds.height;var width=bounds.width;var canvas=$("<canvas></canvas>")[0];var backingScale=morpheus.CanvasUtil.BACKING_SCALE;canvas.height=backingScale*height;canvas.style.height=height+"px";canvas.width=backingScale*width;canvas.style.width=width+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);options.heatMap.snapshot(context);var url=canvas.toDataURL();morpheus.Util.setClipboardData([{format:"text/html",data:'<img src="'+url+'">'}],true)}});this.add({name:"Close Tab",cb:function(options){options.heatMap.getTabManager().remove(options.heatMap.tabId)}});this.add({name:"Rename Tab",ellipsis:true,cb:function(options){options.heatMap.getTabManager().rename(options.heatMap.tabId)}});this.add({which:[88],commandKey:true,name:"New Heat Map",accept:function(options){return!options.isInputField||window.getSelection().toString()===""},cb:function(options){morpheus.HeatMap.showTool(new morpheus.NewHeatMapTool,options.heatMap)}});this.add({which:[67],commandKey:true,name:"Copy"});this.add({which:[86],commandKey:true,name:"Paste Dataset"});this.add({global:true,name:"Open",ellipsis:true,cb:function(options){morpheus.HeatMap.showTool(new morpheus.OpenFileTool,options.heatMap)},which:[79],commandKey:true,icon:"fa fa-folder-open-o"});this.add({ellipsis:true,name:"Save Image",gui:function(){return new morpheus.SaveImageTool},cb:function(options){morpheus.HeatMap.showTool(this.gui(),options.heatMap)},which:[83],commandKey:true,global:true,icon:"fa fa-file-image-o"});this.add({ellipsis:true,name:"Save Dataset",gui:function(){return new morpheus.SaveDatasetTool},cb:function(options){morpheus.HeatMap.showTool(this.gui(),options.heatMap)},icon:"fa fa-floppy-o"});this.add({ellipsis:true,name:"Save Session",gui:function(){return new morpheus.SaveSessionTool},cb:function(options){morpheus.HeatMap.showTool(this.gui(),options.heatMap)},icon:"fa fa-anchor"});if(typeof echarts!=="undefined"){this.add({name:"Chart",cb:function(options){new morpheus.ChartTool({project:options.heatMap.getProject(),heatmap:options.heatMap,getVisibleTrackNames:_.bind(options.heatMap.getVisibleTrackNames,options.heatMap)})},icon:"fa fa-line-chart"})}this.add({name:"Zoom In",cb:function(options){options.heatMap.zoom(true)},which:[107,61,187]});this.add({name:"Zoom Out",cb:function(options){options.heatMap.zoom(false)},which:[173,189,109]});this.add({name:"Fit To Window",cb:function(options){options.heatMap.fitToWindow({fitRows:true,fitColumns:true,repaint:true})},which:[48],commandKey:true,icon:"fa fa-compress"});this.add({name:"Fit Columns To Window",cb:function(options){options.heatMap.fitToWindow({fitRows:false,fitColumns:true,repaint:true})}});this.add({name:"Fit Rows To Window",cb:function(options){options.heatMap.fitToWindow({fitRows:true,fitColumns:false,repaint:true})}});this.add({name:"100%",cb:function(options){options.heatMap.resetZoom()},button:"100%"});this.add({which:[35],name:"Go To End",cb:function(options){options.heatMap.scrollLeft(options.heatMap.heatmap.getPreferredSize().width);options.heatMap.scrollTop(options.heatMap.heatmap.getPreferredSize().height)}});this.add({which:[36],name:"Go To Start",cb:function(options){options.heatMap.scrollLeft(0);options.heatMap.scrollTop(0)}});this.add({which:[34],commandKey:true,name:"Go To Bottom",cb:function(options){options.heatMap.scrollTop(options.heatMap.heatmap.getPreferredSize().height)}});this.add({which:[34],commandKey:false,name:"Scroll Page Down",cb:function(options){var pos=options.heatMap.scrollTop();options.heatMap.scrollTop(pos+options.heatMap.heatmap.getUnscaledHeight()-2)}});this.add({which:[33],commandKey:true,name:"Go To Top",cb:function(options){options.heatMap.scrollTop(0)}});this.add({which:[33],commandKey:false,name:"Scroll Page Up",cb:function(options){var pos=options.heatMap.scrollTop();options.heatMap.scrollTop(pos-options.heatMap.heatmap.getUnscaledHeight()+2)}});this.add({which:[38],commandKey:true,name:"Zoom Out Rows",cb:function(options){options.heatMap.zoom(false,{columns:false,rows:true})}});this.add({which:[38],commandKey:false,name:"Scroll Up",cb:function(options){options.heatMap.scrollTop(options.heatMap.scrollTop()-8)}});this.add({which:[40],commandKey:true,name:"Zoom In Rows",cb:function(options){options.heatMap.zoom(true,{columns:false,rows:true})}});this.add({which:[40],commandKey:false,name:"Scroll Down",cb:function(options){options.heatMap.scrollTop(options.heatMap.scrollTop()+8)}});this.add({which:[37],commandKey:true,name:"Zoom Out Columns",cb:function(options){options.heatMap.zoom(false,{columns:true,rows:false})}});this.add({which:[37],commandKey:false,name:"Scroll Left",cb:function(options){options.heatMap.scrollLeft(options.heatMap.scrollLeft()-8)}});this.add({which:[39],commandKey:true,name:"Zoom In Columns",cb:function(options){options.heatMap.zoom(true,{columns:true,rows:false})}});this.add({which:[39],commandKey:false,name:"Scroll Right",cb:function(options){options.heatMap.scrollLeft(options.heatMap.scrollLeft()+8)}});this.add({name:"Tutorial",cb:function(){window.open("https://software.broadinstitute.org/morpheus/tutorial.html")}});this.add({icon:"fa fa-code",name:"Source Code",cb:function(){window.open("https://github.com/cmap/morpheus.js")}});var $findModal;var $search;this.add({which:[65],ellipsis:true,shiftKey:true,commandKey:true,name:"Search Menus",cb:function(options){if($findModal==null){var findModal=[];var id=_.uniqueId("morpheus");findModal.push('<div class="modal" tabindex="1" role="dialog" aria-labelledby="'+id+'">');findModal.push('<div class="modal-dialog" role="document">');findModal.push('<div class="modal-content">');findModal.push('<div class="modal-header">');findModal.push('<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>');findModal.push('<h4 class="modal-title" id="'+id+'">Enter action</h4>');findModal.push("</div>");findModal.push('<div class="modal-body ui-front"><input class="form-control input-sm"></div>');findModal.push("</div>");findModal.push("</div>");findModal.push("</div>");$findModal=$(findModal.join(""));$findModal.appendTo(options.heatMap.$content);var allActions=options.heatMap.getActionManager().getActions();$search=$findModal.find("input");$search.on("keyup",function(e){if(e.which===13){var text=$search.val().trim();if(text!==""){var action=_this.getAction(text);if(action){$findModal.modal("hide");_this.execute(text,{event:e})}}}});morpheus.Util.autosuggest({$el:$search,multi:false,suggestWhenEmpty:false,filter:function(tokens,response){var token=tokens[0].trim();var matches=[];var replaceRegex=new RegExp("("+morpheus.Util.escapeRegex(token)+")","i");for(var i=0;i<allActions.length;i++){if(allActions[i].cb){var name=allActions[i].name;if(replaceRegex.test(name)){matches.push({clear:true,value:name,label:'<span style="margin-left: 10px">'+name.replace(replaceRegex,"<b>$1</b>")+"</span>"})}}}response(matches)},select:function(){setTimeout(function(){var text=$search.val().trim();if(text!==""){var action=_this.getAction(text);if(action){$findModal.modal("hide");_this.execute(text)}}},20)}});$findModal.on("hidden.bs.modal",function(){options.heatMap.focus()})}$findModal.modal("show");$search.focus()}});this.add({name:"Keyboard Shortcuts",cb:function(options){new morpheus.HeatMapKeyListener(options.heatMap).showKeyMapReference()}});this.add({name:"Configuration",cb:function(){window.open("https://software.broadinstitute.org/morpheus/configuration.html")}});this.add({name:"Contact",icon:"fa fa-envelope-o",cb:function(options){morpheus.FormBuilder.showInModal({title:"Contact",html:"Please email us at morpheus@broadinstitute.org",focus:options.heatMap.getFocusEl()})}});this.add({which:[65],commandKey:true,name:"Select All",accept:function(options){var active=options.heatMap.getActiveComponent();return active==="rowTrack"||active==="columnTrack"},cb:function(options){var active=options.heatMap.getActiveComponent();var selectionModel=active==="rowTrack"?options.heatMap.getProject().getRowSelectionModel():options.heatMap.getProject().getColumnSelectionModel();var count=active==="rowTrack"?options.heatMap.getProject().getSortedFilteredDataset().getRowCount():options.heatMap.getProject().getSortedFilteredDataset().getColumnCount();var indices=new morpheus.Set;for(var i=0;i<count;i++){indices.add(i)}selectionModel.setViewIndices(indices,true)}});var invertAction=function(options,isColumns){var model=isColumns?options.heatMap.getProject().getColumnSelectionModel():options.heatMap.getProject().getRowSelectionModel();var viewIndices=model.getViewIndices();var inverse=new morpheus.Set;var n=n=isColumns?options.heatMap.getProject().getSortedFilteredDataset().getColumnCount():options.heatMap.getProject().getSortedFilteredDataset().getRowCount();for(var i=0;i<n;i++){if(!viewIndices.has(i)){inverse.add(i)}}model.setViewIndices(inverse,true)};this.add({name:"Invert Selected Rows",cb:function(options){invertAction(options,false)}});this.add({name:"Invert Selected Columns",cb:function(options){invertAction(options,true)}});var clearAction=function(options,isColumns){var model=isColumns?options.heatMap.getProject().getColumnSelectionModel():options.heatMap.getProject().getRowSelectionModel();model.setViewIndices(new morpheus.Set,true)};this.add({name:"Clear Selected Rows",cb:function(options){clearAction(options,false)}});this.add({name:"Clear Selected Columns",cb:function(options){clearAction(options,true)}});var moveToTop=function(options,isColumns){var project=options.heatMap.getProject();var selectionModel=!isColumns?project.getRowSelectionModel():project.getColumnSelectionModel();var viewIndices=selectionModel.getViewIndices().values();if(viewIndices.length===0){return}viewIndices.sort(function(a,b){return a===b?0:a<b?-1:1});var converter=isColumns?project.convertViewColumnIndexToModel:project.convertViewRowIndexToModel;converter=_.bind(converter,project);var modelIndices=[];for(var i=0,n=viewIndices.length;i<n;i++){modelIndices.push(converter(viewIndices[i]))}var sortKey=new morpheus.MatchesOnTopSortKey(project,modelIndices,"selection on top",isColumns);sortKey.setLockOrder(1);sortKey.setUnlockable(false);if(isColumns){project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getColumnSortKeys().filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.toString()===sortKey.toString())})),true)}else{project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getRowSortKeys().filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.toString()===sortKey.toString())})),true)}};this.add({name:"Move Selected Rows To Top",cb:function(options){moveToTop(options,false)}});this.add({name:"Move Selected Columns To Top",cb:function(options){moveToTop(options,true)}});var selectAll=function(options,isColumns){var project=options.heatMap.getProject();var selectionModel=!isColumns?project.getRowSelectionModel():project.getColumnSelectionModel();var count=!isColumns?project.getSortedFilteredDataset().getRowCount():project.getSortedFilteredDataset().getColumnCount();var indices=new morpheus.Set;for(var i=0;i<count;i++){indices.add(i)}selectionModel.setViewIndices(indices,true)};this.add({name:"Select All Rows",cb:function(options){selectAll(options,false)}});this.add({name:"Select All Columns",cb:function(options){selectAll(options,true)}});var copySelection=function(options,isColumns){var project=options.heatMap.getProject();var dataset=project.getSortedFilteredDataset();var activeTrackName=options.heatMap.getSelectedTrackName(isColumns);var v;if(activeTrackName==null){v=isColumns?dataset.getColumnMetadata().get(0):dataset.getRowMetadata().get(0)}else{v=isColumns?dataset.getColumnMetadata().getByName(activeTrackName):dataset.getRowMetadata().getByName(activeTrackName)}var selectionModel=isColumns?project.getColumnSelectionModel():project.getRowSelectionModel();var text=[];var toStringFunction=morpheus.VectorTrack.vectorToString(v);selectionModel.getViewIndices().forEach(function(index){text.push(toStringFunction(v.getValue(index)))});morpheus.Util.setClipboardData([{format:"text/plain",data:text.join("\n")}])};this.add({name:"Copy Selected Rows",cb:function(options){copySelection(options,false)}});this.add({name:"Copy Selected Columns",cb:function(options){copySelection(options,true)}});var annotateSelection=function(options,isColumns){var project=options.heatMap.getProject();var selectionModel=isColumns?project.getColumnSelectionModel():project.getRowSelectionModel();if(selectionModel.count()===0){morpheus.FormBuilder.showMessageModal({title:"Annotate Selection",html:"No "+(isColumns?"columns":"rows")+" selected.",focus:options.heatMap.getFocusEl()});return}var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"annotation_name",type:"text",required:true});formBuilder.append({name:"annotation_value",type:"text",required:true});morpheus.FormBuilder.showOkCancel({title:"Annotate",content:formBuilder.$form,focus:options.heatMap.getFocusEl(),okCallback:function(){var value=formBuilder.getValue("annotation_value");var annotationName=formBuilder.getValue("annotation_name");var dataset=project.getSortedFilteredDataset();var fullDataset=project.getFullDataset();if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset);fullDataset=morpheus.DatasetUtil.transposedView(fullDataset)}var existingVector=fullDataset.getRowMetadata().getByName(annotationName);var v=dataset.getRowMetadata().add(annotationName);selectionModel.getViewIndices().forEach(function(index){v.setValue(index,value)});morpheus.VectorUtil.maybeConvertStringToNumber(v);project.trigger("trackChanged",{vectors:[v],display:existingVector!=null?[]:[morpheus.VectorTrack.RENDER.TEXT],columns:isColumns})}})};this.add({ellipsis:true,name:"Annotate Selected Rows",cb:function(options){annotateSelection(options,false)}});this.add({ellipsis:true,name:"Annotate Selected Columns",cb:function(options){annotateSelection(options,true)}});this.add({name:"Copy Selected Dataset",cb:function(options){var project=options.heatMap.getProject();var dataset=project.getSelectedDataset({emptyToAll:false});var columnMetadata=dataset.getColumnMetadata();var rowMetadata=dataset.getRowMetadata();var visibleColumnFields=options.heatMap.getVisibleTrackNames(true);var columnFieldIndices=[];_.each(visibleColumnFields,function(name){var index=morpheus.MetadataUtil.indexOf(columnMetadata,name);if(index!==-1){columnFieldIndices.push(index)}});columnMetadata=new morpheus.MetadataModelColumnView(columnMetadata,columnFieldIndices);var rowMetadata=dataset.getRowMetadata();var visibleRowFields=options.heatMap.getVisibleTrackNames(false);var rowFieldIndices=[];_.each(visibleRowFields,function(name){var index=morpheus.MetadataUtil.indexOf(rowMetadata,name);if(index!==-1){rowFieldIndices.push(index)}});rowMetadata=new morpheus.MetadataModelColumnView(rowMetadata,rowFieldIndices);var text=(new morpheus.GctWriter).write(dataset);morpheus.Util.setClipboardData([{format:"text/plain",data:text}])}});var _this=this;[new morpheus.HClusterTool,new morpheus.KMeansTool,new morpheus.MarkerSelection,new morpheus.NearestNeighbors,new morpheus.AdjustDataTool,new morpheus.CollapseDatasetTool,new morpheus.CreateAnnotation,new morpheus.SimilarityMatrixTool,new morpheus.TransposeTool,new morpheus.TsneTool,new morpheus.DevAPI].forEach(function(tool){_this.add({ellipsis:true,name:tool.toString(),gui:function(){return tool},cb:function(options){morpheus.HeatMap.showTool(tool,options.heatMap)}})});this.add({name:"Edit Fonts",ellipse:true,cb:function(options){var trackInfo=options.heatMap.getLastSelectedTrackInfo();var project=options.heatMap.getProject();var model=trackInfo.isColumns?project.getColumnFontModel():project.getRowFontModel();var chooser=new morpheus.FontChooser({fontModel:model,track:options.heatMap.getTrack(trackInfo.name,trackInfo.isColumns),heatMap:options.heatMap});morpheus.FormBuilder.showInModal({title:"Edit Fonts",html:chooser.$div,close:"Close",focus:options.heatMap.getFocusEl()})}})};morpheus.ActionManager.prototype={getActions:function(){return this.actions},getAction:function(name){return this.actionNameToAction.get(name)},execute:function(name,args){var action=this.getAction(name);if(args==null){args={}}args.heatMap=this.heatMap;action.cb(args);morpheus.Util.trackEvent({eventCategory:"Tool",eventAction:name})},add:function(action){this.actions.push(action);this.actionNameToAction.set(action.name,action)}};morpheus.CanvasUtil=function(){};morpheus.CanvasUtil.dragging=false;morpheus.CanvasUtil.FONT_NAME='"Helvetica Neue",Helvetica,Arial,sans-serif';morpheus.CanvasUtil.FONT_COLOR="rgb(0, 0, 0)";morpheus.CanvasUtil.getFontFamily=function(context){return typeof C2S!=="undefined"&&context instanceof C2S||typeof canvas2pdf!=="undefined"&&context instanceof canvas2pdf.PdfContext?"Helvetica":morpheus.CanvasUtil.FONT_NAME};morpheus.CanvasUtil.getPreferredSize=function(c){var size=c.getPreferredSize();var prefWidth=c.getPrefWidth();var prefHeight=c.getPrefHeight();if(prefWidth!==undefined){size.widthSet=true;size.width=prefWidth}if(prefHeight!==undefined){size.heightSet=true;size.height=prefHeight}return size};morpheus.CanvasUtil.BACKING_SCALE=1;if(typeof window!=="undefined"&&"devicePixelRatio"in window){if(window.devicePixelRatio>1){morpheus.CanvasUtil.BACKING_SCALE=window.devicePixelRatio}}morpheus.CanvasUtil.setBounds=function(canvas,bounds){var backingScale=morpheus.CanvasUtil.BACKING_SCALE;if(bounds.height!=null){canvas.height=bounds.height*backingScale;canvas.style.height=bounds.height+"px"}if(bounds.width!=null){canvas.width=bounds.width*backingScale;canvas.style.width=bounds.width+"px"}if(bounds.left!=null){canvas.style.left=bounds.left+"px"}if(bounds.top!=null){canvas.style.top=bounds.top+"px"}};morpheus.CanvasUtil.drawShape=function(context,shape,x,y,size2,isFill){if(size2<0){return}context.beginPath();if(shape==="circle-minus"){context.arc(x,y,size2,0,2*Math.PI,false);context.moveTo(x-size2,y);context.lineTo(x+size2,y)}else if(shape==="circle"){context.arc(x,y,size2,0,2*Math.PI,false)}else if(shape==="square"){context.rect(x-size2,y-size2,size2*2,size2*2)}else if(shape==="plus"){context.moveTo(x,y-size2);context.lineTo(x,y+size2);context.moveTo(x-size2,y);context.lineTo(x+size2,y)}else if(shape==="x"){context.moveTo(x-size2,y-size2);context.lineTo(x+size2,y+size2);context.moveTo(x+size2,y-size2);context.lineTo(x-size2,y+size2)}else if(shape==="asterisk"){context.moveTo(x-size2,y-size2);context.lineTo(x+size2,y+size2);context.moveTo(x+size2,y-size2);context.lineTo(x-size2,y+size2);context.moveTo(x,y-size2);context.lineTo(x,y+size2)}else if(shape==="diamond"){context.moveTo(x,y-size2);context.lineTo(x+size2,y);context.lineTo(x,y+size2);context.lineTo(x-size2,y);context.lineTo(x,y-size2)}else if(shape==="triangle-up"){context.moveTo(x,y-size2);context.lineTo(x+size2,y+size2);context.lineTo(x-size2,y+size2);context.lineTo(x,y-size2)}else if(shape==="triangle-down"){context.moveTo(x,y+size2);context.lineTo(x-size2,y-size2);context.lineTo(x+size2,y-size2);context.lineTo(x,y+size2)}else if(shape==="triangle-left"){context.moveTo(x-size2,y);context.lineTo(x+size2,y-size2);context.lineTo(x+size2,y+size2);context.lineTo(x-size2,y)}else if(shape==="triangle-right"){context.moveTo(x+size2,y);context.lineTo(x-size2,y+size2);context.lineTo(x-size2,y-size2);context.lineTo(x+size2,y)}isFill?context.fill():context.stroke()};morpheus.CanvasUtil.drawLine=function(context,x1,y1,x2,y2){context.beginPath();context.moveTo(x1,y1);context.lineTo(x2,y2);context.stroke()};morpheus.CanvasUtil.resetTransform=function(context){context.setTransform(1,0,0,1,0,0);if(morpheus.CanvasUtil.BACKING_SCALE!==1){context.scale(morpheus.CanvasUtil.BACKING_SCALE,morpheus.CanvasUtil.BACKING_SCALE)}};morpheus.CanvasUtil.bezierCurveTo=function(context,start,end){var m1=(start[1]+end[1])/2;context.beginPath();context.moveTo(start[0],start[1]);context.bezierCurveTo(start[0],m1,end[0],m1,end[0],end[1]);context.stroke()};morpheus.CanvasUtil.createCanvas=function(){var $c=$("<canvas></canvas>");$c.attr("tabindex","0");$c.css({cursor:"default",outline:0,overflow:"hidden",position:"absolute","z-index":1});return $c[0]};morpheus.CanvasUtil.getHeaderStringWidth=function(context,s){context.font="14px "+morpheus.CanvasUtil.getFontFamily(context);return context.measureText(s).width+18};morpheus.CanvasUtil.forceSubPixelRendering=function(context){context.getImageData(0,0,1,1)};morpheus.CanvasUtil.getVectorStringWidth=function(context,vector,positions,end){if(positions.getSize()<6){return 0}var fontSize=Math.min(morpheus.VectorTrack.MAX_FONT_SIZE,positions.getSize()-2);if(fontSize<=0){return 0}context.font=fontSize+"px "+morpheus.CanvasUtil.getFontFamily(context);var toString=morpheus.VectorTrack.vectorToString(vector);var maxWidth=0;var n=end<=0?vector.size():Math.min(end,vector.size());for(var i=0;i<n;i++){var value=vector.getValue(i);if(value!=null&&value!=""){value=toString(value)}else{continue}var width=context.measureText(value).width;if(width>maxWidth){maxWidth=width}}return maxWidth===0?maxWidth:maxWidth+2};morpheus.CanvasUtil.clipString=function(context,string,availTextWidth){var textWidth=context.measureText(string).width;if(textWidth<=availTextWidth){return string}var clipString="...";availTextWidth-=context.measureText(clipString).width;if(availTextWidth<=0){return clipString}var width=0;for(var nChars=0,stringLength=string.length;nChars<stringLength;nChars++){width+=context.measureText(string[nChars]).width;if(width>availTextWidth){string=string.substring(0,nChars);break}}return string+clipString};morpheus.CanvasUtil.toSVG=function(drawable,file){var totalSize={width:drawable.getWidth(),height:drawable.getHeight()};var context=new C2S(totalSize.width,totalSize.height);context.save();drawable.draw({x:0,y:0,width:totalSize.width,height:totalSize.height},context);context.restore();var svg=context.getSerializedSvg();var blob=new Blob([svg],{type:"text/plain;charset=utf-8"});saveAs(blob,file)};morpheus.CanvasUtil.getMousePos=function(element,event,useDelta){return morpheus.CanvasUtil.getMousePosWithScroll(element,event,0,0,useDelta)};morpheus.CanvasUtil.getClientXY=function(event,useDelta){var clientX;var clientY;if(event.pointers){if(event.pointers.length>0){clientX=event.pointers[0].clientX-(useDelta?event.deltaX:0);clientY=event.pointers[0].clientY-(useDelta?event.deltaY:0)}else{clientX=event.srcEvent.clientX-(useDelta?event.deltaX:0);clientY=event.srcEvent.clientY-(useDelta?event.deltaY:0)}}else{clientX=event.clientX;clientY=event.clientY}return{x:clientX,y:clientY}};morpheus.CanvasUtil.getMousePosWithScroll=function(element,event,scrollX,scrollY,useDelta){return morpheus.CanvasUtil._getMousePosWithScroll(element,scrollX,scrollY,morpheus.CanvasUtil.getClientXY(event,useDelta))};morpheus.CanvasUtil._getMousePosWithScroll=function(element,scrollX,scrollY,clientXY){var rect=element.getBoundingClientRect();return{x:clientXY.x-rect.left+scrollX,y:clientXY.y-rect.top+scrollY}};morpheus.CheckBoxList=function(options){var _this=this;var set=options.set||new morpheus.Set;options=$.extend(true,{},{height:"150px",showHeader:false,select:false,search:true,checkBoxSelectionOnTop:false,rowHeader:function(item){var header=[];header.push('<span><input name="toggle" type="checkbox" '+(set.has(_this.getter(item))?" checked":"")+"/> ");header.push("</span>");return header.join("")}},options);options=morpheus.Table.createOptions(options);if(options.columns.length===1){options.maxWidth=583}var idColumn=options.columns[0];for(var i=0;i<options.columns.length;i++){if(options.columns[i].idColumn){idColumn=options.columns[i];break}}this.getter=idColumn.getter;var html=[];var table=new morpheus.Table(options);if(options.columns.length===1){options.$el.find(".slick-table-header").find("[name=right]").remove()}this.table=table;var html=[];html.push('<div style="display:inline;">');html.push('<div style="display:inline;" class="dropdown">');html.push('<button class="btn btn-default btn-xs dropdown-toggle" type="button"'+' data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">');html.push('<i data-name="checkbox" class="fa fa-square-o"'+' aria-hidden="true"></i>');html.push(' <span class="fa fa-caret-down"></span>');html.push("</button>");html.push('<ul style="font-size:12px;" class="dropdown-menu">');html.push('<li><a name="selectAll" href="#">Select All</a></li>');html.push('<li><a name="selectNone" href="#">Select None</a></li>');html.push('<li><a name="invertSel" href="#">Invert Selection</a></li>');html.push("</ul>");html.push("</div>");html.push('<span data-name="available" style="font-size:12px;padding-left:6px;"></span>');html.push("</div>");var $checkBoxEl=$(html.join(""));table.$header.find("[name=left]").html($checkBoxEl);var $selection=$checkBoxEl.find("[data-name=available]");var $selectAll=$checkBoxEl.find("[name=selectAll]");var $selectNone=$checkBoxEl.find("[name=selectNone]");var $cb=$checkBoxEl.find("[data-name=checkbox]");var updateLabel=function(){var label=[];label.push("selected ");label.push(morpheus.Util.intFormat(set.size()));label.push(" of ");label.push(morpheus.Util.intFormat(table.getAllItemCount()));if(table.getFilteredItemCount()!==table.getAllItemCount()){label.push(", ");label.push(morpheus.Util.intFormat(table.getFilteredItemCount()));label.push(table.getFilteredItemCount()===1?" match":" matches")}$selection.html(label.join(""))};table.grid.on("filter",function(e){updateLabel()});$cb.on("click",function(e){if($cb.hasClass("fa-square-o")){var items=table.getItems();for(var i=0;i<items.length;i++){set.add(_this.getter(items[i]))}}else{var items=table.getItems();for(var i=0;i<items.length;i++){set.remove(_this.getter(items[i]))}}table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();e.stopPropagation()});$selectAll.on("click",function(e){var items=table.getItems();for(var i=0,nitems=items.length;i<nitems;i++){set.add(_this.getter(items[i]))}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();_this.table.redraw()});$checkBoxEl.find("[name=invertSel]").on("click",function(e){var items=table.getItems();for(var i=0,nitems=items.length;i<nitems;i++){var val=_this.getter(items[i]);if(set.has(val)){set.remove(val)}else{set.add(val)}}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();_this.table.redraw()});$selectNone.on("click",function(e){var items=table.getItems();for(var i=0,nitems=items.length;i<nitems;i++){set.remove(_this.getter(items[i]))}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();_this.table.redraw()});this.set=set;this.table=table;updateLabel();var priorCount=0;this.table.on("checkBoxSelectionChanged",function(){if(set.size()===0){$cb.attr("class","fa fa-square-o")}else{var items=table.getItems();var count=0;var found=false;var notFound=false;for(var i=0;i<items.length;i++){if(set.has(_this.getter(items[i]))){count++;found=true;if(notFound){break}}else{notFound=true;if(found){break}}}if(count===0){$cb.attr("class","fa fa-square-o")}else if(count===items.length){$cb.attr("class","fa fa-check-square-o")}else{$cb.attr("class","fa fa-minus-square-o")}}updateLabel();_this.table.redraw()});table.on("click",function(e){var $target=$(e.target);var item=table.getItems()[e.row];var value=_this.getter(item);if($target.is(".morpheus-hover-show")){set.clear();set.add(value);_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set})}else if(!options.select||$target.is("[type=checkbox]")&&$target.attr("name")==="toggle"){if(set.has(value)){set.remove(value)}else{set.add(value)}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set})}})};morpheus.CheckBoxList.prototype={searchWithPredicates:function(predicates){this.table.searchWithPredicates(predicates)},autocomplete:function(tokens,cb){this.table.autocomplete(tokens,cb)},setHeight:function(height){this.table.setHeight(height)},resize:function(){this.table.resize()},setSearchVisible:function(visible){this.table.setSearchVisible(visible)},getSelectedRows:function(){return this.table.getSelectedRows()},getSelectedItems:function(){return this.table.getSelectedItems()},setSelectedRows:function(rows){this.table.setSelectedRows(rows)},getItems:function(items){return this.table.getItems()},getAllItemCount:function(){return this.table.getAllItemCount()},getFilteredItemCount:function(){return this.table.getFilteredItemCount()},setFilter:function(f){this.table.setFilter(f)},redraw:function(){this.table.redraw()},getSelection:function(){return this.set},clearSelection:function(values){this.set.clear();this.table.redraw()},setValue:function(values){this.setSelectedValues(values)},setSelectedValues:function(values){this.set.clear();if(morpheus.Util.isArray(values)){for(var i=0;i<values.length;i++){this.set.add(values[i])}}else{this.set.add(values)}this.table.redraw()},val:function(){return this.set.values()},on:function(evtStr,handler){this.table.on(evtStr,handler);return this},off:function(evtStr,handler){this.table.off(evtStr,handler)},setItems:function(items){var newItems=new morpheus.Set;var getter=this.getter;for(var i=0;i<items.length;i++){newItems.add(getter(items[i]))}var selection=this.set;selection.forEach(function(val){if(!newItems.has(val)){selection.remove(val)}});this.table.setItems(items);this.table.trigger("checkBoxSelectionChanged",{source:this,set:selection})}};morpheus.ColorSchemeChooser=function(options){var colorModel=options.colorModel;var track=options.track;var heatMap=options.heatMap;colorModel.getMappedValue(track.getVector(track.settings.colorByField),track.getVector(track.settings.colorByField).getValue(0));var formBuilder=new morpheus.FormBuilder;if(track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)){formBuilder.append({value:track.settings.colorByField!=null,type:"checkbox",name:"use_another_annotation_to_determine_color"});var annotationNames=morpheus.MetadataUtil.getMetadataNames(track.isColumns?heatMap.getProject().getFullDataset().getColumnMetadata():heatMap.getProject().getFullDataset().getRowMetadata());annotationNames.splice(annotationNames.indexOf(track.getName()),1);formBuilder.append({name:"annotation_name",type:"bootstrap-select",options:annotationNames,search:annotationNames.length>10,value:track.settings.colorByField})}formBuilder.append({name:"discrete",type:"checkbox",value:track.getVector(track.settings.colorByField).getProperties().get(morpheus.VectorKeys.DISCRETE)});var dataType=morpheus.VectorUtil.getDataType(track.getVector(track.settings.colorByField));var isNumber=dataType==="number"||dataType==="[number]";formBuilder.setVisible("discrete",isNumber);formBuilder.setVisible("annotation_name",track.settings.colorByField!=null);var $chooser=$("<div></div>");$chooser.appendTo(formBuilder.$form);var updateChooser=function(){var colorSchemeChooser;var v=track.getVector(track.settings.colorByField);formBuilder.setValue("discrete",v.getProperties().get(morpheus.VectorKeys.DISCRETE));if(v.getProperties().get(morpheus.VectorKeys.DISCRETE)){colorModel.getMappedValue(v,v.getValue(0));colorSchemeChooser=new morpheus.DiscreteColorSchemeChooser({colorScheme:{scale:colorModel.getDiscreteColorScheme(track.getVector(track.settings.colorByField))}});colorSchemeChooser.on("change",function(event){colorModel.setMappedValue(track.getVector(track.settings.colorByField),event.value,event.color);track.setInvalid(true);track.repaint()})}else{colorModel.getContinuousMappedValue(v,v.getValue(0));colorSchemeChooser=new morpheus.HeatMapColorSchemeChooser({showRelative:false});colorSchemeChooser.setColorScheme(colorModel.getContinuousColorScheme(v));colorSchemeChooser.on("change",function(event){track.setInvalid(true);track.repaint()})}$chooser.html(colorSchemeChooser.$div);track.setInvalid();track.repaint()};formBuilder.find("use_another_annotation_to_determine_color").on("change",function(){var checked=$(this).prop("checked");formBuilder.setValue("annotation_name",null);formBuilder.setVisible("annotation_name",checked);if(!checked){track.settings.colorByField=null;updateChooser()}else{$chooser.empty()}formBuilder.setVisible("discrete",false)});formBuilder.find("annotation_name").on("change",function(){var annotationName=$(this).val();colorModel.getMappedValue(track.getVector(annotationName),track.getVector(annotationName).getValue(0));track.settings.colorByField=annotationName;var dataType=morpheus.VectorUtil.getDataType(track.getVector(track.settings.colorByField));var isNumber=dataType==="number"||dataType==="[number]";formBuilder.setVisible("discrete",isNumber);updateChooser();track.setInvalid(true);track.repaint()});formBuilder.find("discrete").on("change",function(){track.getVector(track.settings.colorByField).getProperties().set(morpheus.VectorKeys.DISCRETE,$(this).prop("checked"));updateChooser();track.setInvalid(true);track.repaint()});updateChooser();this.$div=formBuilder.$form};morpheus.ColumnDendrogram=function(heatMap,tree,positions,project){morpheus.AbstractDendrogram.call(this,heatMap,tree,positions,project,morpheus.AbstractDendrogram.Type.COLUMN)};morpheus.ColumnDendrogram.prototype={drawNode:function(context,node){var radius=this.getNodeRadius(node);var pix=this.toPix(node);context.beginPath();context.arc(pix[0],pix[1],4,Math.PI*2,false);context.fill()},isDragHotSpot:function(p){return Math.abs(this.scale(this.cutHeight)-p.y)<=2},drawCutSlider:function(clip,context){if(context.setLineDash){context.setLineDash([5])}context.strokeStyle="black";var ny=this.scale(this.cutHeight);context.beginPath();context.moveTo(clip.x,ny);context.lineTo(this.getUnscaledWidth(),ny);context.stroke();if(context.setLineDash){context.setLineDash([])}},createScale:function(){return d3.scale.linear().domain([this.tree.maxHeight,0]).range([0,this.getUnscaledHeight()])},paintMouseOver:function(clip,context){if(this.project.getHoverColumnIndex()!==-1){morpheus.CanvasUtil.resetTransform(context);context.translate(-clip.x,0);this.drawColumnBorder(context,this.positions,this.project.getHoverColumnIndex(),this.getUnscaledWidth())}},drawColumnBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(pix+size,0);context.lineTo(pix+size,gridSize);context.stroke();context.beginPath();context.moveTo(pix,0);context.lineTo(pix,gridSize);context.stroke()},getMaxIndex:function(clip){return morpheus.Positions.getRight(clip,this.positions)},getMinIndex:function(clip){return morpheus.Positions.getLeft(clip,this.positions)},getPreferredSize:function(context){return{width:Math.ceil(this.positions.getPosition(this.positions.getLength()-1)+this.positions.getItemSize(this.positions.getLength()-1)),height:100}},toPix:function(node){var min=this.positions.getPosition(node.minIndex)+this.positions.getItemSize(node.minIndex)/2;var max=this.positions.getPosition(node.maxIndex)+this.positions.getItemSize(node.maxIndex)/2;return[(min+max)/2,this.scale(node.height)]},drawPathFromNodeToParent:function(context,node){var pix=this.toPix(node);var parentPix=this.toPix(node.parent);context.beginPath();context.moveTo(pix[0],pix[1]);context.lineTo(pix[0],parentPix[1]);context.lineTo(parentPix[0],parentPix[1]);context.stroke()},drawNodePath:function(context,node,minIndex,maxIndex){var children=node.children;var left=children[0];var right=children[1];var ny=this.scale(node.height);var rx=this.toPix(right)[0];var ry=this.scale(right.height);var lx=this.toPix(left)[0];var ly=this.scale(left.height);var x,y;if(!this.drawLeafNodes){var leftIsLeaf=left.children!==undefined;var rightIsLeaf=right.children!==undefined;if(leftIsLeaf){ly=ny+4}if(rightIsLeaf){ry=ny+4}x=[rx,rx,lx,lx];y=[ry,ny,ny,ly]}else{x=[rx,rx,lx,lx];y=[ry,ny,ny,ly]}context.beginPath();context.moveTo(x[0],y[0]);for(var i=1,length=x.length;i<length;i++){context.lineTo(x[i],y[i])}context.stroke()}};morpheus.Util.extend(morpheus.ColumnDendrogram,morpheus.AbstractDendrogram);morpheus.ConditionalRenderingUI=function(heatmap){var _this=this;this.heatmap=heatmap;var $div=$('<div class="container-fluid" style="min-width:180px;"></div>');$div.on("click","[data-name=add]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index();var condition={seriesName:null,color:"rgb(0,0,0)",shape:null,inheritColor:true,accept:function(val){return false}};heatmap.heatmap.getColorScheme().getConditions().insert(index,condition);$row.after(_this.add(condition));e.preventDefault()});$div.on("click","[data-name=delete]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index()-1;heatmap.heatmap.getColorScheme().getConditions().remove(index);heatmap.revalidate();$row.remove();e.preventDefault()});var html=[];html.push('<div class="morpheus-entry">');html.push('<div class="row">');html.push('<div style="padding-bottom:20px;" class="col-xs-8"><a class="btn btn-default btn-xs"'+' role="button"'+' data-name="add" href="#">Add Condition</a></div>');html.push("</div>");html.push("</div>");$div.append(html.join(""));this.$div=$div;heatmap.heatmap.getColorScheme().getConditions().getConditions().forEach(function(c){_this.add(c).appendTo($div)})};morpheus.ConditionalRenderingUI.prototype={add:function(condition){var _this=this;var html=[];html.push('<div style="border-top:1px solid LightGrey;padding-bottom:6px;padding-top:6px;"'+' class="morpheus-entry">');html.push('<form class="form-horizontal">');html.push('<div class="form-group">');html.push('<label class="col-xs-2">Series</label>');html.push('<div class="col-xs-6">');html.push('<select class="form-control morpheus-form-control-inline" name="cond_series">');html.push(morpheus.Util.createOptions(morpheus.DatasetUtil.getSeriesNames(this.heatmap.getProject().getFullDataset())));html.push("</select>");html.push("</div>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-2">Condition</label>');html.push('<div class="col-xs-6">');html.push('<select class="form-control morpheus-form-control-inline" name="lower"><option value="gte">&gt;=</option><option value="gt">&gt;</option></select>');html.push('<input class="form-control morpheus-form-control-inline" name="v1" size="5" type="text">');html.push('<span style="margin-right:1em;">and</span>');html.push('<select class="form-control morpheus-form-control-inline" name="upper"><option value="lte">&lt;=</option><option value="lt">&lt;</option></select>');html.push('<input class="form-control morpheus-form-control-inline" name="v2" size="5" type="text">');html.push("</div>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-2">Shape</label>');var shapeField=new morpheus.ShapeField({shapes:morpheus.VectorShapeModel.FILLED_SHAPES,showNone:false});html.push('<div class="col-xs-4">');html.push('<div style="display:inline;" data-name="shapeHolder"></div>');html.push("</div>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-offset-2 col-xs-4"><input name="inherit_color"'+' type="checkbox" checked> Inherit'+" color</label>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-2">Color</label>');html.push('<div class="col-xs-4">');html.push('<input class="form-control" type="color" name="color" style="display:inline;'+' width:6em;" disabled>');html.push("</div>");html.push("</div>");html.push('<div class="row"><div class="col-xs-11">');html.push('<a class="btn btn-default btn-xs" role="button" data-name="delete"'+' href="#">Delete Condition</a>');html.push("</div></div>");html.push("</div>");var $el=$(html.join(""));console.log($el.find("form").length);$el.find("form").on("submit",function(e){e.preventDefault()});shapeField.$el.appendTo($el.find("[data-name=shapeHolder]"));var $color=$el.find("[name=color]");var $series=$el.find("[name=cond_series]");var $v1=$el.find("[name=v1]");var $v2=$el.find("[name=v2]");var $v1Op=$el.find("[name=lower]");var $v2Op=$el.find("[name=upper]");var $inherit_color=$el.find("[name=inherit_color]");$color.prop("disabled",condition.inheritColor);$color.val(condition.color);$series.val(condition.seriesName);shapeField.setShapeValue(condition.shape);if(condition.v1!=null&&!isNaN(condition.v1)){$v1.val(condition.v1)}if(condition.v2!=null&&!isNaN(condition.v2)){$v2.val(condition.v2)}$v1Op.val(condition.v1Op);$v2Op.val(condition.v2Op);function updateAccept(){var v1=parseFloat($($v1).val());var v2=parseFloat($($v2).val());var v1Op=$v1Op.val();var v2Op=$v2Op.val();condition.v1=v1;condition.v2=v2;condition.v1Op=v1Op;condition.v2Op=v2Op;var gtf=function(){return true};var ltf=function(){return true};if(!isNaN(v1)){gtf=v1Op==="gt"?function(val){return val>v1}:function(val){return val>=v1}}if(!isNaN(v2)){ltf=v2Op==="lt"?function(val){return val<v2}:function(val){return val<=v2}}condition.accept=function(val){return gtf(val)&&ltf(val)};_this.heatmap.revalidate()}$v1Op.on("change",function(e){updateAccept()});$v2Op.on("change",function(e){updateAccept()});$v1.on("keyup",_.debounce(function(e){updateAccept()},100));$v2.on("keyup",_.debounce(function(e){updateAccept()},100));$inherit_color.on("click",function(e){condition.inheritColor=$(this).prop("checked");$color.prop("disabled",condition.inheritColor);_this.heatmap.revalidate()});$color.on("change",function(e){condition.color=$(this).val();_this.heatmap.revalidate()});shapeField.on("change",function(e){condition.shape=e.shape;_this.heatmap.revalidate()});$series.on("change",function(e){condition.seriesName=$(this).val();_this.heatmap.revalidate()});condition.seriesName=$series.val();return $el}};morpheus.DendrogramUtil={};morpheus.DendrogramUtil.setIndices=function(root,counter){counter=counter||0;var setIndex=function(node){var children=node.children;var maxIndex=children[0].maxIndex;var minIndex=children[0].minIndex;var sum=children[0].index;for(var i=1,length=children.length;i<length;i++){var child=children[i];sum+=child.index;minIndex=Math.min(minIndex,child.minIndex);maxIndex=Math.max(maxIndex,child.maxIndex)}node.minIndex=minIndex;node.maxIndex=maxIndex;node.index=sum/children.length;node.children.sort(function(a,b){return a.index===b.index?0:a.index<b.index?-1:1})};var visit=function(node,callback){var children=node.children;var n;if(children&&(n=children.length)){var i=-1;while(++i<n){visit(children[i],callback)}}callback(node)};visit(root,function(n){if(n.children===undefined){n.minIndex=counter;n.maxIndex=counter;n.index=counter;counter++}else{setIndex(n)}return true})};morpheus.DendrogramUtil.convertEdgeLengthsToHeights=function(rootNode){var maxHeight=0;function setHeights(node,height){var newHeight=height;if(node.length!==undefined){newHeight+=node.length}node.height=newHeight;maxHeight=Math.max(maxHeight,node.height);if(node.children!=null){node.children.forEach(function(child){setHeights(child,newHeight)})}}setHeights(rootNode,0);var counter=0;morpheus.DendrogramUtil.dfs(rootNode,function(node){node.id=counter;counter++;node.height=maxHeight-node.height;return true});return{maxHeight:maxHeight,n:counter}};morpheus.DendrogramUtil.writeNewick=function(node,out,leafNodeIdFunction){if(node.children!=null&&node.children.length>0){out.push("(");for(var i=0;i<node.children.length;i++){if(i>0){out.push(",")}morpheus.DendrogramUtil.writeNewick(node.children[i],out,leafNodeIdFunction)}out.push(")")}out.push(node.index!=null?leafNodeIdFunction(node):"");out.push(":");var parentHeight=node.parent?node.parent.height:node.height;out.push(parentHeight-node.height)};morpheus.DendrogramUtil.parseNewick=function(text){var rootNode=Newick.parse(text);var counter=0;var leafNodes=[];function visit(node){var children=node.children;if(children!==undefined){var left=children[0];var right=children[1];left.parent=node;right.parent=node;visit(left);visit(right)}else{node.minIndex=counter;node.maxIndex=counter;node.index=counter;leafNodes.push(node);counter++}}visit(rootNode);var maxHeight=morpheus.DendrogramUtil.convertEdgeLengthsToHeights(rootNode).maxHeight;morpheus.DendrogramUtil.setNodeDepths(rootNode);morpheus.DendrogramUtil.setIndices(rootNode);return{maxHeight:rootNode.height,rootNode:rootNode,leafNodes:leafNodes,nLeafNodes:leafNodes.length}};morpheus.DendrogramUtil.cutAtHeight=function(rootNode,h){var roots=[];morpheus.DendrogramUtil.dfs(rootNode,function(node){if(node.height<h){roots.push(node);return false}return true});roots.sort(function(a,b){return a.index<b.index?-1:a.index==b.index?0:1});return roots};morpheus.DendrogramUtil.getDeepestChild=function(node,isMin){while(true){if(node.children===undefined){return node}var index;if(isMin){index=node.children[0].index<node.children[node.children.length-1].index?0:node.children.length-1}else{index=node.children[0].index>node.children[node.children.length-1].index?0:node.children.length-1}node=node.children[index]}};morpheus.DendrogramUtil.dfs=function(node,callback,childrenAccessor){if(childrenAccessor===undefined){childrenAccessor=function(n){return n.children}}if(callback(node)){var children=childrenAccessor(node);var n;if(children&&(n=children.length)){var i=-1;while(++i<n){morpheus.DendrogramUtil.dfs(children[i],callback,childrenAccessor)}}}};morpheus.DendrogramUtil.copyTree=function(tree){var counter=0;function recurse(node){var children=node.children;if(children!==undefined){var newChildren=[];for(var i=0,n=children.length;i<n;i++){var copy=$.extend({},children[i]);copy.parent=node;newChildren.push(copy)}node.children=newChildren;for(var i=0,n=newChildren.length;i<n;i++){recurse(newChildren[i])}}else{node.index=counter;node.minIndex=counter;node.maxIndex=counter;counter++}}var rootNode=$.extend({},tree.rootNode);rootNode.parent=undefined;recurse(rootNode);return{nLeafNodes:tree.nLeafNodes,maxDepth:tree.maxDepth,rootNode:rootNode}};morpheus.DendrogramUtil.collapseAtDepth=function(rootNode,maxDepth){morpheus.DendrogramUtil.dfs(rootNode,function(d){if(d.collapsedChildren){d.children=d.collapsedChildren;d.collapsedChildren=undefined}return true});morpheus.DendrogramUtil.dfs(rootNode,function(d){var depth=d.depth;if(depth>maxDepth){d.collapsedChildren=d.children;d.children=undefined;return false}return true})};morpheus.DendrogramUtil.setNodeDepths=function(rootNode){var max=0;function recurse(node,depth){var children=node.children;node.depth=depth;max=Math.max(depth,max);if(children!==undefined){var i=-1;var j=depth+1;var n=children.length;while(++i<n){var d=recurse(children[i],j)}}return node}recurse(rootNode,0);return max};morpheus.DendrogramUtil.sortDendrogram=function(root,vectorToSortBy,project,summaryFunction){summaryFunction=summaryFunction||function(array){var min=Number.MAX_VALUE;for(var i=0;i<array.length;i++){min=Math.min(min,array[i].weight)}return min};var setWeights=function(node){if(node.children!==undefined){var children=node.children;for(var i=0;i<children.length;i++){setWeights(children[i])}node.weight=summaryFunction(children)}else{node.weight=vectorToSortBy.getValue(node.index)}};setWeights(root);var nodeIdToModelIndex={};var leafNodes=morpheus.DendrogramUtil.getLeafNodes(root);_.each(leafNodes,function(node){nodeIdToModelIndex[node.id]=project.convertViewColumnIndexToModel(node.index)});morpheus.DendrogramUtil.dfs(root,function(node){if(node.children){node.children.sort(function(a,b){return a.weight===b.weight?0:a.weight<b.weight?-1:1})}return true});morpheus.DendrogramUtil.setIndices(root);var sortOrder=[];_.each(leafNodes,function(node){var oldModelIndex=nodeIdToModelIndex[node.id];var newIndex=node.index;sortOrder[newIndex]=oldModelIndex});return sortOrder};morpheus.DendrogramUtil.leastCommonAncestor=function(leafNodes){function getPathToRoot(node){var path=new morpheus.Map;while(node!=null){path.set(node.id,node);node=node.parent}return path}var path=getPathToRoot(leafNodes[0]);for(var i=1;i<leafNodes.length;i++){var path2=getPathToRoot(leafNodes[i]);path.forEach(function(node,id){if(!path2.has(id)){path.remove(id)}})}var max=-Number.MAX_VALUE;var maxNode;path.forEach(function(n,id){if(n.depth>max){max=n.depth;maxNode=n}});return maxNode};morpheus.DendrogramUtil.search=function(options){var searchText=options.text;var rootNode=options.rootNode;var tokens=morpheus.Util.getAutocompleteTokens(searchText);var predicates;var nmatches=0;var matchAllPredicates=options.matchAllPredicates===true;if(tokens==null||tokens.length==0){morpheus.DendrogramUtil.dfs(rootNode,function(node){node.search=false;return true});nmatches=-1}else{predicates=morpheus.Util.createSearchPredicates({tokens:tokens,defaultMatchMode:options.defaultMatchMode});var npredicates=predicates.length;morpheus.DendrogramUtil.dfs(rootNode,function(node){var matches=false;if(node.info){searchLabel:if(!matchAllPredicates){for(var p=0;p<npredicates;p++){var predicate=predicates[p];var filterColumnName=predicate.getField();if(filterColumnName!=null){var vals=node.info[filterColumnName];for(var i=0,nvals=vals.length;i<nvals;i++){if(predicate.accept(vals[i])){matches=true;break searchLabel}}}else{for(var name in node.info){var vals=node.info[name];for(var i=0,nvals=vals.length;i<nvals;i++){if(predicate.accept(vals[i])){matches=true;break searchLabel}}}}}}else{matches=true;for(var p=0;p<npredicates;p++){var predicate=predicates[p];var filterColumnName=predicate.getField();if(filterColumnName!=null){var vals=node.info[filterColumnName];for(var i=0,nvals=vals.length;i<nvals;i++){if(!predicate.accept(vals[i])){matches=false;break searchLabel}}}else{for(var name in node.info){var vals=node.info[name];for(var i=0,nvals=vals.length;i<nvals;i++){if(!predicate.accept(vals[i])){matches=false;break searchLabel}}}}}}}node.search=matches;if(matches){nmatches++}return true})}return nmatches};morpheus.DendrogramUtil.squishNonSearchedNodes=function(heatMap,isColumns){if(isColumns){heatMap.getHeatMapElementComponent().getColumnPositions().setSize(13)}else{heatMap.getHeatMapElementComponent().getRowPositions().setSize(13)}var expandedLeafNodes={};var dendrogram=isColumns?heatMap.columnDendrogram:heatMap.rowDendrogram;morpheus.DendrogramUtil.dfs(dendrogram.tree.rootNode,function(node){for(var i=node.minIndex;i<=node.maxIndex;i++){if(node.search){expandedLeafNodes[i]=true}}return true});var clusterIds=[];var previous=expandedLeafNodes[0];var squishedIndices={};if(!previous){squishedIndices[0]=true}var clusterNumber=0;clusterIds.push(clusterNumber);for(var i=1,nleaves=dendrogram.tree.leafNodes.length;i<nleaves;i++){var expanded=expandedLeafNodes[i];if(expanded!==previous){clusterNumber++;previous=expanded}if(!expanded){squishedIndices[i]=true}clusterIds.push(clusterNumber)}if(isColumns){heatMap.getHeatMapElementComponent().getColumnPositions().setSquishedIndices(squishedIndices);heatMap.getProject().setGroupColumns([new morpheus.SpecifiedGroupByKey(clusterIds)],false)}else{heatMap.getHeatMapElementComponent().getRowPositions().setSquishedIndices(squishedIndices);heatMap.getProject().setGroupRows([new morpheus.SpecifiedGroupByKey(clusterIds)],false)}};morpheus.DendrogramUtil.getLeafNodes=function(rootNode){var leafNodes=[];morpheus.DendrogramUtil.dfs(rootNode,function(node){if(node.children===undefined){leafNodes.push(node)}return true});return leafNodes};morpheus.DiscreteColorSchemeChooser=function(options){var formBuilder=new morpheus.FormBuilder;var map=options.colorScheme.scale;formBuilder.append({name:"selected_value",type:"bootstrap-select",options:map.keys()});var $select=formBuilder.find("selected_value");formBuilder.append({style:"max-width:50px;",name:"selected_color",type:"color"});var selectedVal=$select.val();var _this=this;var $color=formBuilder.find("selected_color");$color.val(map.get(selectedVal));$color.on("change",function(e){var color=$(this).val();map.set(selectedVal,color);_this.trigger("change",{value:selectedVal,color:color})});$select.on("change",function(){selectedVal=$select.val();var c=map.get(selectedVal);$color.val(c)});this.$div=formBuilder.$form};morpheus.DiscreteColorSchemeChooser.prototype={};morpheus.Util.extend(morpheus.DiscreteColorSchemeChooser,morpheus.Events);morpheus.DiscreteColorSupplier=function(){this.colorMap=new morpheus.Map;this.hiddenValue=0;this.hiddenValues=new morpheus.Set;morpheus.AbstractColorSupplier.call(this);this.scalingMode=morpheus.HeatMapColorScheme.ScalingMode.FIXED};morpheus.DiscreteColorSupplier.prototype={createInstance:function(){return new morpheus.DiscreteColorSupplier},setColorMap:function(array){this.colorMap=new morpheus.Map;this.colors=[];this.fractions=[];this.names=[];this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;for(var i=0;i<array.length;i++){this.colorMap.set(array[i].value,array[i].color);this.fractions.push(array[i].value);this.names.push(array[i].name);this.colors.push(array[i].color);this.min=Math.min(this.min,array[i].value);this.max=Math.max(this.max,array[i].value)}},copy:function(){var c=this.createInstance();c.names=this.names.slice(0);c.colorMap=new morpheus.Map;this.colorMap.forEach(function(color,value){c.colorMap.set(value,color)});c.colors=this.colors.slice(0);c.fractions=this.fractions.slice(0);this.hiddenValues.forEach(function(val){c.hiddenValues.add(val)});c.missingColor=this.missingColor;return c},isStepped:function(){return true},getColor:function(row,column,value){if(this.hiddenValues.has(value)){value=this.hiddenValue}if(isNaN(value)){return this.missingColor}return this.colorMap.get(value)}};morpheus.Util.extend(morpheus.DiscreteColorSupplier,morpheus.AbstractColorSupplier);morpheus.Divider=function(vertical){morpheus.AbstractCanvas.call(this,false);this.vertical=vertical;var that=this;var canvas=this.canvas;canvas.style.cursor=vertical?"ew-resize":"ns-resize";if(vertical){this.setBounds({height:15,width:4})}else{this.setBounds({height:4,width:15})}this.hammer=morpheus.Util.hammer(canvas,["pan"]).on("panstart",this.panstart=function(event){that.trigger("resizeStart");morpheus.CanvasUtil.dragging=true}).on("panmove",this.panmove=function(event){if(that.vertical){that.trigger("resize",{delta:event.deltaX})}else{that.trigger("resize",{delta:event.deltaY})}}).on("panend",this.panend=function(event){morpheus.CanvasUtil.dragging=false;that.trigger("resizeEnd")});this.paint()};morpheus.Divider.prototype={dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.hammer.off("panstart",this.panstart).off("panmove",this.panmove).off("panend",this.panend);this.hammer.destroy()},getPreferredSize:function(){return{width:3,height:this.getUnscaledHeight()}},draw:function(clip,context){var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();context.clearRect(0,0,width,height);context.strokeStyle="#ddd";if(!this.vertical){context.beginPath();context.moveTo(0,1.5);context.lineTo(width,1.5);context.stroke()}else{context.beginPath();context.moveTo(0,0);context.lineTo(0,height);context.stroke()}}};morpheus.Util.extend(morpheus.Divider,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.Divider,morpheus.Events);morpheus.DualList=function(leftOptions,rightOptions){var html=[];html.push('<div class="container-fluid">');html.push('<div class="row">');html.push('<div class="col-xs-4"><label>Available Fields</label></div>');html.push('<div class="col-xs-2"></div>');html.push('<div class="col-xs-4"><label>Selected Fields</label></div>');html.push("</div>");html.push('<div class="row">');html.push('<div class="col-xs-4"><select class="form-control" name="left" multiple></select></div>');html.push('<div class="col-xs-2"><div class="btn-group-vertical" role="group">'+'<button name="add" type="button" class="btn btn-xs btn-default">Add</button>'+'<button name="remove" type="button" class="btn btn-xs btn-default">Remove</button>'+'<button name="up" type="button" class="btn btn-xs btn-default">Move Up</button>'+'<button name="down" type="button" class="btn btn-xs btn-default">Move Down</button>'+"</div></div>");html.push('<div class="col-xs-4"><select class="form-control" name="right" multiple></select></div>');html.push("</div>");html.push("</div>");this.$el=$(html.join(""));var _this=this;this.$el.find("[name=add]").on("click",function(){_this.addSelected()});this.$el.find("[name=remove]").on("click",function(){_this.removeSelected()});this.$el.find("[name=up]").on("click",function(){_this.moveUp()});this.$el.find("[name=down]").on("click",function(){_this.moveDown()});this.left=this.$el.find("[name=left]")[0];this.right=this.$el.find("[name=right]")[0];for(var i=0;i<leftOptions.length;i++){this.left.options[i]=leftOptions[i]}for(var i=0;i<rightOptions.length;i++){this.right.options[i]=rightOptions[i]}};morpheus.DualList.prototype={addSelected:function(){var left=this.left;var right=this.right;for(var i=0;i<left.options.length;i++){if(left.options[i].selected){var opt=left.options[i];right.options[right.options.length]=new Option(opt.innerHTML,opt.value);left.options[i]=null;i--}}},addAll:function(){var left=this.left;var right=this.right;for(var i=0;i<left.options.length;i++){var opt=left.options[i];right.options[right.options.length]=new Option(opt.innerHTML,opt.value)}left.options.length=0},removeSelected:function(){var left=this.left;var right=this.right;for(var i=0;i<right.options.length;i++){if(right.options[i].selected){var opt=right.options[i];left.options[left.options.length]=new Option(opt.innerHTML,opt.value);right.options[i]=null;i--}}},getOptions:function(isLeft){var sel=isLeft?this.left:this.right;var options=[];for(var i=0;i<sel.options.length;i++){options.push(sel.options[i].value)}return options},removeAll:function(){var left=this.left;var right=this.right;for(var i=0;i<right.options.length;i++){var opt=right.options[i];left.options[left.options.length]=new Option(opt.innerHTML,opt.value)}right.options.length=0},moveUp:function(){var right=this.right;var selectedOptions=right.selectedOptions;var indices=[];for(var i=0;i<selectedOptions.length;i++){indices.push(selectedOptions[i].index)}var index=morpheus.Util.indexSort(indices,false);for(var i=0;i<selectedOptions.length;i++){var sel=selectedOptions[index[i]].index;var optHTML=right.options[sel].innerHTML;var optVal=right.options[sel].value;var opt1HTML=right.options[sel-1].innerHTML;var opt1Val=right.options[sel-1].value;right.options[sel]=new Option(opt1HTML,opt1Val);right.options[sel-1]=new Option(optHTML,optVal);right.options.selectedIndex=sel-1}},moveDown:function(){var right=this.right;var selectedOptions=right.selectedOptions;var indices=[];for(var i=0;i<selectedOptions.length;i++){indices.push(selectedOptions[i].index)}var index=morpheus.Util.indexSort(indices,false);for(var i=0;i<selectedOptions.length;i++){var sel=selectedOptions[index[i]].index;var optHTML=right.options[sel].innerHTML;var optVal=right.options[sel].value;var opt1HTML=right.options[sel+1].innerHTML;var opt1Val=right.options[sel+1].value;right.options[sel]=new Option(opt1HTML,opt1Val);right.options[sel+1]=new Option(optHTML,optVal);right.options.selectedIndex=sel+1}}};morpheus.FilePicker=function(options){var html=[];html.push("<div>");var myComputer=_.uniqueId("morpheus");var url=_.uniqueId("morpheus");var googleId=_.uniqueId("morpheus");var dropbox=_.uniqueId("morpheus");var preloaded=_.uniqueId("morpheus");html.push('<ul style="margin-bottom:10px;" class="nav nav-pills morpheus">');html.push('<li role="presentation" class="active"><a href="#'+myComputer+'"'+' aria-controls="'+myComputer+'" role="tab" data-toggle="tab"><i class="fa fa-desktop"></i>'+" My Computer</a></li>");html.push('<li role="presentation"><a href="#'+url+'"'+' aria-controls="'+url+'" role="tab" data-toggle="tav"><i class="fa fa-link"></i>'+" URL</a></li>");if(typeof gapi!=="undefined"){html.push('<li role="presentation"><a href="#'+googleId+'"'+' aria-controls="'+googleId+'" role="tab" data-toggle="tab"><i class="fa'+' fa-google"></i>'+" Google</a></li>")}if(typeof Dropbox!=="undefined"){html.push('<li role="presentation"><a href="#'+dropbox+'"'+' aria-controls="'+dropbox+'" role="tab" data-toggle="tab"><i class="fa fa-dropbox"></i>'+" Dropbox</a></li>")}var $sampleDatasetsEl=$('<div class="morpheus-preloaded"></div>');if(navigator.onLine){html.push('<li role="presentation"><a href="#'+preloaded+'"'+' aria-controls="'+preloaded+'" role="tab" data-toggle="tab"><i class="fa fa-database"></i>'+" Preloaded Datasets</a></li>");new morpheus.SampleDatasets({$el:$sampleDatasetsEl,show:true,callback:function(heatMapOptions){options.optionsCallback(heatMapOptions)}})}html.push("</ul>");html.push('<div class="tab-content"'+' style="text-align:center;cursor:pointer;height:300px;">');html.push('<div role="tabpanel" class="tab-pane active" id="'+myComputer+'">');html.push('<div data-name="drop" class="morpheus-file-drop morpheus-landing-panel">');html.push('<button class="btn btn-default"><span class="fa-stack"><i'+' class="fa fa-file-o'+' fa-stack-2x"></i> <i class="fa fa-plus fa-stack-1x"></i></span> Select File</button>'+' <div style="padding-top:10px;">or Copy and Paste Clipboard Data, <span'+' class="morpheus-drag-text">Drag and'+" Drop</span></div>");html.push('<input name="hiddenFile" style="display:none;" type="file">');html.push("</div>");html.push("</div>");html.push('<div role="tabpanel" class="tab-pane" id="'+url+'">');html.push('<div class="morpheus-landing-panel">');html.push('<input name="url" placeholder="Enter a URL" class="form-control"'+' style="display:inline;max-width:400px;'+' type="text"><button name="openUrl" class="btn btn-default"'+' type="button">Go</button>');html.push("</div>");html.push("</div>");if(typeof Dropbox!=="undefined"){html.push('<div role="tabpanel" class="tab-pane" id="'+dropbox+'">');html.push('<div class="morpheus-landing-panel">');html.push('<button name="dropbox" class="btn btn-default">Browse Dropbox</button>');html.push("</div>");html.push("</div>")}if(typeof gapi!=="undefined"){html.push('<div role="tabpanel" class="tab-pane" id="'+googleId+'">');html.push('<div class="morpheus-landing-panel">');html.push('<button name="google" class="btn btn-default">Browse Google Drive</button>');html.push("</div>");html.push("</div>")}if(navigator.onLine){html.push('<div role="tabpanel" class="tab-pane" id="'+preloaded+'">');html.push('<div class="morpheus-landing-panel">');html.push("</div>");html.push("</div>")}html.push("</div>");html.push("</div>");var $el=$(html.join(""));$sampleDatasetsEl.appendTo($el.find("#"+preloaded+" > .morpheus-landing-panel"));this.$el=$el;var $file=$el.find("[name=hiddenFile]");var $myComputer=$el.find("[id="+myComputer+"]");this.$el.find(".nav").on("click","li > a",function(e){e.preventDefault();$(this).tab("show")});var $url=$el.find("[name=url]");$url.on("keyup",function(evt){if(evt.which===13){var text=$.trim($(this).val());if(text!==""){options.fileCallback(text)}}});$el.find("[name=openUrl]").on("click",function(evt){var text=$.trim($url.val());if(text!==""){options.fileCallback(text)}});var $dropbox=$el.find("[name=dropbox]");$dropbox.on("click",function(e){Dropbox.choose({success:function(results){var val=results[0].link;options.fileCallback(val)},linkType:"direct",multiselect:false})});var $google=$el.find("[name=google]");$google.on("click",function(){var developerKey="AIzaSyBCRqn5xgdUsJZcC6oJnIInQubaaL3aYvI";var clientId="936482190815-85k6k06b98ihv272n0b7f7fm33v5mmfa.apps.googleusercontent.com";var scope=["https://www.googleapis.com/auth/drive"];var oauthToken;var pickerApiLoaded=false;var oauthToken;function onApiLoad(){gapi.load("auth",{callback:onAuthApiLoad});gapi.load("picker",{callback:onPickerApiLoad})}function onAuthApiLoad(){window.gapi.auth.authorize({client_id:clientId,scope:scope,immediate:false},handleAuthResult)}function onPickerApiLoad(){pickerApiLoaded=true;createPicker()}function handleAuthResult(authResult){if(authResult&&!authResult.error){oauthToken=authResult.access_token;createPicker()}}function createPicker(){if(pickerApiLoaded&&oauthToken){var picker=(new google.picker.PickerBuilder).addView(google.picker.ViewId.DOCS).setOAuthToken(oauthToken).setDeveloperKey(developerKey).setCallback(pickerCallback).build();picker.setVisible(true);$(".picker-dialog-bg").css("z-index",1052);$(".picker-dialog").css("z-index",1053)}}function pickerCallback(data){if(data.action==google.picker.Action.PICKED){var file=data.docs[0];var fileName=file.name;var accessToken=gapi.auth.getToken().access_token;var xhr=new XMLHttpRequest;var url=new String("https://www.googleapis.com/drive/v3/files/"+file.id+"?alt=media");url.name=fileName;url.headers={Authorization:"Bearer "+accessToken};options.fileCallback(url)}}onApiLoad()});$file.on("change",function(evt){var files=evt.target.files;for(var i=0;i<files.length;i++){options.fileCallback(files[i])}});$(window).on("paste.morpheus",this.paste=function(e){if($myComputer.is(":visible")){var text=e.originalEvent.clipboardData.getData("text/plain");if(text!=null&&text.length>0){e.preventDefault();e.stopPropagation();var url;if(text.indexOf("http")===0){url=text}else{var blob=new Blob([text]);url=new String(window.URL.createObjectURL(blob));url.name="clipboard"}options.fileCallback(url)}}});var $drop=$el.find("[data-name=drop]");var _this=this;$el.on("remove",function(){$(window).off(_this.paste).off(_this.dragover).off(_this.dragenter).off(_this.dragleave).off(_this.drop)});var clicking=false;$drop.on("click",function(e){if(!clicking){clicking=true;$file.click();clicking=false}});$(window).on("dragover",this.dragover=function(e){if($myComputer.is(":visible")){$drop.addClass("drag");e.preventDefault();e.stopPropagation()}}).on("dragenter",this.dragenter=function(e){if($myComputer.is(":visible")){$drop.addClass("drag");e.preventDefault();e.stopPropagation()}}).on("dragleave",this.dragleave=function(e){if($myComputer.is(":visible")){$drop.removeClass("drag");e.preventDefault();e.stopPropagation()}}).on("drop",this.drop=function(e){if($myComputer.is(":visible")){$drop.removeClass("drag");if(e.originalEvent.dataTransfer){if(e.originalEvent.dataTransfer.files.length){e.preventDefault();e.stopPropagation();var files=e.originalEvent.dataTransfer.files;for(var i=0;i<files.length;i++){options.fileCallback(files[i])}}else{var url=e.originalEvent.dataTransfer.getData("URL");options.fileCallback(url);e.preventDefault();e.stopPropagation()}}}})};morpheus.FilterUI=function(project,isColumns){var _this=this;this.project=project;this.isColumns=isColumns;var $div=$('<div style="min-width:180px;"></div>');this.$div=$div;$div.append(this.addBase());var $filterMode=$div.find("[name=filterMode]");$filterMode.on("change",function(e){var isAndFilter=$filterMode.prop("checked");(isColumns?project.getColumnFilter():project.getRowFilter()).setAnd(isAndFilter);isColumns?_this.project.setColumnFilter(_this.project.getColumnFilter(),true):_this.project.setRowFilter(_this.project.getRowFilter(),true);e.preventDefault()});$div.on("click","[data-name=add]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index();var newFilter=new morpheus.AlwaysTrueFilter;(isColumns?project.getColumnFilter():project.getRowFilter()).insert(index,newFilter);$row.after(_this.add(newFilter));e.preventDefault()});$div.on("click","[data-name=delete]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index()-1;(isColumns?project.getColumnFilter():project.getRowFilter()).remove(index);$row.remove();isColumns?_this.project.setColumnFilter(_this.project.getColumnFilter(),true):_this.project.setRowFilter(_this.project.getRowFilter(),true);e.preventDefault()});$div.on("submit","form",function(e){var $this=$(this);e.preventDefault()});$div.on("change","[name=by]",function(e){var $this=$(this);var fieldName=$this.val();var $row=$this.closest(".morpheus-entry");var index=$row.index()-1;if(fieldName==""){$row.find("[data-name=ui]").empty()}else{_this.createFilter({fieldName:fieldName,$div:$this})}isColumns?_this.project.setColumnFilter(_this.project.getColumnFilter(),true):_this.project.setRowFilter(_this.project.getRowFilter(),true)});var combinedFilter=isColumns?project.getColumnFilter():project.getRowFilter();var filters=combinedFilter.getFilters?combinedFilter.getFilters():[];for(var i=0;i<filters.length;i++){this.createFilter({filter:filters[i]})}if(combinedFilter.on){combinedFilter.on("add",function(e){_this.createFilter({filter:e.filter})});combinedFilter.on("remove",function(e){var $row=$div.find(".morpheus-entry")[1+e.index].remove()});combinedFilter.on("and",function(e){$filterMode.prop("checked",e.source.isAnd())})}};morpheus.FilterUI.rangeFilter=function(project,name,isColumns,$ui,filter){$ui.empty();var html=[];html.push("<label>Range of values</label><br />");html.push('<label>>= </label> <input style="max-width:200px;" class="form-control input-sm" name="min" type="text" />');html.push('<label> and <= </label> <input style="max-width:200px;" class="form-control input-sm" name="max" type="text" />');html.push('<br /><a data-name="switch" href="#">Switch to top filter</a>');var $form=$(html.join(""));$form.appendTo($ui);$ui.find("[data-name=switch]").on("click",function(e){e.preventDefault();var newFilter=morpheus.FilterUI.topFilter(project,name,isColumns,$ui);var index=-1;var filters=isColumns?project.getColumnFilter().getFilters():project.getRowFilter().getFilters();for(var i=0;i<filters.length;i++){if(filters[i]===filter){index=i;break}}if(index===-1){throw new Error("Filter not found.")}(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,newFilter);isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)});var $min=$ui.find("[name=min]");var $max=$ui.find("[name=max]");if(!filter){filter=new morpheus.RangeFilter(-Number.MAX_VALUE,Number.MAX_VALUE,name,isColumns)}else{$min.val(filter.min);$max.val(filter.max)}$min.on("keyup",_.debounce(function(e){filter.setMin(parseFloat($.trim($(this).val())));isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)},500));$max.on("keyup",_.debounce(function(e){filter.setMax(parseFloat($.trim($(this).val())));isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)},500));return filter};morpheus.FilterUI.topFilter=function(project,name,isColumns,$ui,filter){$ui.empty();var html=[];html.push("<label>Top</label><br />");html.push('<select style="width:auto;" class="form-control input-sm" name="direction"><option value="Top">Top</option><option value="Bottom">Bottom</option><option value="TopBottom">Top/Bottom</option></select>');html.push(' <label>N </label> <input style="max-width:200px;" class="form-control input-sm" name="n" type="text" />');html.push('<br /><a data-name="switch" href="#">Switch to range filter</a>');var $form=$(html.join(""));$form.appendTo($ui);var $n=$ui.find("[name=n]");var $direction=$ui.find("[name=direction]");$ui.find("[data-name=switch]").on("click",function(e){e.preventDefault();var newFilter=morpheus.FilterUI.rangeFilter(project,name,isColumns,$ui);var index=-1;var filters=isColumns?project.getColumnFilter().getFilters():project.getRowFilter().getFilters();for(var i=0;i<filters.length;i++){if(filters[i]===filter){index=i;break}}if(index===-1){throw new Error("Filter not found.")}(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,newFilter);isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)});if(!filter){filter=new morpheus.TopNFilter(NaN,morpheus.TopNFilter.TOP,name,isColumns)}else{var dirVal;if(filter.direction===morpheus.TopNFilter.TOP){dirVal="Top"}else if(filter.direction===morpheus.TopNFilter.BOTTOM){dirVal="Bottom"}else{dirVal="TopBottom"}$direction.val(dirVal);$n.val(filter.n)}$direction.on("change",function(){var dir=$(this).val();var dirVal;if(dir==="Top"){dirVal=morpheus.TopNFilter.TOP}else if(dir==="Bottom"){dirVal=morpheus.TopNFilter.BOTTOM}else{dirVal=morpheus.TopNFilter.TOP_BOTTOM}filter.setDirection(dirVal);isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)});$n.on("keyup",_.debounce(function(e){filter.setN(parseInt($.trim($(this).val())));isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)},500));return filter};morpheus.FilterUI.prototype={createFilter:function(options){var index=-1;var $div=options.$div;var isColumns=this.isColumns;var filter=options.filter;var project=this.project;var fieldName=filter?filter.name:options.fieldName;var $ui;if(!$div){var $add=$(this.add(filter));$add.appendTo(this.$div);$ui=$add.find("[data-name=ui]")}else{var $row=$div.closest(".morpheus-entry");index=$row.index()-1;$ui=$row.find("[data-name=ui]")}$ui.empty();var vector=(isColumns?this.project.getFullDataset().getColumnMetadata():this.project.getFullDataset().getRowMetadata()).getByName(fieldName);if(filter instanceof morpheus.RangeFilter){morpheus.FilterUI.rangeFilter(project,fieldName,isColumns,$ui,filter)}else if(filter instanceof morpheus.TopNFilter){morpheus.FilterUI.topFilter(project,fieldName,isColumns,$ui,filter)}else if(filter==null&&morpheus.VectorUtil.isNumber(vector)&&morpheus.VectorUtil.containsMoreThanNValues(vector,9)){filter=morpheus.FilterUI.rangeFilter(project,fieldName,isColumns,$ui,filter)}else{var set=morpheus.VectorUtil.getSet(vector);var array=set.values();array.sort(morpheus.SortKey.ASCENDING_COMPARATOR);if(!filter){filter=new morpheus.VectorFilter(new morpheus.Set,set.size(),fieldName,isColumns)}else{filter.maxSetSize=array.length}var checkBoxList=new morpheus.CheckBoxList({responsive:false,$el:$ui,items:array,set:filter.set});checkBoxList.on("checkBoxSelectionChanged",function(){isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)})}if(index!==-1){if(fieldName!==""){(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,filter)}else{(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,new morpheus.AlwaysTrueFilter)}}return filter},addBase:function(){var html=[];html.push('<div style="padding-bottom:2px;border-bottom:1px solid #eee" class="morpheus-entry">');html.push('<div class="row">');html.push('<div class="col-xs-12">'+'<div class="checkbox"><label><input type="checkbox" name="filterMode">Pass all filters</label></div> '+"</div>");html.push("</div>");html.push('<div class="row">');html.push('<div class="col-xs-8"><a class="btn btn-default btn-xs" role="button"'+' data-name="add" href="#">Add</a></div>');html.push("</div>");html.push("</div>");return html.join("")},add:function(filter){var project=this.project;var isColumns=this.isColumns;var fields=morpheus.MetadataUtil.getMetadataNames(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata());var html=[];html.push('<div class="morpheus-entry">');html.push('<div class="form-group">');html.push("<label>Field</label>");html.push('<select style="max-width:160px;overflow-x:hidden;" name="by" class="form-control input-sm">');html.push('<option value=""></option>');var filterField=filter?filter.toString():null;_.each(fields,function(field){html.push('<option value="'+field+'"');if(field===filterField){html.push(" selected")}html.push(">");html.push(field);html.push("</option>")});html.push("</select>");html.push("</div>");html.push('<div class="row">');html.push('<div data-name="ui" class="col-xs-12"></div>');html.push("</div>");html.push('<div style="padding-bottom:6px; border-bottom:1px solid #eee" class="row">');html.push('<div class="col-xs-11">');html.push('<a class="btn btn-default btn-xs" role="button" data-name="delete"'+' href="#">Remove</a>');html.push("</div>");html.push("</div>");html.push("</div>");return html.join("")}};morpheus.FontChooser=function(options){var _this=this;var fontModel=options.fontModel;var track=options.track;var heatMap=options.heatMap;fontModel.getMappedValue(track.getVector(track.settings.fontField),track.getVector(track.settings.fontField).getValue(0));var formBuilder=new morpheus.FormBuilder;formBuilder.append({value:track.settings.fontField!=null,type:"checkbox",name:"use_another_annotation_to_determine_font"});var annotationNames=morpheus.MetadataUtil.getMetadataNames(track.isColumns?heatMap.getProject().getFullDataset().getColumnMetadata():heatMap.getProject().getFullDataset().getRowMetadata());annotationNames.splice(annotationNames.indexOf(track.getName()),1);formBuilder.append({name:"annotation_name",type:"bootstrap-select",options:annotationNames,search:annotationNames.length>10,value:track.settings.fontField});formBuilder.setVisible("annotation_name",track.settings.fontField!=null);formBuilder.append({name:"selected_value",type:"bootstrap-select",search:true,options:fontModel.getMap(track.settings.fontField!=null?track.settings.fontField:track.getName()).keys()});var $selectedValue=formBuilder.find("selected_value");formBuilder.append({name:"selected_font",type:"bootstrap-select",options:[{name:"normal",value:400},{name:"bold",value:700},{name:"bolder",value:900}]});var repaint=function(){track.setInvalid(true);track.repaint()};formBuilder.find("use_another_annotation_to_determine_font").on("change",function(){var checked=$(this).prop("checked");formBuilder.setValue("annotation_name",null);formBuilder.setValue("selected_value",null);formBuilder.setVisible("annotation_name",checked);if(!checked){track.settings.fontField=null}repaint()});formBuilder.find("annotation_name").on("change",function(){var annotationName=$(this).val();fontModel.getMappedValue(track.getVector(annotationName),track.getVector(annotationName).getValue(0));track.settings.fontField=annotationName;formBuilder.setOptions("selected_value",fontModel.getMap(track.settings.fontField!=null?track.settings.fontField:track.getName()).keys());formBuilder.setValue("selected_value",null);repaint()});var $selectedFont=formBuilder.find("selected_font");$selectedFont.on("change",function(e){fontModel.setMappedValue(track.getVector(track.settings.fontField),$selectedValue.val(),{weight:$(this).val()});repaint()});var updateMappedValue=function(){var selectedVal=$selectedValue.val();var mappedValue=fontModel.getMappedValue(track.getVector(track.settings.fontField),selectedVal);formBuilder.setValue("selected_font",mappedValue.weight)};$selectedValue.on("change",function(){updateMappedValue()});updateMappedValue();this.$div=formBuilder.$form};morpheus.Util.extend(morpheus.FontChooser,morpheus.Events);morpheus.FormBuilder=function(options){var _this=this;this.prefix=_.uniqueId("form");this.$form=$("<form></form>");this.$form.attr("role","form").attr("id",this.prefix);this.formStyle=options==null||options.formStyle==null?"horizontal":options.formStyle;this.$form.addClass("morpheus");if(this.formStyle==="horizontal"){this.titleClass="col-xs-12 control-label";this.labelClass="col-xs-4 control-label";this.$form.addClass("form-horizontal")}else if(this.formStyle==="vertical"){this.labelClass="control-label";this.titleClass="control-label"}else if(this.formStyle==="inline"){this.titleClass="";this.labelClass="";this.$form.addClass("form-inline")}this.$form.on("submit",function(e){e.preventDefault()});this.$form.on("dragover",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){$(e.originalEvent.srcElement).parent().css("border","1px solid black");e.preventDefault();e.stopPropagation()}}).on("dragenter",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){$(e.originalEvent.srcElement).parent().css("border","1px solid black");e.preventDefault();e.stopPropagation()}}).on("dragleave",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){$(e.originalEvent.srcElement).parent().css("border","");e.preventDefault();e.stopPropagation()}}).on("drop",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){var isMultiple=node.data("multiple");$(e.originalEvent.srcElement).parent().css("border","");var name=node.attr("name");name=name.substring(0,name.length-"_picker".length);if(e.originalEvent.dataTransfer){if(e.originalEvent.dataTransfer.files.length){e.preventDefault();e.stopPropagation();var files=e.originalEvent.dataTransfer.files;_this.setValue(name,isMultiple?files:files[0]);_this.trigger("change",{name:name,value:files[0]})}else{var url=e.originalEvent.dataTransfer.getData("URL");e.preventDefault();e.stopPropagation();_this.setValue(name,isMultiple?[url]:url);_this.trigger("change",{name:name,value:url})}}}})};morpheus.FormBuilder.showProgressBar=function(options){var content=[];content.push('<div class="container-fluid">');content.push('<div class="row">');content.push('<div class="col-xs-8">');content.push('<div class="progress progress-striped active"><div class="progress-bar" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width: 100%"></div></div>');content.push("</div>");content.push('<div class="col-xs-2">');content.push('<input class="btn btn-default" type="button" name="stop" value="Cancel">');content.push("</div>");content.push("</div>");if(options.subtitle){content.push('<div class="row"><div class="col-xs-8">');content.push('<p class="text-muted">');content.push(options.subtitle);content.push("</p>");content.push("</div></div>")}content.push("</div>");var $content=$(content.join(""));$content.find("[name=stop]").on("click",function(e){options.stop();e.preventDefault()});return morpheus.FormBuilder.showInDraggableDiv({title:options.title,$content:$content})};morpheus.FormBuilder.showInDraggableDiv=function(options){var width=options.width||"300px";var html=[];html.push('<div style="z-index: 1050; top: 100px; position:absolute; padding-left:10px; padding-right:10px; width:'+width+' ; background:white; box-shadow: 0 5px 15px rgba(0,0,0,0.5); border: 1px solid rgba(0,0,0,0.2); border-radius: 6px;">');if(options.title!=null){html.push('<h4 style="cursor:move; border-bottom: 1px solid #e5e5e5;" name="header">'+options.title+"</h4>")}html.push('<div name="content"></div>');html.push("</div>");var $div=$(html.join(""));var $content=$div.find("[name=content]");$div.find("[name=header]").on("dblclick",function(){if($content.css("display")==="none"){$content.css("display","")}else{$content.css("display","none")}});options.$content.appendTo($content);$div.css("left",$(window).width()/2-$content.outerWidth()/2);$div.draggable({containment:"document"});$div.appendTo(options.appendTo!=null?options.appendTo:$(document.body));return $div};morpheus.FormBuilder.showMessageModal=function(options){var $div=morpheus.FormBuilder._showInModal({modalClass:options.modalClass,title:options.title,html:options.html,footer:'<button type="button" class="btn btn-default"'+' data-dismiss="modal">OK</button>',backdrop:options.backdrop,size:options.size,focus:options.focus,appendTo:options.appendTo});$div.find("button").focus();return $div};morpheus.FormBuilder._showInModal=function(options){var html=[];options=$.extend({},{size:"",close:true,modalClass:""},options);html.push('<div tabindex="-1" class="modal'+(options.modalClass?" "+options.modalClass:"")+'" role="dialog"'+' aria-hidden="false"');if(options.z){html.push(' style="z-index: '+options.z+' !important;"')}html.push(">");html.push('<div class="modal-dialog '+options.size+'">');html.push('<div class="modal-content">');html.push(' <div class="modal-header">');if(options.close){html.push('  <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>')}if(options.title!=null){html.push('<h4 class="modal-title">'+options.title+"</h4>")}html.push("</div>");html.push('<div class="modal-body">');html.push("</div>");if(options.footer){html.push('<div class="modal-footer">');html.push(options.footer)}html.push("</div>");html.push("</div>");html.push("</div>");html.push("</div>");var $div=$(html.join(""));$div.on("mousewheel",function(e){e.stopPropagation()});$div.find(".modal-body").html(options.html);$div.prependTo(options.appendTo!=null?options.appendTo:$(document.body));$div.modal({keyboard:true,backdrop:options.backdrop===true?true:false}).on("hidden.bs.modal",function(e){$div.remove();if(options.onClose){options.onClose()}if(options.focus){$(options.focus).focus()}});return $div};morpheus.FormBuilder.showInModal=function(options){return morpheus.FormBuilder._showInModal({modalClass:options.modalClass,title:options.title,html:options.html,footer:options.close?'<button type="button" class="btn btn-default" data-dismiss="modal">'+options.close+"</button>":null,onClose:options.onClose,appendTo:options.appendTo,backdrop:options.backdrop,size:options.size,focus:options.focus})};morpheus.FormBuilder.showOkCancel=function(options){options=$.extend({},{ok:true,cancel:true},options);var footer=[];if(options.ok){footer.push('<button name="ok" type="button" class="btn btn-default">OK</button>')}if(options.apply){footer.push('<button name="apply" type="button" class="btn btn-default">Apply</button>')}if(options.cancel){footer.push('<button name="cancel" type="button" data-dismiss="modal" class="btn btn-default">Cancel</button>')}var $div=morpheus.FormBuilder._showInModal({title:options.title,html:options.content,footer:footer.join(""),size:options.size,close:options.close,onClose:options.onClose,focus:options.focus,appendTo:options.appendTo});var $ok=$div.find("[name=ok]");$ok.on("click",function(e){if(options.okCallback){options.okCallback()}$div.modal("hide")});$div.find("[name=cancel]").on("click",function(e){if(options.cancelCallback){options.cancelCallback()}$div.modal("hide")});if(options.okFocus){$ok.focus()}if(options.draggable){$div.draggable({handle:".modal-header",containment:"document"})}return $div};morpheus.FormBuilder.hasChanged=function(object,keyToUIElement){var keys=_.keys(keyToUIElement);for(var i=0;i<keys.length;i++){var key=keys[i];var value=object[key];var $element=keyToUIElement[key];if(value!==morpheus.FormBuilder.getValue($element)){return true}}return false};morpheus.FormBuilder.getValue=function($element){var list=$element.data("morpheus.checkbox-list");if(list!=null){return list.val()}if($element.attr("type")==="radio"){return $element.filter(":checked").val()}if($element.data("type")==="file"){return $element.data("files")}return $element.attr("type")==="checkbox"?$element.prop("checked"):$element.val()};morpheus.FormBuilder.prototype={appendContent:function($content){this.$form.append($content)},addSeparator:function(){var html=[];html.push('<div class="form-group">');if(this.formStyle==="horizontal"){html.push('<div class="col-xs-12">')}html.push("<hr />");if(this.formStyle==="horizontal"){html.push("</div>")}html.push("</div>");this.$form.append(html.join(""))},_append:function(html,field,isFieldStart){var _this=this;var required=field.required;var name=field.name;var type=field.type;if(type=="separator"){if(this.formStyle==="horizontal"){html.push('<div class="col-xs-12">')}else{html.push('<div class="form-group">')}html.push("<hr />");html.push("</div>");return}var title=field.title;var disabled=field.disabled;var help=field.help;var value=field.value;var showLabel=field.showLabel;var style=field.style||"";var col="";var labelColumn="";if(this.formStyle==="horizontal"){col=field.col||"col-xs-8"}if(showLabel===undefined){showLabel="checkbox"!==type&&"button"!==type&&"radio"!==type;showLabel=showLabel||field.options!==undefined}var id=_this.prefix+"_"+name;if(title===undefined){title=name.replace(/_/g," ");title=title[0].toUpperCase()+title.substring(1)}var endingDiv=false;if(showLabel){html.push('<label for="'+id+'" class="'+this.labelClass+'">');html.push(title);html.push("</label>");if(isFieldStart&&this.formStyle!=="inline"){html.push('<div class="'+col+'">');endingDiv=true}}else if(isFieldStart&&this.formStyle==="horizontal"){html.push('<div class="col-xs-offset-4 '+col+'">');endingDiv=true}if("radio"===type){if(field.options){_.each(field.options,function(choice){var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;var selected=value===optionValue;html.push('<div class="radio"><label>');html.push('<input style="'+style+'" value="'+optionValue+'" name="'+field.name+'" type="radio"');if(selected){html.push(" checked")}html.push("> ");if(choice.icon){html.push('<span class="'+choice.icon+'"></span> ')}optionText=optionText[0].toUpperCase()+optionText.substring(1);html.push(optionText);html.push("</label></div>")})}else{html.push('<div class="radio"><label>');html.push('<input style="'+style+'" value="'+value+'" name="'+name+'" id="'+id+'" type="radio"');if(field.checked){html.push(" checked")}html.push("> ");html.push(value[0].toUpperCase()+value.substring(1));html.push("</label></div>")}}else if("checkbox"===type){html.push('<div class="checkbox"><label>');html.push('<input style="'+style+'" name="'+name+'" id="'+id+'" type="checkbox"');if(value){html.push(" checked")}if(disabled){html.push(" disabled")}html.push("> ");html.push(title);html.push("</label></div>")}else if("checkbox-list"===type){html.push('<div name="'+name+'" class="checkbox-list"><div>')}else if("select"==type||type=="bootstrap-select"){if(type=="bootstrap-select"){html.push('<select style="'+style+'" data-live-search="'+(field.search?true:false)+'" data-selected-text-format="count" name="'+name+'" id="'+id+'" data-actions-box="'+(field.selectAll?true:false)+'" class="selectpicker'+(this.formStyle!=="inline"?" form-control":"")+'"')}else{html.push('<select style="'+style+'" name="'+name+'" id="'+id+'" class="form-control"')}if(disabled){html.push(" disabled")}if(field.multiple){html.push(" multiple")}html.push(">");_.each(field.options,function(choice){if(choice&&choice.divider){html.push('<option data-divider="true"></option>')}else{html.push('<option value="');var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;html.push(optionValue);html.push('"');var selected=false;if(_.isObject(value)){selected=value[optionValue]}else if(_.isArray(value)){selected=value.indexOf(optionValue)!==-1}else{selected=value==optionValue}if(selected){html.push(" selected")}html.push(">");html.push(optionText);html.push("</option>")}});html.push("</select>");if(field.type=="bootstrap-select"&&field.toggle){html.push('<p class="help-block"><a data-name="'+name+'_all" href="#">All</a>&nbsp;|&nbsp;<a data-name="'+name+'_none" href="#">None</a></p>');_this.$form.on("click","[data-name="+name+"_all]",function(evt){evt.preventDefault();var $select=_this.$form.find("[name="+name+"]");$select.selectpicker("val",$.map($select.find("option"),function(o){return $(o).val()}));$select.trigger("change")});_this.$form.on("click","[data-name="+name+"_none]",function(evt){evt.preventDefault();var $select=_this.$form.find("[name="+name+"]");$select.selectpicker("val",[]);$select.trigger("change")})}}else if("textarea"==type){html.push('<textarea style="'+style+'" id="'+id+'" class="form-control" name="'+name+'"');if(required){html.push(" required")}if(field.placeholder){html.push(' placeholder="'+field.placeholder+'"')}if(disabled){html.push(" disabled")}html.push(">");if(value!=null){html.push(value)}html.push("</textarea>")}else if("button"==type){html.push('<button style="'+style+'" id="'+id+'" name="'+name+'" type="button" class="btn btn-default btn-sm">');if(field.icon){html.push('<span class="'+field.icon+'"></span> ')}html.push(value?value:title);html.push("</button>")}else if("custom"===type){html.push(value)}else if("file"===type){var isMultiple=field.multiple==null?false:field.multiple;html.push('<select data-multiple="'+isMultiple+'" data-type="file" title="'+(field.placeholder||(isMultiple?"Choose one or more files...":"Choose a file..."))+'" name="'+name+'_picker" data-width="35%" class="file-input selectpicker form-control">');var options=[];if(field.options){options=options.concat(field.options)}options.push("My Computer");options.push("URL");if(field.text!=null){options.push(field.text)}_.each(options,function(choice,index){var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;html.push('<option value="');html.push(optionValue);html.push('"');if(isChoiceObject&&choice.disabled){html.push(" disabled")}if(optionValue==="Dropbox"){html.push(' data-icon="fa fa-dropbox"')}else if(optionValue==="My Computer"){html.push(' data-icon="fa fa-desktop"')}else if(optionValue==="URL"){html.push(' data-icon="fa fa-external-link"')}html.push(">");html.push(optionText);html.push("</option>")});html.push("</select>");html.push("<div>");html.push('<input placeholder="'+(isMultiple?"Enter one or more URLs":"Enter a URL")+'" class="form-control" style="width:50%; display:none;" type="text" name="'+name+'_url">');if(field.text){html.push('<input class="form-control" style="width:50%; display:none;" type="text" name="'+name+'_text">')}html.push("</div>");html.push('<input style="display:none;" type="file" name="'+name+'_file"'+(isMultiple?" multiple":"")+">");_this.$form.on("change","[name="+name+"_picker]",function(evt){var $this=$(this);var val=$this.val();var showUrlInput=val==="URL";var showTextInput=val===field.text;if("Dropbox"===val){var options={success:function(results){var val=!isMultiple?results[0].link:results.map(function(result){return result.link});_this.setValue(name,val);_this.trigger("change",{name:name,value:val})},linkType:"direct",multiselect:isMultiple};Dropbox.choose(options);_this.$form.find("[name="+name+"_picker]").selectpicker("val","")}else if("My Computer"===val){_this.$form.find("[name="+name+"_file]").click();_this.$form.find("[name="+name+"_picker]").selectpicker("val","")}_this.$form.find("[name="+name+"_url]").css("display",showUrlInput?"":"none");_this.$form.find("[name="+name+"_text]").css("display",showTextInput?"":"none")});_this.$form.on("keyup","[name="+name+"_url]",function(evt){var text=$.trim($(this).val());if(isMultiple){text=text.split(",").filter(function(t){t=$.trim(t);return t!==""})}_this.setValue(name,text);if(evt.which===13){_this.trigger("change",{name:name,value:text})}});_this.$form.on("keyup","[name="+name+"_text]",function(evt){var text=$.trim($(this).val());_this.setValue(name,text);if(evt.which===13){_this.trigger("change",{name:name,value:text})}});_this.$form.on("change","[name="+name+"_file]",function(evt){var files=evt.target.files;_this.setValue(name,isMultiple?files:files[0]);_this.trigger("change",{name:name,value:isMultiple?files:files[0]})})}else{type=type==null?"text":type;if(type==="div"){html.push('<div name="'+name+'" id="'+id+'"')}else{html.push('<input style="'+style+'" type="'+type+'" class="form-control" name="'+name+'" id="'+id+'"')}if(value!=null){html.push(' value="'+value+'"')}if(field.placeholder){html.push(' placeholder="'+field.placeholder+'"')}if(field.min!=null){html.push(' min="'+field.min+'"')}if(field.max!=null){html.push(' max="'+field.max+'"')}if(field.step){html.push(' step="'+field.step+'"')}if(required){html.push(" required")}if(disabled){html.push(" disabled")}if(field.autocomplete!=null){html.push(' autocomplete="'+field.autocomplete+'"')}html.push(">");if(type==="div"){html.push("</div>")}}if(help!==undefined){html.push('<span data-name="'+name+'_help" class="help-block">');html.push(help);html.push("</span>")}return endingDiv},append:function(fields){var html=[];var _this=this;var isArray=morpheus.Util.isArray(fields);if(!isArray){fields=[fields]}html.push('<div class="form-group">');var endingDiv=false;_.each(fields,function(field,index){endingDiv||_this._append(html,field,index===0)});html.push("</div>");if(endingDiv){html.push("</div>")}var $div=$(html.join(""));this.$form.append($div);var checkBoxLists=$div.find(".checkbox-list");if(checkBoxLists.length>0){var checkBoxIndex=0;_.each(fields,function(field){if(field.type==="checkbox-list"){var list=new morpheus.CheckBoxList({responsive:false,$el:$(checkBoxLists[checkBoxIndex]),items:field.options});$(checkBoxLists[checkBoxIndex]).data("morpheus.checkbox-list",list);checkBoxIndex++}})}$div.find(".selectpicker").selectpicker({iconBase:"fa",tickIcon:"fa-check",style:"btn-default btn-sm"})},clear:function(){this.$form.empty()},getValue:function(name){var $v=this.$form.find("[name="+name+"]");if($v.length===0){$v=this.$form.find("[name="+name+"_picker]")}return morpheus.FormBuilder.getValue($v)},setOptions:function(name,options,selectFirst){var $select=this.$form.find("[name="+name+"]");var checkBoxList=$select.data("morpheus.checkbox-list");if(checkBoxList){checkBoxList.setItems(options)}else{var html=[];var selection=$select.val();_.each(options,function(choice){var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;if(choice&&choice.divider){html.push('<option data-divider="true"></option>')}else{html.push('<option value="');var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;html.push(optionValue);html.push('"');html.push(">");html.push(optionText);html.push("</option>")}});$select.html(html.join(""));$select.val(selection);if(selectFirst&&$select.val()==null){if($select[0].options.length>0){$select.val($select[0].options[0].value)}}if($select.hasClass("selectpicker")){$select.selectpicker("refresh");$select.selectpicker("render")}}},find:function(name){return this.$form.find("[name="+name+"]")},setHelpText:function(name,value){var v=this.$form.find("[data-name="+name+"_help]");v.html(value)},setValue:function(name,value){var v=this.$form.find("[name="+name+"]");if(v.length===0){v=this.$form.find("[name="+name+"_picker]");if(v.data("type")==="file"){v.val(value);v.selectpicker("render");v.data("files",value);return}}var type=v.attr("type");var list=v.data("morpheus.checkbox-list");if(list){list.setValue(value)}else{if(type==="radio"){v.filter("[value="+value+"]").prop("checked",true)}else if(type==="checkbox"){v.prop("checked",value)}else{v.val(value)}if(v.hasClass("selectpicker")){v.selectpicker("render")}}},setVisible:function(name,visible){var $div=this.$form.find("[name="+name+"]").parents(".form-group");if(visible){$div.show()}else{$div.hide()}},remove:function(name){var $div=this.$form.find("[name="+name+"]").parents(".form-group");$div.remove()},setEnabled:function(name,enabled){var $div=this.$form.find("[name="+name+"]");$div.attr("disabled",!enabled);if(!enabled){$div.parents(".form-group").find("label").addClass("text-muted")}else{$div.parents(".form-group").find("label").removeClass("text-muted")}}};morpheus.Util.extend(morpheus.FormBuilder,morpheus.Events);morpheus.GradientColorSupplier=function(){morpheus.AbstractColorSupplier.call(this);this._updateScale()};morpheus.GradientColorSupplier.prototype={createInstance:function(){return new morpheus.GradientColorSupplier},getColor:function(row,column,value){if(isNaN(value)){return this.missingColor}var min=this.min;var max=this.max;var colors=this.colors;if(value<=min){return colors[0]}else if(value>=max){return colors[colors.length-1]}var fraction=morpheus.SteppedColorSupplier.linearScale(value,min,max,0,100)/100;return this.colorScale(fraction)},setFractions:function(options){morpheus.AbstractColorSupplier.prototype.setFractions.call(this,options);this._updateScale()},_updateScale:function(){this.colorScale=d3.scale.linear().domain(this.fractions).range(this.colors).clamp(true)}};morpheus.Util.extend(morpheus.GradientColorSupplier,morpheus.AbstractColorSupplier);morpheus.Grid=function(options){this.options=options;var _this=this;var grid;this.items=options.items;this.modelToView=null;this.viewOrder=null;function getItemColumnValue(item,column){return column.getter(item)}this.filter=new morpheus.CombinedGridFilter;var model={getLength:function(){return _this.viewOrder!=null?_this.viewOrder.length:_this.items.length},getItem:function(index){return _this.items[_this.viewOrder!=null?_this.viewOrder[index]:index]}};this.$el=options.$el;var gridOptions=$.extend({},{select:true,headerRowHeight:0,showHeaderRow:false,multiColumnSort:true,multiSelect:false,topPanelHeight:0,enableColumnReorder:false,enableTextSelectionOnCells:true,forceFitColumns:true,dataItemColumnValueExtractor:getItemColumnValue,defaultFormatter:function(row,cell,value,columnDef,dataContext){if(_.isNumber(value)){return morpheus.Util.nf(value)}else if(morpheus.Util.isArray(value)){var s=[];for(var i=0,length=value.length;i<length;i++){if(i>0){s.push(", ")}var val=value[i];s.push(value[i])}return s.join("")}else{return value}}},options.gridOptions||{});grid=new Slick.Grid(options.$el,model,options.columns,gridOptions);this.grid=grid;grid.registerPlugin(new morpheus.AutoTooltips2);grid.onCellChange.subscribe(function(e,args){_this.trigger("edit",args)});if(gridOptions.select){grid.setSelectionModel(new Slick.RowSelectionModel({selectActiveRow:true,multiSelect:gridOptions.multiSelect}));grid.getSelectionModel().onSelectedRangesChanged.subscribe(function(e){var nitems=grid.getDataLength();_this.trigger("selectionChanged",{selectedRows:grid.getSelectedRows().filter(function(row){return row>=0&&row<=nitems})})})}grid.onSort.subscribe(function(e,args){_this.sortCols=args.sortCols;_this._updateMappings();grid.invalidate()});options.$el.on("click",function(e){var cell=grid.getCellFromEvent(e);if(cell){_this.trigger("click",{row:cell.row,target:e.target})}});options.$el.on("dblclick",function(e){var cell=grid.getCellFromEvent(e);if(cell){_this.trigger("dblclick",{row:cell.row,target:e.target})}});if(options.sort){var gridSortColumns=[];var gridColumns=grid.getColumns();var sortCols=[];options.sort.forEach(function(c){var column=null;for(var i=0;i<gridColumns.length;i++){if(gridColumns[i].name===c.name){column=gridColumns[i];break}}if(column!=null){gridSortColumns.push({columnId:column.id,sortAsc:c.sortAsc})}else{console.log(c.name+" not found.")}});this.setSortColumns(gridSortColumns)}this.grid.invalidate()};morpheus.Grid.prototype={columnsAutosized:false,setSortColumns:function(gridSortColumns){this.grid.setSortColumns(gridSortColumns);this.sortCols=[];for(var i=0;i<gridSortColumns.length;i++){var column=this.grid.getColumns()[this.grid.getColumnIndex(gridSortColumns[i].columnId)];if(column==null){throw"Unable to find column "+gridSortColumns[i]}this.sortCols.push({sortCol:column,sortAsc:gridSortColumns[i].sortAsc})}this._updateMappings();this.grid.invalidate()},setColumns:function(columns){this.grid.setColumns(columns);this.grid.resizeCanvas();this.grid.invalidate()},getColumns:function(){return this.grid.getColumns()},getSelectedRows:function(){var nitems=this.grid.getDataLength();return this.grid.getSelectedRows().filter(function(row){return row>=0&&row<=nitems})},getSelectedItems:function(){var rows=this.grid.getSelectedRows();var selection=[];for(var i=0,nrows=rows.length;i<nrows;i++){selection.push(this.items[this.convertViewIndexToModel(rows[i])])}return selection},getSelectedItem:function(){var rows=this.grid.getSelectedRows();if(rows.length===1){return this.items[this.convertViewIndexToModel(rows[0])]}return null},getItems:function(){var items=[];for(var i=0,length=this.getFilteredItemCount();i<length;i++){items.push(this.items[this.convertViewIndexToModel(i)])}return items},getAllItemCount:function(){return this.items.length},getAllItems:function(){return this.items},getFilteredItemCount:function(){return this.viewOrder?this.viewOrder.length:this.items.length},redraw:function(){this.grid.invalidate()},redrawRows:function(rows){this.grid.invalidateRows(rows);this.grid.render()},setItems:function(items){this.items=items;if(this.grid.getSelectionModel()){this.grid.setSelectedRows([])}this.setFilter(this.filter);this.maybeAutoResizeColumns()},maybeAutoResizeColumns:function(){if(!this.columnsAutosized){this.autosizeColumns()}},convertModelIndexToView:function(modelIndex){if(this.modelToView!==null){var index=this.modelToView.get(modelIndex);return index!==undefined?index:-1}return modelIndex},convertViewIndexToModel:function(viewIndex){return this.viewOrder!=null?viewIndex<this.viewOrder.length&&viewIndex>=0?this.viewOrder[viewIndex]:-1:viewIndex},_updateMappings:function(){var selectedViewIndices=this.grid.getSelectionModel()!=null?this.grid.getSelectedRows():null;var selectedModelIndices=[];if(selectedViewIndices){for(var i=0,length=selectedViewIndices.length;i<length;i++){selectedModelIndices.push(this.convertViewIndexToModel(selectedViewIndices[i]))}}this.viewOrder=null;if(this.filter!=null){this.filter.init();if(!this.filter.isEmpty()){this.viewOrder=[];for(var i=0,length=this.items.length;i<length;i++){if(this.filter.accept(this.items[i])){this.viewOrder.push(i)}}}}var cols=this.sortCols;if(cols&&cols.length>0){if(this.viewOrder==null){this.viewOrder=[];for(var i=0,length=this.items.length;i<length;i++){this.viewOrder.push(i)}}var ncols=cols.length;var items=this.items;this.viewOrder.sort(function(index1,index2){for(var i=0;i<ncols;i++){var getter=cols[i].sortCol.getter;var comparator=cols[i].sortAsc?morpheus.SortKey.ASCENDING_COMPARATOR:morpheus.SortKey.DESCENDING_COMPARATOR;var value1=getter(items[index1]);var value2=getter(items[index2]);var result=comparator(value1,value2);if(result!==0){return result}}return 0})}if(this.viewOrder!=null){this.modelToView=new morpheus.Map;for(var i=0,length=this.viewOrder.length;i<length;i++){this.modelToView.set(this.viewOrder[i],i)}}else{this.modelToView=null}if(this.grid.getSelectionModel()!=null){var newSelectedViewIndices=[];for(var i=0,length=selectedModelIndices.length;i<length;i++){var index=this.convertModelIndexToView(selectedModelIndices[i]);if(index!==undefined){newSelectedViewIndices.push(index)}}this.grid.setSelectedRows(newSelectedViewIndices)}},setSelectedRows:function(rows){this.grid.setSelectedRows(rows)},setFilter:function(filter){this.filter=filter;this._updateMappings();this.grid.invalidate();this.trigger("filter")},getFilter:function(){return this.filter},autosizeColumns:function(){var columns=this.grid.getColumns();var items=this.getItems();if(!items||items.length===0||!columns||columns.length===0){return}var gridWidth=this.options.$el.width()-30;if(gridWidth<=0){return}this.columnsAutosized=true;if(columns.length>-1){var div=document.createElement("div");document.body.appendChild(div);var $d=$(div);$d.css({position:"absolute",left:-1e3,top:-1e3});var $row=$('<div class="slick-table">'+'<div class="ui-state-default slick-header-column slick-header-sortable ui-sortable-handle"></div>'+'<div class="ui-widget-content slick-row"><div class="slick-cell selected"></div></div>'+"</div>");var $cell=$row.find(".slick-cell");var $header=$row.find(".slick-header-column");$row.appendTo($d);var maxWidth=Math.min(parseInt(gridWidth/2),400);var getColumnWidth=function(column){var w=$header.html(column.name).outerWidth()+13;if(column.prototypeValue){$cell.html(column.prototypeValue);w=Math.max($cell.outerWidth(),w)}else{for(var i=0,nrows=Math.min(items.length,10);i<nrows;i++){var html=column.formatter(i,null,column.getter(items[i]),column,items[i]);var $html=$(html);$html.find(".slick-cell-wrapper").attr("class","");$cell.html($html);w=Math.max($cell.outerWidth(),w)}}column.width=parseInt(Math.min(maxWidth,w))};var totalWidth=0;for(var i=0;i<columns.length;i++){getColumnWidth(columns[i]);totalWidth+=columns[i].width}if(totalWidth<gridWidth){}else if(totalWidth>gridWidth){}$d.remove();this.grid.resizeCanvas()}}};morpheus.Util.extend(morpheus.Grid,morpheus.Events);morpheus.AutoTooltips2=function(options){var _grid;var _self=this;var tip;function init(grid){_grid=grid;$(_grid.getCanvasNode()).on("mouseover",".slick-row",showToolTip);$(_grid.getCanvasNode()).on("mouseout",".slick-row",hideToolTip);$(_grid.getCanvasNode()).on("mouseup",hideAll)}function destroy(){$(_grid.getCanvasNode()).off("mouseover",showToolTip);$(_grid.getCanvasNode()).off("mouseout",hideToolTip);$(_grid.getCanvasNode()).off("mouseup",hideAll)}function hideToolTip(e){var cell=_grid.getCellFromEvent(e);if(cell){var $node=$(_grid.getCellNode(cell.row,cell.cell));if($node.data("bs.tooltip")){$node.tooltip("hide")}}}function hideAll(){$(_grid.getCanvasNode()).find("[data-original-title]").attr("data-original-title","").tooltip("hide")}function hideHeaderToolTip(e){var $node=$(e.target);if($node.data("bs.tooltip")){$node.tooltip("hide")}}function showHeaderToolTip(e){var show=false;var $node=$(e.target);if($node[0].scrollWidth>$node[0].offsetWidth){show=true;var $name=$node.find(".slick-column-name");if(!$node.data("bs.tooltip")){$node.tooltip({placement:"auto",html:true,container:"body",trigger:"manual"})}$node.attr("data-original-title",$name.text());if(show){$node.tooltip("show")}else{$node.tooltip("hide")}}}function showToolTip(e){var cell=_grid.getCellFromEvent(e);if(cell){var $node=$(_grid.getCellNode(cell.row,cell.cell));var text="";var c=_grid.getColumns()[cell.cell];var show=false;var $checkNode=$node.find(".slick-cell-wrapper");if(c.alwaysShowTooltip||$checkNode[0].scrollWidth>$checkNode[0].offsetWidth){var item=_grid.getDataItem(cell.row);text=c.tooltip(item,c.getter(item));show=true}$node.attr("data-original-title",text);var hasTip=$node.data("bs.tooltip");if(!hasTip){$node.tooltip({placement:"auto",html:true,container:"body",trigger:"manual"})}if(show){$node.tooltip("show")}else if(hasTip){$node.tooltip("hide")}}}function handleHeaderMouseEnter(e,args){var column=args.column,$node=$(e.target).closest(".slick-header-column");if(!column.toolTip){$node.attr("title",$node.innerWidth()<$node[0].scrollWidth?column.name:"")}}$.extend(this,{init:init,destroy:destroy})};morpheus.CombinedGridFilter=function(){this.filters=[]};morpheus.CombinedGridFilter.prototype={add:function(filter){this.filters.push(filter)},getFilters:function(){return this.filters},get:function(index){return this.filters[index]},set:function(index,f){this.filters[index]=f},init:function(){for(var i=0;i<this.filters.length;i++){this.filters[i].init()}this.activeFilters=this.filters.filter(function(f){return!f.isEmpty()});this.nActiveFilters=this.activeFilters.length},accept:function(item){for(var i=0;i<this.nActiveFilters;i++){if(!this.activeFilters[i].accept(item)){return false}}return true},isEmpty:function(){return this.activeFilters.length===0}};morpheus.HeatMapColorSchemeChooser=function(options){var _this=this;this.$div=$("<div></div>");this.currentValue=null;this.legend=new morpheus.LegendWithStops;this.colorScheme=options.colorScheme||new morpheus.HeatMapColorScheme(new morpheus.Project(new morpheus.Dataset({rows:0,columns:0})));this.legend.on("added",function(e){var fractions=_this.colorScheme.getFractions();fractions.push(e.fraction);var colors=_this.colorScheme.getColors();colors.push("black");_this.colorScheme.setFractions({fractions:fractions,colors:colors});var newIndex=_this.getFractionIndex(e.fraction,"black");_this.setSelectedIndex(newIndex);_this.fireChanged()}).on("selectedIndex",function(e){_this.setSelectedIndex(e.selectedIndex)}).on("delete",function(index){_this.deleteSelectedStop()}).on("moved",function(e){var fraction=e.fraction;var fractions=_this.colorScheme.getFractions();fractions[_this.legend.selectedIndex]=fraction;var color=_this.colorScheme.getColors()[_this.legend.selectedIndex];_this.colorScheme.setFractions({fractions:fractions,colors:_this.colorScheme.getColors()});_this.legend.selectedIndex=_this.getFractionIndex(e.fraction,color);var fractionToValue=d3.scale.linear().domain([0,1]).range([_this.colorScheme.getMin(),_this.colorScheme.getMax()]).clamp(true);_this.formBuilder.setValue("selected_value",fractionToValue(fractions[_this.legend.selectedIndex]));_this.fireChanged()});var $row=$("<div></div>");$row.css("height","50px").css("width","300px").css("margin-left","auto").css("margin-right","auto");$row.appendTo(this.$div);$(this.legend.canvas).appendTo($row);var formBuilder=new morpheus.FormBuilder;var items=[];items=items.concat({name:"selected_color",type:"color",style:"max-width: 50px;"},{name:"selected_value",type:"text",style:"max-width: 100px;"},[{name:"delete",type:"button",value:"Delete Selected Color Stop"},{name:"add",type:"button",value:"Add Color Stop"}],{name:"minimum",type:"text",style:"max-width: 100px;"},{name:"maximum",type:"text",style:"max-width: 100px;"});if(options.showRelative){items=items.concat({name:"relative_color_scheme",type:"checkbox",help:"A relative color scheme uses the minimum and maximum values in each row"+" to convert values to colors"});items=items.concat({name:"transform_values",type:"select",value:0,options:[{name:"None",value:0},{name:"Subtract row mean, divide by row standard deviation",value:morpheus.AbstractColorSupplier.Z_SCORE},{name:"Subtract row median, divide by row median absolute deviation",value:morpheus.AbstractColorSupplier.ROBUST_Z_SCORE}]})}items=items.concat({name:"missing_color",type:"color",style:"max-width: 50px;"});items.push({name:"stepped_colors",type:"checkbox",value:false,help:"Intervals include left end point and exclude right end point, except for the highest interval"});_.each(items,function(item){formBuilder.append(item)});this.getFractionIndex=function(fraction,color){var fractions=_this.colorScheme.getFractions();var colors=_this.colorScheme.getColors();for(var i=0,len=fractions.length;i<len;i++){if(fractions[i]===fraction&&colors[i]===color){return i}}return-1};this.$div.append(formBuilder.$form);formBuilder.$form.find("[name^=selected],[name=delete]").prop("disabled",true);formBuilder.$form.find("[name=add]").on("click",function(e){var fractions=_this.colorScheme.getFractions();var val=.5;while(val>=0&&_.indexOf(fractions,val)!==-1){val-=.1}val=Math.max(0,val);fractions.push(val);var colors=_this.colorScheme.getColors();colors.push("black");_this.colorScheme.setFractions({fractions:fractions,colors:colors});var newIndex=_this.getFractionIndex(e.fraction,"black");_this.setSelectedIndex(newIndex);_this.fireChanged()});formBuilder.$form.find("[name=delete]").on("click",function(e){_this.deleteSelectedStop()});formBuilder.$form.find("[name=transform_values]").on("change",function(e){_this.colorScheme.setTransformValues(parseInt(formBuilder.getValue("transform_values")));_this.fireChanged()});formBuilder.$form.on("keyup","[name=selected_value]",_.debounce(function(e){var val=parseFloat($(this).val());if(!isNaN(val)){_this.setSelectedValue(val);_this.fireChanged()}},100));formBuilder.$form.on("change","[name=selected_color]",function(e){var colors=_this.colorScheme.getColors();colors[_this.legend.selectedIndex]=$(this).val();_this.colorScheme.setFractions({fractions:_this.colorScheme.getFractions(),colors:colors});_this.fireChanged()});formBuilder.$form.on("change","[name=missing_color]",function(e){var color=$(this).val();_this.colorScheme.setMissingColor(color);_this.fireChanged(false)});formBuilder.$form.on("change","[name=stepped_colors]",function(e){_this.colorScheme.setStepped($(this).prop("checked"));_this.fireChanged()});formBuilder.$form.on("keyup","[name=minimum]",_.debounce(function(e){var val=parseFloat($(this).val());if(!isNaN(val)){_this.colorScheme.setMin(val);_this.setSelectedIndex(_this.legend.selectedIndex);_this.fireChanged(false)}},100));formBuilder.$form.on("keyup","[name=maximum]",_.debounce(function(e){var val=parseFloat($(this).val());if(!isNaN(val)){_this.colorScheme.setMax(val);_this.setSelectedIndex(_this.legend.selectedIndex);_this.fireChanged(false)}},100));formBuilder.$form.on("change","[name=relative_color_scheme]",_.throttle(function(e){_this.legend.selectedIndex=-1;var scalingMode=$(this).prop("checked")?morpheus.HeatMapColorScheme.ScalingMode.RELATIVE:morpheus.HeatMapColorScheme.ScalingMode.FIXED;_this.colorScheme.setScalingMode(scalingMode);_this.setColorScheme(_this.colorScheme);_this.fireChanged()},100));this.formBuilder=formBuilder};morpheus.HeatMapColorSchemeChooser.prototype={deleteSelectedStop:function(){var fractions=this.colorScheme.getFractions();fractions.splice(this.legend.selectedIndex,1);var colors=this.colorScheme.getColors();colors.splice(this.legend.selectedIndex,1);this.colorScheme.setFractions({fractions:fractions,colors:colors});this.formBuilder.$form.find("[name^=selected],[name=delete]").prop("disabled",true);this.legend.setSelectedIndex(-1);this.fireChanged()},setSelectedValue:function(val){var valueToFraction=d3.scale.linear().domain([this.colorScheme.getMin(),this.colorScheme.getMax()]).range([0,1]).clamp(true);var fractions=this.colorScheme.getFractions();var fraction=valueToFraction(val);fractions[this.legend.selectedIndex]=fraction;var color=this.colorScheme.getColors()[this.legend.selectedIndex];this.colorScheme.setFractions({fractions:fractions,colors:this.colorScheme.getColors()});this.legend.selectedIndex=this.getFractionIndex(fraction,color)},setSelectedIndex:function(index){var fractions=this.colorScheme.getFractions();if(index>=fractions.length){index=-1}this.legend.setSelectedIndex(index);var formBuilder=this.formBuilder;formBuilder.$form.find("[name^=selected],[name=delete]").prop("disabled",this.legend.selectedIndex===-1);if(this.legend.selectedIndex!==-1){var fractionToValue=d3.scale.linear().domain([0,1]).range([this.colorScheme.getMin(),this.colorScheme.getMax()]).clamp(true);formBuilder.setValue("selected_value",fractionToValue(fractions[this.legend.selectedIndex]));var context=this.legend.canvas.getContext("2d");var colors=this.colorScheme.getColors();context.fillStyle=colors[this.legend.selectedIndex];formBuilder.setValue("selected_color",context.fillStyle)}else{formBuilder.setValue("selected_value","")}this.draw()},setMinMax:function(){if(this.colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){this.colorScheme.setMin(0);this.colorScheme.setMax(1)}},dispose:function(){this.off("change");this.legend.destroy();this.formBuilder.$form.off("keyup","input");this.formBuilder.$form.off("change","[name=relative_color_scheme]")},restoreCurrentValue:function(){if(this.colorScheme.setCurrentValue){this.colorScheme.setCurrentValue(this.currentValue)}},setCurrentValue:function(value){this.currentValue=value;if(this.colorScheme&&this.colorScheme.setCurrentValue){this.colorScheme.setCurrentValue(this.currentValue)}this.setColorScheme(this.colorScheme)},setColorScheme:function(colorScheme){this.colorScheme=colorScheme;this.setMinMax();if(colorScheme.setCurrentValue){colorScheme.setCurrentValue(this.currentValue)}this.formBuilder.setValue("relative_color_scheme",colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE?true:false);this.formBuilder.setValue("transform_values",colorScheme.getTransformValues());this.formBuilder.setEnabled("transform_values",colorScheme.getScalingMode()!==morpheus.HeatMapColorScheme.ScalingMode.RELATIVE);this.formBuilder.$form.find("[name=minimum],[name=maximum]").prop("disabled",colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE);this.formBuilder.setValue("minimum",this.colorScheme.getMin());this.formBuilder.setValue("maximum",this.colorScheme.getMax());this.formBuilder.setValue("stepped_colors",this.colorScheme.isStepped());this.formBuilder.setValue("missing_color",this.colorScheme.getMissingColor());this.draw()},getFractionToStopPix:function(){return d3.scale.linear().clamp(true).domain([0,1]).range([this.legend.border,this.legend.getUnscaledWidth()-this.legend.border])},fireChanged:function(noreset){this.trigger("change");if(noreset!==false){this.setColorScheme(this.colorScheme)}},draw:function(){var colorScheme=this.colorScheme;if(colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){colorScheme.setMin(0);colorScheme.setMax(1)}var fractions=colorScheme.getFractions();var colors=colorScheme.getColors();var fractionToStopPix=this.getFractionToStopPix();this.legend.draw(fractions,colors,colorScheme.isStepped(),fractionToStopPix)}};morpheus.Util.extend(morpheus.HeatMapColorSchemeChooser,morpheus.Events);morpheus.HeatMapColorSchemeLegend=function(heatMap,$keyContent){var colorScheme=heatMap.heatmap.getColorScheme();var colorByValues=colorScheme.getColorByValues();var totalHeight;$keyContent.empty();var ntracks=colorByValues.length;colorByValues.forEach(function(value){if(value!=null||ntracks===1){if(value!="null"){var $label=$('<div style="overflow:hidden;text-overflow:'+' ellipsis;width:250px;max-width:250px;">'+value+"</div>");$keyContent.append($label);totalHeight+=$label.height()}var trackLegend=new morpheus.ColorSupplierLegend(colorScheme,value);$(trackLegend.canvas).css("position","");trackLegend.repaint();trackLegend.on("selectionChanged",function(){heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()});$keyContent.append($(trackLegend.canvas));totalHeight+=trackLegend.getUnscaledHeight()}});if(heatMap.options.$key){$keyContent.append(heatMap.options.$key);totalHeight+=heatMap.options.$key.height()}var $edit=$('<div style="padding-left:4px; display:inline;"><a data-name="options"'+' href="#">Edit</a></div>');$edit.find("[data-name=options]").on("click",function(e){e.preventDefault();heatMap.showOptions();morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"options"})});totalHeight+=$edit.height();$keyContent.append($edit);$keyContent.css({"text-overflow":"ellipsis",overflow:"hidden",width:250+"px",height:totalHeight+"px"})};morpheus.HeatMapColorSchemeLegend.drawColorScheme=function(context,colorScheme,width,printing,hideText,legendHeight){if(!legendHeight){legendHeight=12}context.font="11px "+morpheus.CanvasUtil.getFontFamily(context);var names=colorScheme.getNames();var hasNames=names!=null;if(hasNames){morpheus.HeatMapColorSchemeLegend.drawColorSchemeVertically(context,colorScheme,colorScheme.getHiddenValues(),printing)}else{morpheus.HeatMapColorSchemeLegend.draw(context,colorScheme.getFractions(),colorScheme.getColors(),width,legendHeight,colorScheme.isStepped());context.strokeStyle="LightGrey";context.strokeRect(0,0,width,legendHeight);if(hideText){return}var map=d3.scale.linear().domain([0,1]).range([0,width]).clamp(true);var fractionToValue=d3.scale.linear().domain([0,1]).range([colorScheme.getMin(),colorScheme.getMax()]).clamp(true);context.textAlign="center";context.textBaseline="top";context.fillStyle="black";if(colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){context.fillText("row min",0,14);context.fillText("row max",width,legendHeight+2)}else{var fractions=colorScheme.getFractions();var lastTextPixEnd=-1;var halfway=parseInt(fractions.length/2);for(var i=0;i<halfway;i++){var pix=map(fractions[i]);var text="";if(hasNames){text=names[i]!=""?names[i]+" ("+fractionToValue(fractions[i])+")":names[i]}else{text=morpheus.Util.nf(fractionToValue(fractions[i]))}var textWidth=context.measureText(text).width;if(pix>lastTextPixEnd){context.fillText(text,pix,legendHeight+2)}lastTextPixEnd=pix+textWidth/2}var lastTextPixStart=1e4;for(var i=fractions.length-1;i>=halfway;i--){var pix=map(fractions[i]);var text="";if(hasNames){text=names[i]!=""?names[i]+" ("+fractionToValue(fractions[i])+")":names[i]}else{text=morpheus.Util.nf(fractionToValue(fractions[i]))}var textWidth=context.measureText(text).width;var textPixEnd=pix+textWidth/2;if(textPixEnd<lastTextPixStart){context.fillText(text,pix,legendHeight+2);lastTextPixStart=pix-textWidth/2}}}}};morpheus.HeatMapColorSchemeLegend.drawColorSchemeVertically=function(context,colorScheme,hiddenValues,printing){var fractionToValue=d3.scale.linear().domain([0,1]).range([colorScheme.getMin(),colorScheme.getMax()]).clamp(true);context.textAlign="left";context.textBaseline="top";context.fillStyle="black";var fractions=colorScheme.getFractions();var colors=colorScheme.getColors();var names=colorScheme.getNames();context.strokeStyle="LightGrey";var xpix=0;var ypix=0;context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);for(var i=0;i<colors.length;i++){var name=names[i];if(name!=null){context.fillStyle=colors[i];context.fillRect(xpix,ypix,12,12);context.strokeRect(xpix,ypix,12,12);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;if(hiddenValues&&!printing){var value=fractionToValue(fractions[i]);context.font="12px FontAwesome";if(!hiddenValues.has(value)){context.fillText("",-14,ypix)}context.font="12px "+morpheus.CanvasUtil.getFontFamily(context)}context.fillText(name,xpix+16,ypix)}ypix+=14}};morpheus.HeatMapColorSchemeLegend.draw=function(context,fractions,colors,width,height,stepped){if(!stepped){var gradient=context.createLinearGradient(0,0,width,height);for(var i=0,length=fractions.length;i<length;i++){gradient.addColorStop(fractions[i],colors[i])}context.fillStyle=gradient;context.fillRect(0,0,width,height)}else{var map=d3.scale.linear().domain([0,1]).range([0,width]).clamp(true);for(var i=0,length=fractions.length;i<length;i++){context.fillStyle=colors[i];var x1=map(fractions[i]);var x2=i===length-1?width:map(fractions[i+1]);context.fillRect(Math.min(x1,x2),0,Math.abs(x2-x1),height)}}};morpheus.ColorSupplierLegend=function(colorScheme,value){morpheus.AbstractCanvas.call(this,false);var _this=this;this.value=value;this.colorScheme=colorScheme;colorScheme.setCurrentValue(value);var hiddenValues=colorScheme.getHiddenValues();var names=colorScheme.getNames();var hasNames=names!=null;var legendHeight=hasNames?names.length*14:30;var bounds={width:250,height:legendHeight};this.hasNames=hasNames;this.setBounds(bounds);if(hasNames&&hiddenValues){$(this.canvas).on("click",function(e){e.preventDefault();e.stopPropagation();var clickedRow=Math.floor((e.clientY-_this.canvas.getBoundingClientRect().top)/14);var fractionToValue=d3.scale.linear().domain([0,1]).range([colorScheme.getMin(),colorScheme.getMax()]).clamp(true);var fractions=colorScheme.getFractions();var value=fractionToValue(fractions[clickedRow]);if(!hiddenValues.has(value)){hiddenValues.add(value)}else{hiddenValues.remove(value)}_this.trigger("selectionChanged");_this.repaint()})}};morpheus.ColorSupplierLegend.prototype={draw:function(clip,context){var colorScheme=this.colorScheme;colorScheme.setCurrentValue(this.value);context.translate(this.hasNames?14:(this.getUnscaledWidth()-200)/2,0);morpheus.HeatMapColorSchemeLegend.drawColorScheme(context,colorScheme,200)}};morpheus.Util.extend(morpheus.ColorSupplierLegend,morpheus.Events);morpheus.Util.extend(morpheus.ColorSupplierLegend,morpheus.AbstractCanvas);morpheus.HeatMapColorScheme=function(project,scheme){this.project=project;var _this=this;this.separateColorSchemeForRowMetadataField=null;this.rowValueToColorSupplier={};this.value=null;if(scheme){if(scheme.valueToColorScheme){this.fromJSON(scheme)}else{this.rowValueToColorSupplier[null]=this.fromJSON(scheme);this.currentColorSupplier=this.rowValueToColorSupplier[this.value]}}project.on("rowFilterChanged columnFilterChanged rowSortOrderChanged columnSortOrderChanged datasetChanged",function(){_this.projectUpdated()});this.projectUpdated()};morpheus.HeatMapColorScheme.Predefined={};morpheus.HeatMapColorScheme.Predefined.CN=function(){return{scalingMode:"fixed",values:[-2,-.1,.1,2],colors:["#0000ff","#ffffff","#ffffff","#ff0000"]}};morpheus.HeatMapColorScheme.Predefined.BINARY=function(){return{scalingMode:"fixed",values:[0,1],colors:["#ffffff","black"]}};morpheus.HeatMapColorScheme.Predefined.RELATIVE=function(){return{scalingMode:"relative"}};morpheus.HeatMapColorScheme.Predefined.MAF=function(){return{scalingMode:"fixed",stepped:true,values:[0,1,2,3,4,5,6,7],names:["","Synonymous","In Frame Indel","Other Non-Synonymous","Missense","Splice Site","Frame Shift","Nonsense"],colors:["#ffffff","#4daf4a","#ffff33","#a65628","#377eb8","#984ea3","#ff7f00","#e41a1c"]}};morpheus.HeatMapColorScheme.Predefined.ZS=function(){return{scalingMode:"fixed",values:[-10,-2,2,10],colors:["#0000ff","#ffffff","#ffffff","#ff0000"]}};morpheus.HeatMapColorScheme.ScalingMode={RELATIVE:0,FIXED:1};morpheus.HeatMapConditions=function(){this.array=[]};morpheus.HeatMapConditions.prototype={insert:function(index,c){this.array.splice(index,0,c)},add:function(c){this.array.push(c)},getConditions:function(){return this.array},remove:function(index){this.array.splice(index,1)},copy:function(){var c=new morpheus.HeatMapConditions;this.array.forEach(function(cond){c.array.push(_.clone(cond))});return c}};morpheus.HeatMapColorScheme.prototype={getColors:function(){return this.currentColorSupplier.getColors()},setMissingColor:function(color){this.currentColorSupplier.setMissingColor(color)},getHiddenValues:function(){return this.currentColorSupplier.getHiddenValues?this.currentColorSupplier.getHiddenValues():null},getMissingColor:function(){return this.currentColorSupplier.getMissingColor()},getScalingMode:function(){return this.currentColorSupplier.getScalingMode()},getSizer:function(){return this.currentColorSupplier.getSizer()},getConditions:function(){return this.currentColorSupplier.getConditions()},setScalingMode:function(scalingMode){this.currentColorSupplier.setScalingMode(scalingMode)},getFractions:function(){return this.currentColorSupplier.getFractions()},getNames:function(){return this.currentColorSupplier.getNames()},getMin:function(){return this.currentColorSupplier.getMin()},getMax:function(){return this.currentColorSupplier.getMax()},setMin:function(min){this.currentColorSupplier.setMin(min)},setMax:function(max){this.currentColorSupplier.setMax(max)},isStepped:function(){return this.currentColorSupplier.isStepped()},setFractions:function(options){this.currentColorSupplier.setFractions(options)},setTransformValues:function(options){this.currentColorSupplier.setTransformValues(options);this.cachedRowStats.cachedRow=-1},getTransformValues:function(){return this.currentColorSupplier.getTransformValues()},setStepped:function(stepped){var oldColorSupplier=this.currentColorSupplier;var newColorSupplier=stepped?new morpheus.SteppedColorSupplier:new morpheus.GradientColorSupplier;newColorSupplier.sizer=oldColorSupplier.getSizer();newColorSupplier.array=oldColorSupplier.getConditions();newColorSupplier.setScalingMode(oldColorSupplier.getScalingMode());newColorSupplier.setMin(oldColorSupplier.getMin());newColorSupplier.setMax(oldColorSupplier.getMax());newColorSupplier.setFractions({fractions:oldColorSupplier.getFractions(),colors:oldColorSupplier.getColors()});this.currentColorSupplier=newColorSupplier;this.rowValueToColorSupplier[this.value]=this.currentColorSupplier},toJSON:function(){var json={};var _this=this;if(this.separateColorSchemeForRowMetadataField!=null){json.separateColorSchemeForRowMetadataField=this.separateColorSchemeForRowMetadataField}json.valueToColorScheme={};_.each(_.keys(this.rowValueToColorSupplier),function(key){json.valueToColorScheme[key]=morpheus.AbstractColorSupplier.toJSON(_this.rowValueToColorSupplier[key])});return json},fromJSON:function(json){var _this=this;if(json.separateColorSchemeForRowMetadataField){this.separateColorSchemeForRowMetadataField=json.separateColorSchemeForRowMetadataField;this.vector=this.project.getSortedFilteredDataset().getRowMetadata().getByName(this.separateColorSchemeForRowMetadataField)}this.rowValueToColorSupplier={};var obj=json.valueToColorScheme||json.colorSchemes;if(obj==null){var colorSupplier=morpheus.AbstractColorSupplier.fromJSON(json);_this.rowValueToColorSupplier["null"]=colorSupplier}else{_.each(_.keys(obj),function(key){var colorSupplier=morpheus.AbstractColorSupplier.fromJSON(obj[key]);_this.rowValueToColorSupplier[key]=colorSupplier})}this._ensureColorSupplierExists()},copy:function(project){var _this=this;var c=new morpheus.HeatMapColorScheme(project);c.separateColorSchemeForRowMetadataField=this.separateColorSchemeForRowMetadataField;if(c.separateColorSchemeForRowMetadataField!=null){c.vector=project.getSortedFilteredDataset().getRowMetadata().getByName(c.separateColorSchemeForRowMetadataField)}if(c.vector==null){c.separateColorSchemeForRowMetadataField=null}_.each(_.keys(this.rowValueToColorSupplier),function(key){c.rowValueToColorSupplier[key]=_this.rowValueToColorSupplier[key].copy()});c.value=this.value;c.currentColorSupplier=c.rowValueToColorSupplier[c.value];return c},setSeparateColorSchemeForRowMetadataField:function(separateColorSchemeForRowMetadataField){if(separateColorSchemeForRowMetadataField!=this.separateColorSchemeForRowMetadataField){this.separateColorSchemeForRowMetadataField=separateColorSchemeForRowMetadataField;this.vector=this.project.getSortedFilteredDataset().getRowMetadata().getByName(separateColorSchemeForRowMetadataField);var _this=this;_.each(_.keys(this.rowValueToColorSupplier),function(key){delete _this.rowValueToColorSupplier[key]})}},getProject:function(){return this.project},getSeparateColorSchemeForRowMetadataField:function(){return this.separateColorSchemeForRowMetadataField},getColorByValues:function(){return _.keys(this.rowValueToColorSupplier)},projectUpdated:function(){var dataset=this.project.getSortedFilteredDataset();if(this.separateColorSchemeForRowMetadataField!=null){this.vector=this.project.getSortedFilteredDataset().getRowMetadata().getByName(this.separateColorSchemeForRowMetadataField)}this.cachedRowStats=new morpheus.RowStats(dataset)},setColorSupplierForCurrentValue:function(colorSupplier){this.rowValueToColorSupplier[this.value]=colorSupplier;this.currentColorSupplier=colorSupplier},setCurrentValue:function(value){this.value=value;this._ensureColorSupplierExists()},isSizeBy:function(){this.currentColorSupplier.isSizeBy()},getCurrentColorSupplier:function(){return this.currentColorSupplier},getColor:function(row,column,val){if(this.vector!==undefined){var tmp=this.vector.getValue(row);if(this.value!==tmp){this.value=tmp;this._ensureColorSupplierExists()}}if(this.currentColorSupplier.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){if(this.cachedRowStats.maybeUpdateRelative(row)){this.currentColorSupplier.setMin(this.cachedRowStats.rowCachedMin);this.currentColorSupplier.setMax(this.cachedRowStats.rowCachedMax)}}else if(this.currentColorSupplier.getTransformValues()&&this.cachedRowStats.cachedRow!==row){this.cachedRowStats.cacheTransformValues(row,this.currentColorSupplier.getTransformValues());val=(val-this.cachedRowStats.rowCachedMean)/this.cachedRowStats.rowCachedStandardDeviation}return this.currentColorSupplier.getColor(row,column,val)},_ensureColorSupplierExists:function(){this.currentColorSupplier=this.rowValueToColorSupplier[this.value];if(this.currentColorSupplier===undefined){var cs=morpheus.AbstractColorSupplier.fromJSON({scalingMode:"relative"});this.rowValueToColorSupplier[this.value]=cs;this.currentColorSupplier=cs}}};morpheus.RowStats=function(dataset){this.datasetRowView=new morpheus.DatasetRowView(dataset);this.cachedRow=-1;this.rowCachedMax=0;this.rowCachedMin=0;this.rowCachedStandardDeviation=-1;this.rowCachedMean=-1};morpheus.RowStats.prototype={cacheTransformValues:function(row,transform){var meanFunction=transform===morpheus.AbstractColorSupplier.Z_SCORE?morpheus.Mean:morpheus.Median;var stdevFunction=transform===morpheus.AbstractColorSupplier.Z_SCORE?morpheus.StandardDeviation:morpheus.MAD;this.datasetRowView.setIndex(row);this.rowCachedMean=meanFunction(this.datasetRowView);this.rowCachedStandardDeviation=stdevFunction(this.datasetRowView,this.rowCachedMean)},maybeUpdateRelative:function(row){if(this.cachedRow!==row){this.cachedRow=row;this.datasetRowView.setIndex(row);this.rowCachedMax=-Number.MAX_VALUE;this.rowCachedMin=Number.MAX_VALUE;for(var j=0,ncols=this.datasetRowView.size();j<ncols;j++){var d=this.datasetRowView.getValue(j);if(!isNaN(d)){this.rowCachedMax=d>this.rowCachedMax?d:this.rowCachedMax;this.rowCachedMin=d<this.rowCachedMin?d:this.rowCachedMin}}if(this.rowCachedMin===this.rowCachedMax){this.rowCachedMin--}return true}return false}};morpheus.HeatMapSynchronizer=function(){this.controllers=[]};morpheus.HeatMapSynchronizer.prototype={firing:false,getProject:function(){return this.controllers[0].getProject()},zoom:function(){this.controllers[0].zoom.apply(this.controllers[0],arguments)},setTrackVisible:function(){this.controllers[0].setTrackVisible.apply(this.controllers[0],arguments)},revalidate:function(){this.controllers[0].revalidate.apply(this.controllers[0],arguments)},add:function(heatMap){var that=this;this.controllers.push(heatMap);heatMap.on("change",function(event){if(!that.firing){var source=event.source;var method=event.name;that.firing=true;_.each(that.controllers,function(c){if(c!==source){c[method].apply(c,event.arguments)}});that.firing=false}})}};morpheus.HeatMapElementCanvas=function(project){morpheus.AbstractCanvas.call(this,true);var _this=this;this.colorScheme=null;this.project=project;this.dataset=null;this.columnPositions=new morpheus.Positions;this.rowPositions=new morpheus.Positions;this.lastPosition={left:-1,right:-1,top:-1,bottom:-1};this.selectionBox=null;this.selectedRowElements=[];this.selectedColumnElements=[];project.getElementSelectionModel().on("selectionChanged",function(e){_this.repaint()});this.gridColor=morpheus.HeatMapElementCanvas.GRID_COLOR;this.gridThickness=.1;this.elementDrawCallback=null;this.drawCallback=null;this.drawValuesFormat=morpheus.Util.createNumberFormat(".2f")};morpheus.HeatMapElementCanvas.GRID_COLOR="#808080";morpheus.HeatMapElementCanvas.prototype={drawGrid:true,drawValues:false,setPropertiesFromParent:function(parentHeatMapElementCanvas){this.drawGrid=parentHeatMapElementCanvas.drawGrid;this.gridThickness=parentHeatMapElementCanvas.gridThickness;this.gridColor=parentHeatMapElementCanvas.gridColor;this.drawValues=parentHeatMapElementCanvas.drawValues},updateRowSelectionCache:function(repaint){this.selectedRowElements=morpheus.HeatMapElementCanvas.getSelectedSpans(this.project.getRowSelectionModel().getViewIndices());if(repaint){this.repaint()}},updateColumnSelectionCache:function(repaint){this.selectedColumnElements=morpheus.HeatMapElementCanvas.getSelectedSpans(this.project.getColumnSelectionModel().getViewIndices());if(repaint){this.repaint()}},setGridColor:function(gridColor){this.gridColor=gridColor},getGridColor:function(){return this.gridColor},setGridThickness:function(gridThickness){this.gridThickness=gridThickness},getGridThickness:function(){return this.gridThickness},getColorScheme:function(){return this.colorScheme},isDrawGrid:function(){return this.drawGrid},setDrawGrid:function(drawGrid){this.drawGrid=drawGrid},getDrawValuesFormat:function(){return this.drawValuesFormat},setDrawValuesFormat:function(f){if(typeof f==="object"){f=morpheus.Util.createNumberFormat(f.pattern)}this.drawValuesFormat=f},setDrawValues:function(drawValues){this.drawValues=drawValues},isDrawValues:function(){return this.drawValues},setColorScheme:function(colorScheme){this.colorScheme=colorScheme},setDataset:function(dataset){this.dataset=dataset;this.columnPositions.setLength(this.dataset.getColumnCount());this.rowPositions.setLength(this.dataset.getRowCount());this.updateRowSelectionCache(false);this.updateColumnSelectionCache(false)},getColumnPositions:function(){return this.columnPositions},getRowPositions:function(){return this.rowPositions},getPreferredSize:function(context){var w=Math.ceil(this.columnPositions.getPosition(this.columnPositions.getLength()-1)+this.columnPositions.getItemSize(this.columnPositions.getLength()-1));var h=Math.ceil(this.rowPositions.getPosition(this.rowPositions.getLength()-1)+this.rowPositions.getItemSize(this.rowPositions.getLength()-1));return{width:w,height:h}},prePaint:function(clip,context){var lastPosition=this.lastPosition;var columnPositions=this.columnPositions;var rowPositions=this.rowPositions;var left=morpheus.Positions.getLeft(clip,columnPositions);var right=morpheus.Positions.getRight(clip,columnPositions);var top=morpheus.Positions.getTop(clip,rowPositions);var bottom=morpheus.Positions.getBottom(clip,rowPositions);if(this.invalid||left!==lastPosition.left||right!==lastPosition.right||top!==lastPosition.top||bottom!==lastPosition.bottom){lastPosition.right=right;lastPosition.left=left;lastPosition.top=top;lastPosition.bottom=bottom;this.invalid=true}},postPaint:function(clip,context){morpheus.CanvasUtil.resetTransform(context);var project=this.project;context.strokeStyle="Grey";context.lineWidth=1;var rowPositions=this.getRowPositions();var columnPositions=this.getColumnPositions();if(project.getHoverColumnIndex()>=0||project.getHoverRowIndex()>=0){var height=rowPositions.getItemSize(project.getHoverColumnIndex());var width=columnPositions.getItemSize(project.getHoverColumnIndex());var y=project.getHoverRowIndex()===-1?rowPositions.getPosition(rowPositions.getLength()-1):rowPositions.getPosition(project.getHoverRowIndex());var x=project.getHoverColumnIndex()===-1?columnPositions.getPosition(0):columnPositions.getPosition(project.getHoverColumnIndex());if(project.getHoverColumnIndex()!==-1){context.strokeRect(x-clip.x,0,width,this.getUnscaledHeight())}if(project.getHoverRowIndex()!==-1){context.strokeRect(0,y-clip.y,this.getUnscaledWidth(),height)}if(project.getHoverColumnIndex()!==-1&&project.getHoverRowIndex()!==-1){context.strokeStyle="black";context.lineWidth=3;context.strokeRect(x-clip.x+1.5,y-clip.y+1.5,width-1.5,height-1.5);if(project.isSymmetric()){var y2=rowPositions.getPosition(project.getHoverColumnIndex());var x2=columnPositions.getPosition(project.getHoverRowIndex());context.strokeRect(x2-clip.x+1.5,y2-clip.y+1.5,width-1.5,height-1.5)}}}var left=morpheus.Positions.getLeft(clip,columnPositions);var right=morpheus.Positions.getRight(clip,columnPositions);var top=morpheus.Positions.getTop(clip,rowPositions);var bottom=morpheus.Positions.getBottom(clip,rowPositions);context.strokeStyle="rgb(0,0,0)";context.lineWidth=2;context.translate(-clip.x,-clip.y);var selectedElements=project.getElementSelectionModel().getViewIndices();if(selectedElements!=null){selectedElements.forEach(function(id){var rowIndex=id.getArray()[0];var columnIndex=id.getArray()[1];if(rowIndex>=top&&rowIndex<bottom&&columnIndex>=left&&columnIndex<right){var rowSize=rowPositions.getItemSize(rowIndex);var py=rowPositions.getPosition(rowIndex);var columnSize=columnPositions.getItemSize(columnIndex);var px=columnPositions.getPosition(columnIndex);context.strokeRect(px+1.5,py+1.5,columnSize-1.5,rowSize-1.5)}})}context.strokeStyle="rgb(182,213,253)";var selectedRowElements=this.selectedRowElements;var selectedColumnElements=this.selectedColumnElements;if(!(selectedRowElements.length===0&&selectedColumnElements.length===0)){if(selectedRowElements.length===0){selectedRowElements=[[top,bottom-1]]}if(selectedColumnElements.length===0){selectedColumnElements=[[left,right-1]]}}var nrows=selectedRowElements.length;var ncols=selectedColumnElements.length;if(nrows!==0||ncols!==0){for(var i=0;i<nrows;i++){var r=selectedRowElements[i];var y1=rowPositions.getPosition(r[0]);var y2=rowPositions.getPosition(r[1])+rowPositions.getItemSize(i);for(var j=0;j<ncols;j++){var c=selectedColumnElements[j];var x1=columnPositions.getPosition(c[0]);var x2=columnPositions.getPosition(c[1])+columnPositions.getItemSize(j);context.strokeRect(x1,y1,x2-x1,y2-y1)}}}if(this.selectionBox){context.strokeStyle="rgb(0,0,0)";context.lineWidth=2;if(context.setLineDash){context.setLineDash([5])}var x1=columnPositions.getPosition(this.selectionBox.x[0]);var x2=columnPositions.getPosition(this.selectionBox.x[1]);if(x2<x1){var tmp=x1;x1=x2;x2=tmp+columnPositions.getItemSize(this.selectionBox.x[0])}else{x2+=columnPositions.getItemSize(this.selectionBox.x[1])}var y1=rowPositions.getPosition(this.selectionBox.y[0]);var y2=rowPositions.getPosition(this.selectionBox.y[1]);if(y2<y1){var tmp=y1;y1=y2;y2=tmp+rowPositions.getItemSize(this.selectionBox.y[0])}else{y2+=rowPositions.getItemSize(this.selectionBox.y[1])}context.strokeRect(x1,y1,x2-x1,y2-y1);if(context.setLineDash){context.setLineDash([])}context.lineWidth=1}},setElementDrawCallback:function(elementDrawCallback){this.elementDrawCallback=elementDrawCallback},setSelectionBox:function(selectionBox){this.selectionBox=selectionBox},setDrawCallback:function(drawCallback){this.drawCallback=drawCallback},draw:function(clip,context){var columnPositions=this.columnPositions;var rowPositions=this.rowPositions;var left=morpheus.Positions.getLeft(clip,columnPositions);var right=morpheus.Positions.getRight(clip,columnPositions);var top=morpheus.Positions.getTop(clip,rowPositions);var bottom=morpheus.Positions.getBottom(clip,rowPositions);context.translate(-clip.x,-clip.y);this._draw({left:left,right:right,top:top,bottom:bottom,context:context});context.translate(clip.x,clip.y);if(this.drawCallback){this.drawCallback({clip:clip,context:context})}},_draw:function(options){var left=options.left;var right=options.right;var top=options.top;var bottom=options.bottom;var context=options.context;var fontFamily=morpheus.CanvasUtil.getFontFamily(context);var columnPositions=this.columnPositions;var rowPositions=this.rowPositions;morpheus.CanvasUtil.forceSubPixelRendering(context);context.textAlign="center";context.textBaseline="middle";var dataset=this.dataset;var colorScheme=this.colorScheme;var drawGrid=this.drawGrid;var elementDrawCallback=this.elementDrawCallback;var hasElementDrawCallback=elementDrawCallback!=null;var drawValues=this.drawValues&&columnPositions.getSize()>7&&rowPositions.getSize()>7;var nf;if(drawValues){nf=this.drawValuesFormat;var fontSize=columnPositions.getSize();context.font=fontSize+"px "+fontFamily;var textWidth=context.measureText("-99.9").width;fontSize=(columnPositions.getSize()-1)/textWidth*fontSize;fontSize=Math.min(fontSize,17);context.font=fontSize+"px "+morpheus.CanvasUtil.getFontFamily(context)}var seriesNameToIndex={};for(var i=0;i<dataset.getSeriesCount();i++){seriesNameToIndex[dataset.getName(i)]=i}var sizer;var sizeBySeriesName;var sizeBySeriesIndex;var conditions;var conditionSeriesIndices;var sizeFractionRemapper=d3.scale.linear().domain([0,1]).range([.2,1]);for(var row=top;row<bottom;row++){var rowSize=rowPositions.getItemSize(row);var py=rowPositions.getPosition(row);for(var column=left;column<right;column++){var columnSize=columnPositions.getItemSize(column);var px=columnPositions.getPosition(column);var value=dataset.getValue(row,column);context.fillStyle=colorScheme.getColor(row,column,value);if(column===left){sizer=colorScheme.getSizer();sizeBySeriesName=sizer.getSeriesName();sizeBySeriesIndex=sizeBySeriesName!=null?seriesNameToIndex[sizeBySeriesName]:undefined;conditionSeriesIndices=[];conditions=colorScheme.getConditions().getConditions();for(var ci=0,nconditions=conditions.length;ci<nconditions;ci++){conditionSeriesIndices.push(seriesNameToIndex[conditions[ci].seriesName])}}var yoffset=0;var xoffset=0;var cellRowSize=rowSize;var cellColumnSize=columnSize;if(sizeBySeriesIndex!==undefined){var sizeByValue=dataset.getValue(row,column,sizeBySeriesIndex);if(!isNaN(sizeByValue)){var sizeFraction=sizeFractionRemapper(sizer.valueToFraction(sizeByValue));cellRowSize=cellRowSize*sizeFraction;yoffset=(rowSize-cellRowSize)/2;cellColumnSize=cellColumnSize*sizeFraction;xoffset=(columnSize-cellColumnSize)/2}}if(conditions.length>0){var condition=null;for(var ci=0,nconditions=conditions.length;ci<nconditions;ci++){var cond=conditions[ci];var condValue=dataset.getValue(row,column,conditionSeriesIndices[ci]);if(!isNaN(condValue)&&cond.accept(condValue)){condition=cond;break}}if(condition!==null){if(condition.shape!=null){if(condition.inheritColor){if(sizeBySeriesIndex===undefined){xoffset=1;yoffset=1;cellRowSize-=2;cellColumnSize-=2}var x=px+xoffset+cellRowSize/2;var y=py+yoffset+cellColumnSize/2;morpheus.CanvasUtil.drawShape(context,condition.shape,x,y,Math.min(cellColumnSize,cellRowSize)/2,true)}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize);var x=px+xoffset+cellRowSize/2;var y=py+yoffset+cellColumnSize/2;context.fillStyle=condition.color;morpheus.CanvasUtil.drawShape(context,condition.shape,x,y,Math.min(cellColumnSize,cellRowSize)/4,true)}}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize)}}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize)}}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize)}if(drawValues&&cellColumnSize>7&&cellRowSize>7&&!isNaN(value)){context.fillStyle="rgb(0,0,0)";context.fillText(nf(value),px+xoffset+cellColumnSize/2,py+yoffset+cellRowSize/2,cellColumnSize)}if(hasElementDrawCallback){elementDrawCallback(context,dataset,row,column,px,py,columnSize,rowSize)}}}if(drawGrid&&rowPositions.getSize()>10&&columnPositions.getSize()>10){context.strokeStyle=this.gridColor;context.lineWidth=this.gridThickness;context.beginPath();for(var row=top;row<bottom;row++){var rowSize=rowPositions.getItemSize(row);var py=rowPositions.getPosition(row);for(var column=left;column<right;column++){var columnSize=columnPositions.getItemSize(column);var px=columnPositions.getPosition(column);var grid=columnSize>10&&rowSize>10;if(grid){context.rect(px,py,columnSize,rowSize)}}}context.stroke()}context.lineWidth=1}};morpheus.Util.extend(morpheus.HeatMapElementCanvas,morpheus.AbstractCanvas);morpheus.HeatMapElementCanvas.getSelectedSpans=function(set){var array=[];if(set.size()>0){var index=0;var start=index;var viewIndices=set.values();viewIndices.sort(function(a,b){return a===b?0:a<b?-1:1});var length=viewIndices.length;while(index<length){var prior=index===0?viewIndices[0]:viewIndices[index-1];var current=viewIndices[index];if(current-prior>1){array.push([viewIndices[start],viewIndices[index-1]]);start=index}index++}if(start==0){array.push([viewIndices[0],viewIndices[viewIndices.length-1]])}else{array.push([viewIndices[start],viewIndices[index-1]])}}return array};morpheus.KeyboardCharMap=["","","","CANCEL","","","HELP","","BACKSPACE","TAB","","","CLEAR","ENTER","ENTER_SPECIAL","","SHIFT","CONTROL","ALT","PAUSE","CAPS_LOCK","KANA","EISU","JUNJA","FINAL","HANJA","","Escape","CONVERT","NONCONVERT","ACCEPT","MODECHANGE","Space","Page Up","Page Down","End","Home","Left","Up","Right","Down","SELECT","PRINT","EXECUTE","PRINTSCREEN","INSERT","Delete","","0","1","2","3","4","5","6","7","8","9","COLON","SEMICOLON","LESS_THAN","Equals","GREATER_THAN","QUESTION_MARK","AT","A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z","OS_KEY","","CONTEXT_MENU","","SLEEP","0","1","2","3","4","5","6","7","8","9","MULTIPLY","+","SEPARATOR","SUBTRACT","DECIMAL","DIVIDE","F1","F2","F3","F4","F5","F6","F7","F8","F9","F10","F11","F12","F13","F14","F15","F16","F17","F18","F19","F20","F21","F22","F23","F24","","","","","","","","","NUM_LOCK","SCROLL_LOCK","WIN_OEM_FJ_JISHO","WIN_OEM_FJ_MASSHOU","WIN_OEM_FJ_TOUROKU","WIN_OEM_FJ_LOYA","WIN_OEM_FJ_ROYA","","","","","","","","","","CIRCUMFLEX","EXCLAMATION","DOUBLE_QUOTE","HASH","DOLLAR","PERCENT","AMPERSAND","UNDERSCORE","OPEN_PAREN","CLOSE_PAREN","ASTERISK","Plus","PIPE","-","OPEN_CURLY_BRACKET","CLOSE_CURLY_BRACKET","TILDE","","","","","VOLUME_MUTE","VOLUME_DOWN","VOLUME_UP","","","SEMICOLON","EQUALS","COMMA","MINUS","PERIOD","/","BACK_QUOTE","","","","","","","","","","","","","","","","","","","","","","","","","","","OPEN_BRACKET","BACK_SLASH","CLOSE_BRACKET","QUOTE","","META","ALTGR","","WIN_ICO_HELP","WIN_ICO_00","","WIN_ICO_CLEAR","","","WIN_OEM_RESET","WIN_OEM_JUMP","WIN_OEM_PA1","WIN_OEM_PA2","WIN_OEM_PA3","WIN_OEM_WSCTRL","WIN_OEM_CUSEL","WIN_OEM_ATTN","WIN_OEM_FINISH","WIN_OEM_COPY","WIN_OEM_AUTO","WIN_OEM_ENLW","WIN_OEM_BACKTAB","ATTN","CRSEL","EXSEL","EREOF","PLAY","ZOOM","","PA1","WIN_OEM_CLEAR",""];morpheus.HeatMapKeyListener=function(heatMap){var allActions=heatMap.getActionManager().getActions();var actions=allActions.filter(function(a){return a.cb!=null&&a.which!=null});allActions.sort(function(a,b){a=a.name.toLowerCase();b=b.name.toLowerCase();return a===b?0:a<b?-1:1});var keydown=function(e){var tagName=e.target.tagName;var found=false;var commandKey=morpheus.Util.IS_MAC?e.metaKey:e.ctrlKey;var altKey=e.altKey;var shiftKey=e.shiftKey;var which=e.which;var isInputField=tagName==="INPUT"||tagName==="SELECT"||tagName==="TEXTAREA";var acceptOptions={isInputField:isInputField,heatMap:heatMap};var shortcutMatches=function(sc){if(sc.which.indexOf(which)!==-1&&(sc.commandKey===undefined||commandKey===sc.commandKey)&&(sc.shiftKey===undefined||shiftKey===sc.shiftKey)&&(sc.accept==undefined||sc.accept(acceptOptions))){sc.cb({heatMap:heatMap});return true}};if(!isInputField){for(var i=0,n=actions.length;i<n;i++){var sc=actions[i];if(shortcutMatches(sc)){found=true;break}}}else{for(var i=0,n=actions.length;i<n;i++){var sc=actions[i];if(sc.global&&shortcutMatches(sc)){found=true;break}}}if(found){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();return false}};var $keyelement=heatMap.$tabPanel;$keyelement.on("keydown",keydown);$keyelement.on("dragover.morpheus dragenter.morpheus",function(e){e.preventDefault();e.stopPropagation()}).on("drop.morpheus",function(e){if(heatMap.options.menu.File&&heatMap.options.menu.File.indexOf("Open")!==-1&&e.originalEvent.dataTransfer&&e.originalEvent.dataTransfer.files.length){e.preventDefault();e.stopPropagation();var files=e.originalEvent.dataTransfer.files;for(var i=0;i<files.length;i++){morpheus.HeatMap.showTool(new morpheus.OpenFileTool({file:files[i]}),heatMap)}}});$keyelement.on("paste.morpheus",function(e){if(heatMap.options.toolbar.openFile){var tagName=e.target.tagName;if(tagName=="INPUT"||tagName=="SELECT"||tagName=="TEXTAREA"){return}var text=e.originalEvent.clipboardData.getData("text/plain");if(text!=null&&text.length>0){e.preventDefault();e.stopPropagation();var blob=new Blob([text]);var url=window.URL.createObjectURL(blob);morpheus.HeatMap.showTool(new morpheus.OpenFileTool({file:url}),heatMap)}}});$keyelement.on("mousewheel",function(e){var scrolly=e.deltaY*e.deltaFactor;var scrollx=e.deltaX*e.deltaFactor;var stop=false;if(e.altKey){heatMap.zoom(scrolly>0,{rows:true,columns:true});stop=true}else{if(scrolly!==0){var scrollTop=heatMap.scrollTop();if(heatMap.scrollTop(scrollTop-scrolly)!==scrollTop){stop=true}}if(scrollx!==0){var scrollLeft=heatMap.scrollLeft();if(heatMap.scrollLeft(scrollLeft+scrollx)!==scrollLeft){stop=true}}}if(stop&&heatMap.options.standalone){e.preventDefault();e.stopPropagation()}});function shortcutToString(sc){var s=["<b>"];if(sc.commandKey){s.push(morpheus.Util.COMMAND_KEY)}if(sc.shiftKey){s.push("Shift+")}if(sc.which){s.push(morpheus.KeyboardCharMap[sc.which[0]])}s.push("</b>");return s.join("")}this.showKeyMapReference=function(){var html=[];html.push('<table class="table table-condensed">');allActions.forEach(function(sc){html.push("<tr><td>");html.push(shortcutToString(sc));html.push("</td><td>");if(sc.icon){html.push('<span class="'+sc.icon+'"></span> ')}html.push(sc.name);html.push("</td></tr>")});html.push("</table>");morpheus.FormBuilder.showInModal({title:"Keyboard Shortcuts",html:html.join(""),focus:document.activeElement})}};morpheus.HeatMapOptions=function(heatMap){var items=[{name:"color_by",required:true,help:"Use a different color scheme for distinct row annotation values",type:"select",options:["(None)"].concat(morpheus.MetadataUtil.getMetadataNames(heatMap.getProject().getFullDataset().getRowMetadata())),value:heatMap.heatmap.getColorScheme().getSeparateColorSchemeForRowMetadataField()},{name:"color_by_value",required:true,type:"select",options:[]}];items.push({name:"size_by",required:true,type:"select",options:["(None)"].concat(morpheus.DatasetUtil.getSeriesNames(heatMap.getProject().getFullDataset()))});items.push({name:"size_by_minimum",title:"Size by minimum",required:true,type:"text",style:"max-width: 100px;"});items.push({name:"size_by_maximum",title:"Size by maximum",required:true,type:"text",style:"max-width: 100px;"});items.push({name:"conditional_rendering",required:true,type:"button"});items.push({type:"separator"});var createColorSchemeOptions=function(){var colorSchemeOptions=[{name:"relative",value:"relative"},{name:"binary",value:"binary"},{name:"MAF",value:"MAF"},{name:"fixed (-1.5, -0.1, 0.1, 1.5)",value:"cn"}];var savedColorSchemeKeys=[];if(localStorage.getItem("morpheus-colorScheme")!=null){savedColorSchemeKeys=_.keys(JSON.parse(localStorage.getItem("morpheus-colorScheme")))}if(savedColorSchemeKeys.length>0){colorSchemeOptions.push({divider:true});colorSchemeOptions=colorSchemeOptions.concat(savedColorSchemeKeys)}colorSchemeOptions.push({divider:true});colorSchemeOptions.push("My Computer...");return colorSchemeOptions};items.push([{name:"saved_color_scheme",required:true,type:"bootstrap-select",options:createColorSchemeOptions()},{name:"load_color_scheme",type:"button"},{name:"delete_color_scheme",type:"button"}]);items.push({name:"save_color_scheme",type:"button"});var displayItems=[{disabled:heatMap.getProject().getFullDataset().getColumnCount()!==heatMap.getProject().getFullDataset().getRowCount(),name:"link_rows_and_columns",help:"For square matrices",required:true,type:"checkbox",style:"max-width: 100px;",value:heatMap.getProject().isSymmetric()},{name:"show_row_number",required:true,type:"checkbox",value:heatMap.isShowRowNumber()},{name:"show_grid",required:true,type:"checkbox",value:heatMap.heatmap.isDrawGrid()},{name:"grid_thickness",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.heatmap.getGridThickness())},{name:"grid_color",required:true,type:"color",style:"max-width: 50px;",value:heatMap.heatmap.getGridColor()},{name:"row_size",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.heatmap.getRowPositions().getSize())},{name:"column_size",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.heatmap.getColumnPositions().getSize())},{name:"show_values",required:true,type:"checkbox",value:heatMap.heatmap.isDrawValues()},{name:"number_of_fraction_digits",required:true,type:"number",min:0,step:1,style:"max-width: 100px;",value:morpheus.Util.getNumberFormatPatternFractionDigits(heatMap.heatmap.getDrawValuesFormat().toJSON().pattern)}];if(heatMap.rowDendrogram){displayItems.push({name:"row_dendrogram_line_thickness",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.rowDendrogram?heatMap.rowDendrogram.lineWidth:1)})}if(heatMap.columnDendrogram){displayItems.push({name:"column_dendrogram_line_thickness",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.columnDendrogram?heatMap.columnDendrogram.lineWidth:1)})}displayItems.push({name:"info_window",required:true,type:"select",style:"max-width:130px;",options:[{name:"Fixed To Top",value:0},{name:"New Window",value:1}],value:heatMap.tooltipMode});displayItems.push({name:"inline_tooltip",required:true,type:"checkbox",value:heatMap.options.inlineTooltip});var colorSchemeFormBuilder=new morpheus.FormBuilder;_.each(items,function(item){colorSchemeFormBuilder.append(item)});var displayFormBuilder=new morpheus.FormBuilder;_.each(displayItems,function(item){displayFormBuilder.append(item)});var colorSchemeChooser=new morpheus.HeatMapColorSchemeChooser({showRelative:true,colorScheme:heatMap.heatmap.getColorScheme()});var updatingSizer=false;function colorSchemeChooserUpdated(){if(heatMap.heatmap.getColorScheme().getSizer&&heatMap.heatmap.getColorScheme().getSizer()!=null){colorSchemeFormBuilder.setValue("size_by",heatMap.heatmap.getColorScheme().getSizer().getSeriesName());colorSchemeFormBuilder.setEnabled("size_by_minimum",heatMap.heatmap.getColorScheme().getSizer().getSeriesName()!=null);colorSchemeFormBuilder.setEnabled("size_by_maximum",heatMap.heatmap.getColorScheme().getSizer().getSeriesName()!=null);if(!updatingSizer){colorSchemeFormBuilder.setValue("size_by_minimum",heatMap.heatmap.getColorScheme().getSizer().getMin());colorSchemeFormBuilder.setValue("size_by_maximum",heatMap.heatmap.getColorScheme().getSizer().getMax())}}}colorSchemeChooser.on("change",function(){colorSchemeChooserUpdated();heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint();colorSchemeChooser.restoreCurrentValue()});function createMetadataField(isColumns){var options=[];var value={};_.each(heatMap.getVisibleTrackNames(isColumns),function(name){value[name]=true});_.each(morpheus.MetadataUtil.getMetadataNames(isColumns?heatMap.getProject().getFullDataset().getColumnMetadata():heatMap.getProject().getFullDataset().getRowMetadata()),function(name){options.push(name)});var field={type:"bootstrap-select",search:options.length>10,name:isColumns?"column_annotations":"row_annotations",multiple:true,value:value,options:options,toggle:true};return field}var annotationsBuilder=new morpheus.FormBuilder;annotationsBuilder.append(createMetadataField(false));annotationsBuilder.append(createMetadataField(true));function annotationsListener($select,isColumns){var names=[];_.each(heatMap.getVisibleTrackNames(isColumns),function(name){names.push(name)});var values=$select.val();var selectedNow=_.difference(values,names);var unselectedNow=_.difference(names,values);var tracks=[];_.each(selectedNow,function(name){tracks.push({name:name,isColumns:isColumns,visible:true})});_.each(unselectedNow,function(name){tracks.push({name:name,isColumns:isColumns,visible:false})});heatMap.setTrackVisibility(tracks);colorSchemeChooser.restoreCurrentValue()}var $ca=annotationsBuilder.$form.find("[name=column_annotations]");$ca.on("change",function(e){annotationsListener($(this),true)});var $ra=annotationsBuilder.$form.find("[name=row_annotations]");$ra.on("change",function(e){annotationsListener($(this),false)});var annotationOptionsTabId=_.uniqueId("morpheus");var heatMapOptionsTabId=_.uniqueId("morpheus");var displayOptionsTabId=_.uniqueId("morpheus");var $metadataDiv=$('<div class="tab-pane" id="'+annotationOptionsTabId+'"></div>');$metadataDiv.append($(annotationsBuilder.$form));var $heatMapDiv=$('<div class="tab-pane active" id="'+heatMapOptionsTabId+'"></div>');$heatMapDiv.append(colorSchemeChooser.$div);$heatMapDiv.append($(colorSchemeFormBuilder.$form));var $displayDiv=$('<div class="tab-pane" id="'+displayOptionsTabId+'"></div>');$displayDiv.append($(displayFormBuilder.$form));displayFormBuilder.setEnabled("grid_thickness",heatMap.heatmap.isDrawGrid());displayFormBuilder.setEnabled("grid_color",heatMap.heatmap.isDrawGrid());displayFormBuilder.$form.find("[name=show_grid]").on("click",function(e){var grid=$(this).prop("checked");displayFormBuilder.setEnabled("grid_thickness",grid);displayFormBuilder.setEnabled("grid_color",grid);heatMap.heatmap.setDrawGrid(grid);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()});var $fractionDigits=displayFormBuilder.$form.find("[name=number_of_fraction_digits]");displayFormBuilder.$form.find("[name=show_values]").on("click",function(e){var drawValues=$(this).prop("checked");heatMap.heatmap.setDrawValues(drawValues);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()});$fractionDigits.on("keyup input",_.debounce(function(){var n=parseInt($(this).val());if(n>=0){heatMap.heatmap.setDrawValuesFormat(morpheus.Util.createNumberFormat("."+n+"f"));heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}},100));displayFormBuilder.$form.find("[name=inline_tooltip]").on("click",function(e){heatMap.options.inlineTooltip=$(this).prop("checked")});displayFormBuilder.$form.find("[name=grid_color]").on("change",function(e){var value=$(this).val();heatMap.heatmap.setGridColor(value);heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()});displayFormBuilder.$form.find("[name=grid_thickness]").on("keyup",_.debounce(function(e){var value=parseFloat($(this).val());if(!isNaN(value)){heatMap.heatmap.setGridThickness(value);heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}},100));displayFormBuilder.$form.find("[name=row_size]").on("keyup",_.debounce(function(e){var value=parseFloat($(this).val());if(!isNaN(value)){heatMap.heatmap.getRowPositions().setSize(value);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()}},100));displayFormBuilder.$form.find("[name=info_window]").on("change",function(e){heatMap.setTooltipMode(parseInt($(this).val()))});displayFormBuilder.find("link_rows_and_columns").on("click",function(e){var checked=$(this).prop("checked");if(checked){heatMap.getProject().setSymmetric(heatMap)}else{heatMap.getProject().setSymmetric(null)}});displayFormBuilder.find("show_row_number").on("click",function(e){var checked=$(this).prop("checked");heatMap.setShowRowNumber(checked);heatMap.revalidate()});var $colorByValue=colorSchemeFormBuilder.$form.find("[name=color_by_value]");var separateSchemesField=heatMap.heatmap.getColorScheme().getSeparateColorSchemeForRowMetadataField();if(separateSchemesField!=null){var v=heatMap.project.getFullDataset().getRowMetadata().getByName(separateSchemesField);if(v!=null){$colorByValue.html(morpheus.Util.createOptions(morpheus.VectorUtil.createValueToIndexMap(v).keys()))}}if(separateSchemesField!=null){colorSchemeChooser.setCurrentValue($colorByValue.val())}if(heatMap.heatmap.getColorScheme().getSizer&&heatMap.heatmap.getColorScheme().getSizer()!=null&&heatMap.heatmap.getColorScheme().getSizer().getSeriesName()){colorSchemeFormBuilder.setValue("size_by",heatMap.heatmap.getColorScheme().getSizer().getSeriesName())}colorSchemeFormBuilder.$form.find("[name=size_by]").on("change",function(e){var series=$(this).val();if(series=="(None)"){series=null}colorSchemeChooser.colorScheme.getSizer().setSeriesName(series);colorSchemeChooser.fireChanged()});colorSchemeFormBuilder.$form.find("[name=size_by_minimum]").on("keyup",_.debounce(function(e){updatingSizer=true;colorSchemeChooser.colorScheme.getSizer().setMin(parseFloat($(this).val()));colorSchemeChooser.fireChanged(true);updatingSizer=false},100));colorSchemeFormBuilder.$form.find("[name=size_by_maximum]").on("keyup",_.debounce(function(e){updatingSizer=true;colorSchemeChooser.colorScheme.getSizer().setMax(parseFloat($(this).val()));colorSchemeChooser.fireChanged(true);updatingSizer=false},100));colorSchemeFormBuilder.$form.find("[name=conditional_rendering]").on("click",function(e){e.preventDefault();var conditionalRenderingUI=new morpheus.ConditionalRenderingUI(heatMap);morpheus.FormBuilder.showInModal({title:"Conditional Rendering",html:conditionalRenderingUI.$div,close:"Close",modalClass:"morpheus-sub-modal"})});colorSchemeFormBuilder.find("save_color_scheme").on("click",function(e){e.preventDefault();var saveColorSchemeFormBuilder=new morpheus.FormBuilder;saveColorSchemeFormBuilder.append({name:"save_to",type:"radio",value:"Browser Storage",options:["Browser Storage","File"]});saveColorSchemeFormBuilder.append({name:"color_scheme_name",type:"text"});saveColorSchemeFormBuilder.append({name:"file_name",type:"text"});saveColorSchemeFormBuilder.setVisible("file_name",false);saveColorSchemeFormBuilder.find("save_to").on("change",function(){var isBrowser=$(this).val()==="Browser Storage";saveColorSchemeFormBuilder.setVisible("file_name",!isBrowser);saveColorSchemeFormBuilder.setVisible("color_scheme_name",isBrowser)});morpheus.FormBuilder.showOkCancel({title:"Save Color Scheme",ok:true,cancel:true,draggable:true,content:saveColorSchemeFormBuilder.$form,appendTo:heatMap.getContentEl(),align:"right",okCallback:function(){var colorSchemeText=JSON.stringify(heatMap.heatmap.getColorScheme().toJSON());if(saveColorSchemeFormBuilder.getValue("save_to")==="Browser Storage"){var name=saveColorSchemeFormBuilder.getValue("color_scheme_name").trim();if(name===""){name="my color scheme"}var colorSchemeObject=localStorage.getItem("morpheus-colorScheme");if(colorSchemeObject==null){colorSchemeObject={}}else{colorSchemeObject=JSON.parse(colorSchemeObject)}colorSchemeObject[name]=colorSchemeText;localStorage.setItem("morpheus-colorScheme",JSON.stringify(colorSchemeObject));colorSchemeFormBuilder.setOptions("saved_color_scheme",createColorSchemeOptions())}else{var name=saveColorSchemeFormBuilder.getValue("file_name").trim();if(name===""){name="color_scheme.json"}var blob=new Blob([colorSchemeText],{type:"application/json"});saveAs(blob,name)}},focus:heatMap.getFocusEl()})});colorSchemeFormBuilder.setEnabled("delete_color_scheme",false);colorSchemeFormBuilder.find("delete_color_scheme").on("click",function(){var key=colorSchemeFormBuilder.getValue("saved_color_scheme");var savedColorSchemes=JSON.parse(localStorage.getItem("morpheus-colorScheme"));delete savedColorSchemes[key];localStorage.setItem("morpheus-colorScheme",JSON.stringify(savedColorSchemes));colorSchemeFormBuilder.setOptions("saved_color_scheme",createColorSchemeOptions())});colorSchemeFormBuilder.find("saved_color_scheme").on("change",function(){colorSchemeFormBuilder.setEnabled("delete_color_scheme",["relative","cn","MAF","binary","My Computer..."].indexOf(colorSchemeFormBuilder.getValue("saved_color_scheme"))===-1)});colorSchemeFormBuilder.find("load_color_scheme").on("click",function(e){var val=colorSchemeFormBuilder.getValue("saved_color_scheme");var repaint=true;if(val==="relative"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.RELATIVE()))}else if(val==="cn"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.CN()))}else if(val==="MAF"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.MAF()))}else if(val==="binary"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.BINARY()))}else if(val==="My Computer..."){repaint=false;var $file=$('<input style="display:none;" type="file">');$file.appendTo(heatMap.getContentEl());$file.click();$file.on("change",function(evt){var files=evt.target.files;morpheus.Util.getText(evt.target.files[0]).done(function(text){var json=JSON.parse($.trim(text));heatMap.heatmap.getColorScheme().fromJSON(json);colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme());heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}).fail(function(){morpheus.FormBuilder.showInModal({title:"Error",html:"Unable to read color scheme."})}).always(function(){$file.remove()})})}else{var savedColorSchemes=JSON.parse(localStorage.getItem("morpheus-colorScheme"));var scheme=JSON.parse(savedColorSchemes[val]);heatMap.heatmap.getColorScheme().fromJSON(scheme)}if(repaint){colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme());heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}colorSchemeChooser.restoreCurrentValue()});colorSchemeFormBuilder.$form.find("[name=color_by]").on("change",function(e){var colorByField=$(this).val();if(colorByField=="(None)"){colorByField=null}var colorByValue=null;heatMap.heatmap.getColorScheme().setSeparateColorSchemeForRowMetadataField(colorByField);if(colorByField!=null){$colorByValue.html(morpheus.Util.createOptions(morpheus.VectorUtil.createValueToIndexMap(heatMap.project.getFullDataset().getRowMetadata().getByName(colorByField)).keys()));colorByValue=$colorByValue.val()}else{$colorByValue.html("")}heatMap.heatmap.getColorScheme().setCurrentValue(colorByValue);colorSchemeChooser.setCurrentValue(colorByValue);heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint();colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme())});$colorByValue.on("change",function(e){if(heatMap.heatmap.getColorScheme().getSeparateColorSchemeForRowMetadataField()==null){colorSchemeChooser.setCurrentValue(null);heatMap.heatmap.getColorScheme().setCurrentValue(null);colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme())}else{colorSchemeChooser.setCurrentValue($colorByValue.val());colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme())}});displayFormBuilder.$form.find("[name=column_size]").on("keyup",_.debounce(function(e){heatMap.heatmap.getColumnPositions().setSize(parseFloat($(this).val()));heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=row_gap_size]").on("keyup",_.debounce(function(e){heatMap.rowGapSize=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=column_gap_size]").on("keyup",_.debounce(function(e){heatMap.columnGapSize=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=squish_factor]").on("keyup",_.debounce(function(e){var f=parseFloat($(this).val());heatMap.heatmap.getColumnPositions().setSquishFactor(f);heatMap.heatmap.getRowPositions().setSquishFactor(f);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=row_dendrogram_line_thickness]").on("keyup",_.debounce(function(e){heatMap.rowDendrogram.lineWidth=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=column_dendrogram_line_thickness]").on("keyup",_.debounce(function(e){heatMap.columnDendrogram.lineWidth=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));var $tab=$('<div class="tab-content"></div>');$metadataDiv.appendTo($tab);$heatMapDiv.appendTo($tab);$displayDiv.appendTo($tab);var $div=$("<div></div>");var $ul=$('<ul class="nav nav-tabs" role="tablist">'+'<li><a href="#'+annotationOptionsTabId+'" role="tab" data-toggle="tab">Annotations</a></li>'+'<li><a href="#'+heatMapOptionsTabId+'" role="tab" data-toggle="tab">Color Scheme</a></li>'+'<li><a href="#'+displayOptionsTabId+'" role="tab" data-toggle="tab">Display</a></li>'+"</ul>");$ul.appendTo($div);$tab.appendTo($div);colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme());colorSchemeChooserUpdated();$ul.find("[role=tab]:eq(1)").tab("show");morpheus.FormBuilder.showInModal({title:"Options",html:$div,close:"Close",focus:heatMap.getFocusEl(),onClose:function(){$div.find("input").off("keyup");$ca.off("change");$ra.off("change");$div.remove();colorSchemeChooser.dispose()}})};morpheus.HeatMapSizer=function(){this.seriesName=null;this.sizeByScale=d3.scale.linear().domain([this.min,this.max]).range([0,1]).clamp(true)};morpheus.HeatMapSizer.prototype={min:0,max:1,copy:function(){var sizer=new morpheus.HeatMapSizer;sizer.seriesName=this.seriesName;sizer.min=this.min;sizer.max=this.max;sizer.sizeByScale=this.sizeByScale.copy();return sizer},valueToFraction:function(value){return this.sizeByScale(value)},setMin:function(min){this.min=min;this.sizeByScale=d3.scale.linear().domain([this.min,this.max]).range([0,1]).clamp(true)},setMax:function(max){this.max=max;this.sizeByScale=d3.scale.linear().domain([this.min,this.max]).range([0,1]).clamp(true)},getMin:function(){return this.min},getMax:function(){return this.max},getSeriesName:function(){return this.seriesName},setSeriesName:function(name){this.seriesName=name}};morpheus.HeatMapToolBar=function(heatMap){this.heatMap=heatMap;this.rowSearchResultModelIndices=[];this.columnSearchResultModelIndices=[];var _this=this;var layout=['<div class="hidden-print">'];layout.push('<div data-name="toolbar"></div>');layout.push('<div data-name="tip" style="white-space:nowrap; border-top: thin solid #e7e7e7;margin-bottom:2px;height: 14px; font-size: 10px;overflow:hidden;"></div>');layout.push("</div>");var $el=$(layout.join(""));var searchHtml=[];var $searchForm=$('<form style="display:inline-block;margin-right:14px;" name="searchForm"'+' class="form'+" form-inline"+' form-compact"'+' role="search"></form>');$searchForm.on("submit",function(e){e.preventDefault()});searchHtml.push('<div title="Toggle'+" Search ("+morpheus.Util.COMMAND_KEY+'/)" class="btn-group"'+' data-toggle="buttons">');searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="rows" type="radio" autocomplete="off" name="searchToggle"'+' type="button"> Rows');searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="columns" type="radio" autocomplete="off" name="searchToggle"> Columns');searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="values" type="radio" autocomplete="off" name="searchToggle">'+" Values");searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="rowDendrogram" type="radio" autocomplete="off"'+' name="searchToggle"> Row Dendrogram');searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="columnDendrogram" type="radio" autocomplete="off"'+' name="searchToggle"> Column Dendrogram');searchHtml.push("</label>");searchHtml.push("</div>");function createSearchOptionsMenu(){searchHtml.push('<div style="display:inline-block;" class="dropdown">');searchHtml.push('<button type="button" class="btn btn-default btn-xxs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> <span class="fa fa-caret-down"></span></button>');searchHtml.push('<ul data-name="searchOptions" class="dropdown-menu">');searchHtml.push('<li><a data-group="matchMode" data-name="exact" href="#"><span'+' data-type="toggle"></span>Exact'+" Match</a></li>");searchHtml.push('<li><a data-group="matchMode" data-name="contains" href="#"><span'+' data-type="toggle"'+' class="dropdown-checkbox fa fa-check"></span>Contains</a></li>');searchHtml.push('<li role="separator" class="divider"></li>');searchHtml.push('<li><a data-group="searchMode" data-name="matchAny" href="#"><span'+' data-type="toggle"'+' class="dropdown-checkbox fa fa-check"></span>Match Any Search Term</a></li>');searchHtml.push('<li><a data-group="searchMode" data-name="matchAll" href="#"><span'+' data-type="toggle"></span>Match All Search Terms</a></li>');searchHtml.push('<li role="separator" class="divider"></li>');searchHtml.push('<li><a data-name="searchHelp" href="#">Help</a></li>');searchHtml.push("</ul>");searchHtml.push("</div>")}function createSearchMenu(dataName,navigation){searchHtml.push('<div style="display:inline-block;" data-name="'+dataName+'">');searchHtml.push('<div class="form-group">');searchHtml.push('<input type="text" class="form-control input-sm" autocomplete="off"'+' name="search">');searchHtml.push("</div>");searchHtml.push('<div class="form-group">');searchHtml.push('<span data-name="searchResultsWrapper" style="display:none;">');searchHtml.push('<span style="font-size:12px;" data-name="searchResults"></span>');if(navigation){searchHtml.push('<button name="previousMatch" type="button" class="btn btn-default btn-xxs" data-toggle="tooltip" title="Previous"><i class="fa fa-chevron-up"></i></button>');searchHtml.push('<button name="nextMatch" type="button" class="btn btn-default btn-xxs" data-toggle="tooltip" title="Next"><i class="fa fa-chevron-down"></i></button>');searchHtml.push('<button name="matchesToTop" type="button" class="btn btn-default btn-xxs" data-toggle="tooltip" title="Matches To Top"><i class="fa fa-level-up"></i></button>')}searchHtml.push("</span>");searchHtml.push("</div>");searchHtml.push("</div>");searchHtml.push("</div>")}if(heatMap.options.toolbar.searchRows||heatMap.options.toolbar.searchColumns||heatMap.options.toolbar.searchValues){createSearchOptionsMenu()}if(heatMap.options.toolbar.searchRows){createSearchMenu("searchRowsGroup",true)}if(heatMap.options.toolbar.searchColumns){createSearchMenu("searchColumnsGroup",true)}if(heatMap.options.toolbar.searchValues){createSearchMenu("searchValuesGroup",false)}createSearchMenu("searchRowDendrogramGroup",false);createSearchMenu("searchColumnDendrogramGroup",false);if(heatMap.options.toolbar.dimensions){searchHtml.push('<div class="form-group">');searchHtml.push('<h6 style="display: inline; margin-left:10px;" data-name="dim"></h6>');searchHtml.push('<h6 style="display: inline; margin-left:10px;" data-name="selection"></h6>');searchHtml.push("</div>")}var $menus=$('<div style="display: inline-block;margin-right:14px;"></div>');function createMenu(menuName,actions,minWidth){if(!minWidth){minWidth="0px"}var menu=[];var dropdownId=_.uniqueId("morpheus");menu.push('<div class="dropdown morpheus-menu">');menu.push('<a class="dropdown-toggle morpheus-black-link morpheus-black-link-background" type="button"'+' id="'+dropdownId+'" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">');menu.push(menuName);menu.push("</a>");menu.push('<ul style="min-width:'+minWidth+';" class="dropdown-menu" aria-labelledby="'+dropdownId+'">');actions.forEach(function(name){if(name==null){menu.push('<li role="separator" class="divider"></li>')}else{var action=heatMap.getActionManager().getAction(name);if(action!=null){menu.push("<li>");menu.push('<a class="morpheus-menu-item" data-action="'+action.name+'" href="#">');menu.push(action.name);if(action.ellipsis){menu.push("...")}if(action.icon){menu.push('<span class="'+action.icon+' morpheus-menu-item-icon"></span> ')}if(action.which){menu.push('<span class="pull-right">');if(action.commandKey){menu.push(morpheus.Util.COMMAND_KEY)}if(action.shiftKey){menu.push("Shift+")}menu.push(morpheus.KeyboardCharMap[action.which[0]]);menu.push("</span>")}menu.push("</a>");menu.push("</li>")}}});menu.push("</ul>");menu.push("</div>");$(menu.join("")).appendTo($menus)}if(heatMap.options.menu){if(heatMap.options.menu.File){createMenu("File",heatMap.options.menu.File,"240px")}if(heatMap.options.menu.View){createMenu("Edit",heatMap.options.menu.Edit)}if(heatMap.options.menu.View){createMenu("View",heatMap.options.menu.View,"170px")}if(heatMap.options.menu.Tools){createMenu("Tools",heatMap.options.menu.Tools)}if(heatMap.options.menu.Help){createMenu("Help",heatMap.options.menu.Help,"220px")}}$(searchHtml.join("")).appendTo($searchForm);var $lineOneColumn=$el.find("[data-name=toolbar]");$menus.appendTo($lineOneColumn);$searchForm.appendTo($lineOneColumn);var toolbarHtml=['<div style="display: inline;">'];toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.zoom){var dropdownId=_.uniqueId("morpheus");toolbarHtml.push('<div style="display:inline-block;" class="dropdown">');toolbarHtml.push('<a class="dropdown-toggle morpheus-black-link" type="button" id="'+dropdownId+'" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">');toolbarHtml.push('<button type="button"'+' class="btn btn-default btn-xxs"><span class="fa'+' fa-search-plus"></span>');toolbarHtml.push(' <span style="font-size: .8em;" class="fa fa-caret-down"></span>');toolbarHtml.push("</button>");toolbarHtml.push('<ul style="width:200px;" class="dropdown-menu" aria-labelledby="'+dropdownId+'">');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Zoom In">Zoom In<span class="pull-right">+</span></a></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Zoom Out">Zoom'+' Out<span class="pull-right">-</span></a></li>');toolbarHtml.push('<li role="separator" class="divider"></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Fit To Window">Fit To Window<span'+' class="fa'+' fa-compress morpheus-menu-item-icon"></span><span class="pull-right">'+morpheus.Util.COMMAND_KEY+morpheus.KeyboardCharMap[heatMap.getActionManager().getAction("Fit To Window").which[0]]+"</span> </a></li>");toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Fit Rows To Window">Fit Rows To Window</a></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Fit Columns To Window">Fit Columns To Window</a></li>');toolbarHtml.push('<li role="separator" class="divider"></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="100%">100%</a></li>');toolbarHtml.push("</ul>");toolbarHtml.push("</div>")}toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.sort){toolbarHtml.push('<button data-toggle="tooltip" title="Sort" name="Sort" type="button" class="btn'+' btn-default btn-xxs"><span class="fa fa-sort-alpha-asc"></span></button>')}if(heatMap.options.toolbar.options){toolbarHtml.push('<button data-action="Options" data-toggle="tooltip" title="Options" type="button"'+' class="btn btn-default btn-xxs"><span class="fa fa-cog"></span></button>')}toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.openFile){toolbarHtml.push('<button data-action="Open File" data-toggle="tooltip" title="Open File ('+morpheus.Util.COMMAND_KEY+'O)" type="button" class="btn btn-default btn-xxs"><span class="fa fa-folder-open-o"></span></button>')}if(heatMap.options.toolbar.saveImage){toolbarHtml.push('<button data-action="Save Image" data-toggle="tooltip" title="Save Image ('+morpheus.Util.COMMAND_KEY+'S)" type="button" class="btn btn-default btn-xxs"><span class="fa fa-file-image-o"></span></button>')}if(heatMap.options.toolbar.saveDataset){toolbarHtml.push('<button data-action="Save Dataset" data-toggle="tooltip" title="Save Dataset ('+morpheus.Util.COMMAND_KEY+'Shift+S)" type="button" class="btn btn-default btn-xxs"><span class="fa fa-floppy-o"></span></button>')}if(heatMap.options.toolbar.saveSession){toolbarHtml.push('<button data-action="Save Session" data-toggle="tooltip" title="Save Session" type="button"'+' class="btn btn-default btn-xxs"><span class="fa fa-anchor"></span></button>')}toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.filter){toolbarHtml.push('<button data-action="Filter" data-toggle="tooltip" title="Filter" type="button"'+' class="btn btn-default btn-xxs"><span class="fa fa-filter"></span></button>')}if(heatMap.options.toolbar.chart&&typeof echarts!=="undefined"){toolbarHtml.push('<button data-action="Chart" data-toggle="tooltip" title="Chart" type="button" class="btn'+' btn-default btn-xxs"><span class="fa fa-line-chart"></span></button>')}if(heatMap.options.toolbar.colorKey){toolbarHtml.push('<div class="morpheus-button-divider"></div>');toolbarHtml.push('<div class="btn-group">');toolbarHtml.push('<button type="button" class="btn btn-default btn-xxs" data-toggle="dropdown"><span title="Color Key" data-toggle="tooltip" class="fa fa-key"></span></button>');toolbarHtml.push('<ul data-name="key" class="dropdown-menu" role="menu">');toolbarHtml.push('<li data-name="keyContent"></li>');toolbarHtml.push("</ul>");toolbarHtml.push("</div>")}toolbarHtml.push("</div>");var $toolbar=$(toolbarHtml.join(""));$toolbar.find("[data-action]").on("click",function(e){e.preventDefault();heatMap.getActionManager().execute($(this).data("action"))}).on("blur",function(e){if(document.activeElement===document.body){heatMap.focus()}});$menus.on("click","li > a",function(e){e.preventDefault();heatMap.getActionManager().execute($(this).data("action"))}).on("blur",function(e){if(document.activeElement===document.body){heatMap.focus()}});if(heatMap.options.toolbar.$customButtons){heatMap.options.toolbar.$customButtons.appendTo($toolbar)}$toolbar.appendTo($lineOneColumn);$el.prependTo(heatMap.$content);this.$tip=$el.find("[data-name=tip]");$el.find('[data-toggle="tooltip"]').tooltip({placement:"bottom",container:"body",trigger:"hover"}).on("click",function(){$(this).tooltip("hide")});var $key=$el.find("[data-name=key]");var $keyContent=$el.find("[data-name=keyContent]");$key.dropdown().parent().on("show.bs.dropdown",function(){new morpheus.HeatMapColorSchemeLegend(heatMap,$keyContent);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"colorKey"})});var searchHelpHtml=[];searchHelpHtml.push("<h4>Symbols</h4>");searchHelpHtml.push('<table class="table table-bordered">');searchHelpHtml.push("<tr><th>Term</th><th>Description</th></tr>");searchHelpHtml.push("<tr><td><code><strong>*</strong></code></td><td>Quote a search term for an"+" exact"+" match. <br"+' />Example: <code><strong>"root beer"</strong></code></td></tr>');searchHelpHtml.push("<tr><td><code><strong>-</strong></code></td><td>Exclude matches using -"+" modifier.</td></tr>");searchHelpHtml.push("<tr><td><code><strong>..</strong></code></td><td>Separate numbers by two"+" periods"+" without spaces to"+" see numbers that fall within a range.. <br"+" />Example: <code><strong>1..10</strong></code></td></tr>");searchHelpHtml.push("<tr><td><code><strong><= < > >= =</strong></code></td><td>Perform a"+" numeric"+" search."+" <br"+" />Example: <code><strong>>4</strong></code></td></tr>");searchHelpHtml.push("</table>");searchHelpHtml.push("<h4>Search fields</h4>");searchHelpHtml.push('<p>You can restrict your search to any field by typing the field name followed by a colon ":" and then the term you are looking for. For example, to search for matches containing "beer" in the beverage field, you can enter:'+" <code><strong>beverage:beer</strong></code>");searchHelpHtml.push("Note that searches only include metadata fields that are displayed. You"+" can search a hidden field by performing a field search.");searchHelpHtml.push("<p>You can search for an exact list of values by enclosing the list of"+" values in parentheses. For example: <code><strong>pet:(cat dog)</strong></code>"+" searches all pets that are either cats or dogs.</p>");var $searchHelp=$(searchHelpHtml.join(""));$el.find("[data-name=searchHelp]").on("click",function(e){e.preventDefault();morpheus.FormBuilder.showInModal({title:"Search Help",html:$searchHelp,appendTo:heatMap.getContentEl(),focus:heatMap.getFocusEl()})});var $searchRowsGroup=$searchForm.find("[data-name=searchRowsGroup]");var $searchColumnsGroup=$searchForm.find("[data-name=searchColumnsGroup]");var $searchValuesGroup=$searchForm.find("[data-name=searchValuesGroup]");var $searchRowDendrogramGroup=$searchForm.find("[data-name=searchRowDendrogramGroup]");var $searchColumnDendrogramGroup=$searchForm.find("[data-name=searchColumnDendrogramGroup]");this.$searchRowDendrogramGroup=$searchRowDendrogramGroup;this.$searchColumnDendrogramGroup=$searchColumnDendrogramGroup;this.matchMode="contains";this.matchAllPredicates=false;var $searchToggle=$searchForm.find("[name=searchToggle]");var nameToSearchObject={};function getSearchElements($group,searchName,cb){var obj={$group:$group,$search:$group.find("[name=search]"),$searchResultsWrapper:$group.find("[data-name=searchResultsWrapper]"),$searchResults:$group.find("[data-name=searchResults]"),$previousMatch:$group.find("[name=previousMatch]"),$nextMatch:$group.find("[name=nextMatch]"),$matchesToTop:$group.find("[name=matchesToTop]"),$toggleButton:$searchToggle.filter("[data-search="+searchName+"]").parent()};nameToSearchObject[searchName]=obj;return obj}var $searchOptions=$el.find("[data-name=searchOptions]");$searchOptions.on("click","li > a",function(e){e.preventDefault();var $this=$(this);var group=$this.data("group");if(group==="matchMode"){_this.matchMode=$this.data("name")}else{_this.matchAllPredicates=$this.data("name")==="matchAll"}var $searchField;if(_this.rowSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.columnSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.rowDendrogramSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.columnDendrogramSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.valueSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}if($searchField){$searchField.trigger($.Event("keyup",{keyCode:13,which:13}))}var $span=$(this).find("span");if($span.data("type")==="toggle"){$searchOptions.find("[data-group="+group+"] > [data-type=toggle]").removeClass("dropdown-checkbox"+" fa"+" fa-check");$span.addClass("dropdown-checkbox fa fa-check")}morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchMatchMode"})});this.rowSearchObject=getSearchElements($searchRowsGroup,"rows",function(){_this.search(true)});this.columnSearchObject=getSearchElements($searchColumnsGroup,"columns",function(){_this.search(false)});this.rowDendrogramSearchObject=getSearchElements($searchRowDendrogramGroup,"rowDendrogram",function(){_this.searchDendrogram(false)});this.columnDendrogramSearchObject=getSearchElements($searchColumnDendrogramGroup,"columnDendrogram",function(){_this.searchDendrogram(false)});this.valueSearchObject=getSearchElements($searchValuesGroup,"values",function(){searchValues()});if(!heatMap.options.toolbar.searchRows){this.rowSearchObject.$toggleButton.hide();this.rowSearchObject.$group.css("display","none")}if(!heatMap.options.toolbar.searchColumns){this.columnSearchObject.$toggleButton.hide();this.columnSearchObject.$group.css("display","none")}if(!heatMap.options.toolbar.searchValues){this.valueSearchObject.$toggleButton.hide();this.valueSearchObject.$group.css("display","none")}this.rowDendrogramSearchObject.$toggleButton.hide();this.rowDendrogramSearchObject.$group.hide();this.columnDendrogramSearchObject.$toggleButton.hide();this.columnDendrogramSearchObject.$group.hide();this.rowDendrogramSearchObject.$searchResultsWrapper.show();this.columnDendrogramSearchObject.$searchResultsWrapper.show();this.valueSearchObject.$searchResultsWrapper.show();this.rowSearchObject.$search.css({"border-top":"3.8px solid #e6e6e6","border-bottom":"3.8px solid #e6e6e6",width:"240px"});this.columnSearchObject.$search.css({"border-right":"3.8px solid #e6e6e6","border-left":"3.8px solid #e6e6e6",width:"240px"});this.$valueSearchResults=$searchValuesGroup.find("[name=searchResults]");this.$valueTextField=$searchValuesGroup.find("[name=search]");this.$dimensionsLabel=$el.find("[data-name=dim]");this.$selectionLabel=$el.find("[data-name=selection]");$searchToggle.on("change",function(e){var search=$(this).data("search");for(var name in nameToSearchObject){var searchObject=nameToSearchObject[name];if(name===search){searchObject.$group.css("display","inline-block");searchObject.$search.focus()}else{searchObject.$group.css("display","none")}}});this.toggleSearch=function(){var $visible=$searchToggle.filter(":visible");var $checked=$searchToggle.filter(":checked");var $next=$visible.eq($visible.index($checked)+1);if(!$next.length){$next=$visible.first()}$next.click()};for(var i=0;i<$searchToggle.length;i++){var $button=$($searchToggle[i]);if($button.parent().css("display")==="block"){$button.click();break}}heatMap.on("dendrogramAnnotated",function(e){if(e.isColumns){_this.rowDendrogramSearchObject.$toggleButton.show()}else{_this.columnDendrogramSearchObject.$toggleButton.show()}});heatMap.on("dendrogramChanged",function(e){if(e.isColumns){_this.rowDendrogramSearchObject.$group.hide();_this.rowDendrogramSearchObject.$toggleButton.hide()}else{_this.columnDendrogramSearchObject.$group.hide();_this.columnDendrogramSearchObject.$toggleButton.hide()}});var project=heatMap.getProject();morpheus.Util.autosuggest({$el:this.rowSearchObject.$search,filter:function(terms,cb){var indices=[];var meta=project.getSortedFilteredDataset().getRowMetadata();heatMap.getVisibleTrackNames(false).forEach(function(name){var index=morpheus.MetadataUtil.indexOf(meta,name);if(index!==-1){indices.push(index)}});meta=new morpheus.MetadataModelColumnView(meta,indices);morpheus.MetadataUtil.autocomplete(meta)(terms,cb)},select:function(){_this.search(true)}});this.rowSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.search(true);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchRows"})},500));morpheus.Util.autosuggest({$el:this.columnSearchObject.$search,filter:function(terms,cb){var indices=[];var meta=project.getSortedFilteredDataset().getColumnMetadata();heatMap.getVisibleTrackNames(true).forEach(function(name){var index=morpheus.MetadataUtil.indexOf(meta,name);if(index!==-1){indices.push(index)}});meta=new morpheus.MetadataModelColumnView(meta,indices);morpheus.MetadataUtil.autocomplete(meta)(terms,cb)},select:function(){_this.search(false)}});this.columnSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.search(false);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchColumns"})},500));morpheus.Util.autosuggest({$el:this.rowDendrogramSearchObject.$search,filter:function(tokens,cb){var d=heatMap.getDendrogram(false);if(!d.searchTerms){cb([])}else{var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);if(token===""){cb([])}else{morpheus.Util.autocompleteArrayMatcher(token,cb,d.searchTerms,null,10)}}},select:function(){_this.searchDendrogram(false)}});this.rowDendrogramSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.searchDendrogram(false);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchRowDendrogram"})},500));morpheus.Util.autosuggest({$el:this.columnDendrogramSearchObject.$search,filter:function(tokens,cb){var d=heatMap.getDendrogram(true);if(!d.searchTerms){cb([])}else{var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);if(token===""){cb([])}else{morpheus.Util.autocompleteArrayMatcher(token,cb,d.searchTerms,null,10)}}},select:function(){_this.searchDendrogram(true)}});this.columnDendrogramSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.searchDendrogram(true);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchColumnDendrogram"})},500));function searchValues(){var $searchResultsLabel=_this.$valueSearchResults;var text=$.trim(_this.$valueTextField.val());if(text===""){$searchResultsLabel.html("");project.getElementSelectionModel().setViewIndices(null)}else{var viewIndices=morpheus.DatasetUtil.searchValues({dataset:project.getSortedFilteredDataset(),text:text,matchAllPredicates:_this.matchAllPredicates,defaultMatchMode:_this.matchMode});project.getElementSelectionModel().setViewIndices(viewIndices);$searchResultsLabel.html(viewIndices.size()+" match"+(viewIndices.size()===1?"":"es"))}}morpheus.Util.autosuggest({$el:this.$valueTextField,filter:function(terms,cb){morpheus.DatasetUtil.autocompleteValues(project.getSortedFilteredDataset())(terms,cb)},select:function(){searchValues()}});this.$valueTextField.on("keyup",_.debounce(function(e){if(e.which===13){_this.$valueTextField.autocomplete("close");e.preventDefault()}searchValues()},500));this.toggleControls=function(){if($lineOneColumn.css("display")==="none"){$lineOneColumn.css("display","");_this.rowSearchObject.$search.focus()}else{$lineOneColumn.css("display","none");$(_this.heatMap.heatmap.canvas).focus()}};this.$el=$el;var updateFilterStatus=function(){if(heatMap.getProject().getRowFilter().isEnabled()||heatMap.getProject().getColumnFilter().isEnabled()){_this.$el.find("[name=filterButton]").addClass("btn-primary")}else{_this.$el.find("[name=filterButton]").removeClass("btn-primary")}};updateFilterStatus();this.columnSearchObject.$matchesToTop.on("click",function(e){e.preventDefault();var $this=$(this);$this.toggleClass("btn-primary");_this.setSelectionOnTop({isColumns:true,isOnTop:$this.hasClass("btn-primary"),updateButtonStatus:false});morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"columnMatchesToTop"})});this.rowSearchObject.$matchesToTop.on("click",function(e){e.preventDefault();var $this=$(this);$this.toggleClass("btn-primary");_this.setSelectionOnTop({isColumns:false,isOnTop:$this.hasClass("btn-primary"),updateButtonStatus:false});morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"rowMatchesToTop"})});project.on("rowSortOrderChanged.morpheus",function(e){if(_this.searching){return}_this._updateSearchIndices(false);_this.rowSearchObject.$matchesToTop.removeClass("btn-primary")});project.on("columnSortOrderChanged.morpheus",function(e){if(_this.searching){return}_this._updateSearchIndices(true);_this.columnSearchObject.$matchesToTop.removeClass("btn-primary")});heatMap.getProject().on("rowFilterChanged.morpheus",function(e){_this.search(true);updateFilterStatus()});heatMap.getProject().on("columnFilterChanged.morpheus",function(e){_this.search(false);updateFilterStatus()});heatMap.getProject().on("datasetChanged.morpheus",function(){_this.search(true);_this.search(false);updateFilterStatus()});heatMap.getProject().getRowSelectionModel().on("selectionChanged.morpheus",function(){_this.updateSelectionLabel()});heatMap.getProject().getColumnSelectionModel().on("selectionChanged.morpheus",function(){_this.updateSelectionLabel()});this.rowSearchResultViewIndicesSorted=null;this.currentRowSearchIndex=0;this.columnSearchResultViewIndicesSorted=null;this.currentColumnSearchIndex=-1;this.columnSearchObject.$previousMatch.on("click",function(){_this.currentColumnSearchIndex--;if(_this.currentColumnSearchIndex<0){_this.currentColumnSearchIndex=_this.columnSearchResultViewIndicesSorted.length-1}heatMap.scrollLeft(heatMap.getHeatMapElementComponent().getColumnPositions().getPosition(_this.columnSearchResultViewIndicesSorted[_this.currentColumnSearchIndex]));morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"previousColumnMatch"})});this.rowSearchObject.$previousMatch.on("click",function(){_this.currentRowSearchIndex--;if(_this.currentRowSearchIndex<0){_this.currentRowSearchIndex=_this.rowSearchResultViewIndicesSorted.length-1}heatMap.scrollTop(heatMap.getHeatMapElementComponent().getRowPositions().getPosition(_this.rowSearchResultViewIndicesSorted[_this.currentRowSearchIndex]));morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"previousRowMatch"})});this.columnSearchObject.$nextMatch.on("click",function(){_this.next(true);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"nextColumnMatch"})});this.rowSearchObject.$nextMatch.on("click",function(){_this.next(false);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"nextRowMatch"})});this.updateDimensionsLabel();this.updateSelectionLabel()};morpheus.HeatMapToolBar.HIGHLIGHT_SEARCH_MODE=0;morpheus.HeatMapToolBar.FILTER_SEARCH_MODE=1;morpheus.HeatMapToolBar.MATCHES_TO_TOP_SEARCH_MODE=2;morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE=3;morpheus.HeatMapToolBar.prototype={quickColumnFilter:false,searching:false,rowSearchMode:morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE,columnSearchMode:morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE,_updateSearchIndices:function(isColumns){var project=this.heatMap.getProject();if(isColumns){var viewIndices=[];var modelIndices=this.columnSearchResultModelIndices;for(var i=0,length=modelIndices.length;i<length;i++){var index=project.convertModelColumnIndexToView(modelIndices[i]);if(index!==-1){viewIndices.push(index)}}viewIndices.sort(function(a,b){return a<b?-1:1});this.columnSearchResultViewIndicesSorted=viewIndices;this.currentColumnSearchIndex=-1}else{var viewIndices=[];var modelIndices=this.rowSearchResultModelIndices;for(var i=0,length=modelIndices.length;i<length;i++){var index=project.convertModelRowIndexToView(modelIndices[i]);if(index!==-1){viewIndices.push(index)}}viewIndices.sort(function(a,b){return a<b?-1:1});this.rowSearchResultViewIndicesSorted=viewIndices;this.currentRowSearchIndex=-1}},next:function(isColumns){var heatMap=this.heatMap;if(isColumns){this.currentColumnSearchIndex++;if(this.currentColumnSearchIndex>=this.columnSearchResultViewIndicesSorted.length){this.currentColumnSearchIndex=0}heatMap.scrollLeft(heatMap.getHeatMapElementComponent().getColumnPositions().getPosition(this.columnSearchResultViewIndicesSorted[this.currentColumnSearchIndex]))}else{this.currentRowSearchIndex++;if(this.currentRowSearchIndex>=this.rowSearchResultViewIndicesSorted.length){this.currentRowSearchIndex=0}heatMap.scrollTop(heatMap.getHeatMapElementComponent().getRowPositions().getPosition(this.rowSearchResultViewIndicesSorted[this.currentRowSearchIndex]))}},getSearchField:function(type){if(type===morpheus.HeatMapToolBar.COLUMN_SEARCH_FIELD){return this.columnSearchObject.$search}else if(type===morpheus.HeatMapToolBar.ROW_SEARCH_FIELD){return this.rowSearchObject.$search}else if(type===morpheus.HeatMapToolBar.COLUMN_DENDROGRAM_SEARCH_FIELD){return this.columnDendrogramSearchObject.$search}else if(type===morpheus.HeatMapToolBar.ROW_DENDROGRAM_SEARCH_FIELD){return this.rowDendrogramSearchObject.$search}},setSearchText:function(options){var $tf=options.isColumns?this.columnSearchObject.$search:this.rowSearchObject.$search;var existing=options.append?$.trim($tf.val()):"";if(existing!==""){existing+=" "}if(options.onTop){options.isColumns?this.columnSearchObject.$matchesToTop.addClass("btn-primary"):this.rowSearchObject.$matchesToTop.addClass("btn-primary")}$tf.val(existing+options.text);this.search(!options.isColumns);if(options.scrollTo){this.next(options.isColumns)}},updateDimensionsLabel:function(){var p=this.heatMap.getProject();var d=p.getFullDataset();var f=p.getSortedFilteredDataset();var text=[];if(f.getRowCount()!==d.getRowCount()){text.push("<b>");text.push(morpheus.Util.intFormat(f.getRowCount()));text.push("/");text.push(morpheus.Util.intFormat(d.getRowCount()));text.push("</b>")}else{text.push(morpheus.Util.intFormat(f.getRowCount()))}text.push(" rows by ");if(f.getColumnCount()!==d.getColumnCount()){text.push("<b>");text.push(morpheus.Util.intFormat(f.getColumnCount()));text.push("/");text.push(morpheus.Util.intFormat(d.getColumnCount()));text.push("</b>")}else{text.push(morpheus.Util.intFormat(f.getColumnCount()))}text.push(" columns");this.$dimensionsLabel.html(text.join(""))},updateSelectionLabel:function(){var nc=this.heatMap.getProject().getColumnSelectionModel().count();var nr=this.heatMap.getProject().getRowSelectionModel().count();var text=[];text.push(morpheus.Util.intFormat(nr)+" row");if(nr!==1){text.push("s")}text.push(", ");text.push(morpheus.Util.intFormat(nc)+" column");if(nc!==1){text.push("s")}text.push(" selected");this.$selectionLabel.html(text.join(""))},searchDendrogram:function(isColumns){var searchObject=isColumns?this.columnDendrogramSearchObject:this.rowDendrogramSearchObject;var text=$.trim(searchObject.$search.val());var dendrogram=isColumns?this.heatMap.columnDendrogram:this.heatMap.rowDendrogram;var $searchResults=searchObject.$searchResults;var matches=morpheus.DendrogramUtil.search({rootNode:dendrogram.tree.rootNode,text:text,matchAllPredicates:this.matchAllPredicates,defaultMatchMode:this.matchMode});if(matches===-1){$searchResults.html("")}else{$searchResults.html(matches+" match"+(matches===1?"":"es"))}if(matches<=0){var positions=isColumns?this.heatMap.getHeatMapElementComponent().getColumnPositions():this.heatMap.getHeatMapElementComponent().getRowPositions();positions.setSquishedIndices(null);if(isColumns){this.heatMap.getProject().setGroupColumns([],true)}else{this.heatMap.getProject().setGroupRows([],true)}positions.setSize(isColumns?this.heatMap.getFitColumnSize():this.heatMap.getFitRowSize())}else{morpheus.DendrogramUtil.squishNonSearchedNodes(this.heatMap,isColumns)}this.heatMap.updateDataset();this.heatMap.revalidate()},search:function(isRows){this.searching=true;var isMatchesOnTop=isRows?this.rowSearchObject.$matchesToTop.hasClass("btn-primary"):this.columnSearchObject.$matchesToTop.hasClass("btn-primary");var heatMap=this.heatMap;var project=heatMap.getProject();var sortKeys=isRows?project.getRowSortKeys():project.getColumnSortKeys();sortKeys=sortKeys.filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.toString()==="matches on top")});var dataset=project.getSortedFilteredDataset();var $searchResultsLabel=isRows?this.rowSearchObject.$searchResults:this.columnSearchObject.$searchResults;var searchText=!isRows?$.trim(this.columnSearchObject.$search.val()):$.trim(this.rowSearchObject.$search.val());var metadata=isRows?dataset.getRowMetadata():dataset.getColumnMetadata();var visibleIndices=[];heatMap.getVisibleTrackNames(!isRows).forEach(function(name){var index=morpheus.MetadataUtil.indexOf(metadata,name);if(index!==-1){visibleIndices.push(index)}});var fullModel=metadata;metadata=new morpheus.MetadataModelColumnView(metadata,visibleIndices);var searchResultViewIndices=morpheus.MetadataUtil.search({model:metadata,fullModel:fullModel,text:searchText,isColumns:!isRows,matchAllPredicates:this.matchAllPredicates,defaultMatchMode:this.matchMode});if(searchText===""){$searchResultsLabel.html("");if(isRows){this.rowSearchObject.$searchResultsWrapper.hide()}else{this.columnSearchObject.$searchResultsWrapper.hide()}}else{$searchResultsLabel.html(searchResultViewIndices.length+" match"+(searchResultViewIndices.length===1?"":"es"));if(isRows){this.rowSearchObject.$searchResultsWrapper.show()}else{this.columnSearchObject.$searchResultsWrapper.show()}}var searchResultsModelIndices=[];if(searchResultViewIndices!=null){for(var i=0,length=searchResultViewIndices.length;i<length;i++){var viewIndex=searchResultViewIndices[i];searchResultsModelIndices.push(isRows?project.convertViewRowIndexToModel(viewIndex):project.convertViewColumnIndexToModel(viewIndex))}}if(searchResultViewIndices!==null&&isMatchesOnTop){var key=new morpheus.MatchesOnTopSortKey(project,searchResultsModelIndices,"matches on top",!isRows);searchResultViewIndices=key.indices;sortKeys.splice(0,0,key);if(isRows){project.setRowSortKeys(sortKeys,false)}else{project.setColumnSortKeys(sortKeys,false)}}var searchResultsViewIndicesSet=new morpheus.Set;if(searchResultViewIndices!=null){for(var i=0,length=searchResultViewIndices.length;i<length;i++){var viewIndex=searchResultViewIndices[i];searchResultsViewIndicesSet.add(viewIndex)}}if(searchResultViewIndices==null){searchResultViewIndices=[]}if(isRows){this.rowSearchResultModelIndices=searchResultsModelIndices;this.rowSearchResultViewIndicesSorted=searchResultViewIndices.sort(function(a,b){return a<b?-1:1});this.currentRowSearchIndex=-1}else{this.columnSearchResultModelIndices=searchResultsModelIndices;this.columnSearchResultViewIndicesSorted=searchResultViewIndices.sort(function(a,b){return a<b?-1:1});this.currentColumnSearchIndex=-1}(!isRows?project.getColumnSelectionModel():project.getRowSelectionModel()).setViewIndices(searchResultsViewIndicesSet,true);if(isMatchesOnTop){if(isRows){project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,project.getRowSortKeys()),true)}else{project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,project.getColumnSortKeys()),true)}}this.updateDimensionsLabel();this.updateSelectionLabel();this.searching=false},isSelectionOnTop:function(isColumns){var $btn=isColumns?this.columnSearchObject.$matchesToTop:this.rowSearchObject.$matchesToTop;return $btn.hasClass("btn-primary")},setSelectionOnTop:function(options){if(options.updateButtonStatus){var $btn=options.isColumns?this.columnSearchObject.$matchesToTop:this.rowSearchObject.$matchesToTop;if(options.isOnTop){$btn.addClass("btn-primary")}else{$btn.removeClass("btn-primary")}}var project=this.heatMap.getProject();var sortKeys=options.isColumns?project.getColumnSortKeys():project.getRowSortKeys();sortKeys=sortKeys.filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.name==="matches on top")});if(options.isOnTop){var key=new morpheus.MatchesOnTopSortKey(project,options.isColumns?this.columnSearchResultModelIndices:this.rowSearchResultModelIndices,"matches on top");sortKeys.splice(0,0,key);if(options.isColumns){this.heatMap.scrollLeft(0)}else{this.heatMap.scrollTop(0)}}this.searching=true;if(options.isColumns){project.setColumnSortKeys(sortKeys,true)}else{project.setRowSortKeys(sortKeys,true)}this._updateSearchIndices(options.isColumns);this.searching=false}};morpheus.HeatMapToolBar.COLUMN_SEARCH_FIELD="column";morpheus.HeatMapToolBar.ROW_SEARCH_FIELD="column";morpheus.HeatMapToolBar.COLUMN_DENDROGRAM_SEARCH_FIELD="column_dendrogram";morpheus.HeatMapToolBar.ROW_DENDROGRAM_SEARCH_FIELD="row_dendrogram";morpheus.HeatMapTooltipProvider=function(heatMap,rowIndex,columnIndex,options,separator,quick,tipText){var dataset=heatMap.project.getSortedFilteredDataset();if(!quick){if(options.value){_.each(options.value,function(pair){if(tipText.length>0){tipText.push(separator)}tipText.push(pair.name);tipText.push(": <b>");if(_.isArray(pair.value)){for(var i=0;i<pair.value.length;i++){if(i>0){tipText.push(", ")}tipText.push(pair.value[i])}}else{tipText.push(pair.value)}tipText.push("</b>")})}}if(rowIndex!==-1&&columnIndex!==-1){var tooltipSeriesIndices=options.tooltipSeriesIndices?options.tooltipSeriesIndices:morpheus.Util.sequ32(dataset.getSeriesCount());for(var i=0,nseries=tooltipSeriesIndices.length;i<nseries;i++){morpheus.HeatMapTooltipProvider._matrixValueToString(heatMap,dataset,rowIndex,columnIndex,tooltipSeriesIndices[i],tipText,separator,options.showSeriesNameInTooltip||i>0);if(heatMap.options.symmetric&&dataset.getValue(rowIndex,columnIndex,tooltipSeriesIndices[i])!==dataset.getValue(columnIndex,rowIndex,tooltipSeriesIndices[i])){morpheus.HeatMapTooltipProvider._matrixValueToString(heatMap,dataset,columnIndex,rowIndex,tooltipSeriesIndices[i],tipText,separator,false)}}if(quick){var quickRowTracks=heatMap.rowTracks.filter(function(t){return t.settings.inlineTooltip});morpheus.HeatMapTooltipProvider._tracksToString(quickRowTracks,dataset.getRowMetadata(),rowIndex,tipText,separator);morpheus.HeatMapTooltipProvider._tracksToString(heatMap.columnTracks.filter(function(t){return t.settings.inlineTooltip}),dataset.getColumnMetadata(),columnIndex,tipText,separator)}}else if(quick){if(rowIndex!==-1){morpheus.HeatMapTooltipProvider._tracksToString(heatMap.rowTracks.filter(function(t){return t.settings.inlineTooltip&&options.name!==t.getName()}),dataset.getRowMetadata(),rowIndex,tipText,separator)}if(columnIndex!==-1){morpheus.HeatMapTooltipProvider._tracksToString(heatMap.columnTracks.filter(function(t){return t.settings.inlineTooltip&&options.name!==t.getName()}),dataset.getColumnMetadata(),columnIndex,tipText,separator)}}if(!quick){if(rowIndex!==-1){morpheus.HeatMapTooltipProvider._metadataToString(options,heatMap.rowTracks,dataset.getRowMetadata(),rowIndex,tipText,separator)}if(columnIndex!==-1){morpheus.HeatMapTooltipProvider._metadataToString(options,heatMap.columnTracks,dataset.getColumnMetadata(),columnIndex,tipText,separator)}}else if(options.name!=null){var metadata=rowIndex!==-1?dataset.getRowMetadata():dataset.getColumnMetadata();var vector=metadata.getByName(options.name);var track=heatMap.getTrack(options.name,columnIndex!==-1);var colorByName=track!=null?track.settings.colorByField:null;var additionalVector=colorByName!=null?metadata.getByName(colorByName):null;morpheus.HeatMapTooltipProvider.vectorToString(vector,rowIndex!==-1?rowIndex:columnIndex,tipText,separator,additionalVector)}var rowNodes=[];var columnNodes=[];var selectedRowNodes=[];var selectedColumnNodes=[];if(options.rowNodes){rowNodes=options.rowNodes}if(options.columnNodes){columnNodes=options.columnNodes}if(!quick){if(heatMap.rowDendrogram){selectedRowNodes=_.values(heatMap.rowDendrogram.selectedRootNodeIdToNode)}if(heatMap.columnDendrogram){selectedColumnNodes=_.values(heatMap.columnDendrogram.selectedRootNodeIdToNode)}if(selectedRowNodes.length>0&&rowNodes.length>0){var nodeIds={};_.each(selectedRowNodes,function(n){nodeIds[n.id]=true});rowNodes=_.filter(rowNodes,function(n){return nodeIds[n.id]===undefined})}if(selectedColumnNodes.length>0&&columnNodes.length>0){var nodeIds={};_.each(selectedColumnNodes,function(n){nodeIds[n.id]=true});columnNodes=_.filter(columnNodes,function(n){return nodeIds[n.id]===undefined})}}morpheus.HeatMapTooltipProvider._nodesToString(tipText,rowNodes,null,separator);morpheus.HeatMapTooltipProvider._nodesToString(tipText,columnNodes,null,separator);if(!quick){if(selectedRowNodes.length>0){morpheus.HeatMapTooltipProvider._nodesToString(tipText,selectedRowNodes,heatMap.rowDendrogram._selectedNodeColor,separator)}if(selectedColumnNodes.length>0){morpheus.HeatMapTooltipProvider._nodesToString(tipText,selectedColumnNodes,heatMap.columnDendrogram._selectedNodeColor,separator)}}};morpheus.HeatMapTooltipProvider._matrixValueToString=function(heatMap,dataset,rowIndex,columnIndex,seriesIndex,tipText,separator,showSeriesNameInTooltip){var val=dataset.getValue(rowIndex,columnIndex,seriesIndex);if(val!=null){var nf=heatMap.getHeatMapElementComponent().getDrawValuesFormat();if(val.toObject||!_.isNumber(val)){var obj=val.toObject?val.toObject():val;if(morpheus.Util.isArray(obj)){var v=morpheus.Util.toString(obj);if(tipText.length>0){tipText.push(separator)}if(showSeriesNameInTooltip){tipText.push(dataset.getName(seriesIndex));tipText.push(": ")}tipText.push("<b>");tipText.push(v);tipText.push("</b>")}else{var keys=_.keys(obj);if(keys.length===0){var v=morpheus.Util.toString(obj);if(tipText.length>0){tipText.push(separator)}if(showSeriesNameInTooltip){tipText.push(dataset.getName(seriesIndex));tipText.push(": ")}tipText.push("<b>");tipText.push(v);tipText.push("</b>")}else{for(var i=0,nkeys=keys.length;i<nkeys;i++){var key=keys[i];if(key!=="__v"){var objVal=obj[key];var v;if(morpheus.Util.isArray(objVal)){v=morpheus.Util.arrayToString(objVal,", ")}else{v=morpheus.Util.toString(objVal)}if(tipText.length>0){tipText.push(separator)}tipText.push(key);tipText.push(": <b>");tipText.push(v);tipText.push("</b>")}}if(_.isNumber(val)){tipText.push(separator);tipText.push("Value: <b>");tipText.push(nf(val));tipText.push("</b>")}}}}else{if(tipText.length>0){tipText.push(separator)}if(showSeriesNameInTooltip){tipText.push(dataset.getName(seriesIndex));tipText.push(": ")}tipText.push("<b>");tipText.push(nf(val));tipText.push("</b>")}}};morpheus.HeatMapTooltipProvider.vectorToString=function(vector,index,tipText,separator,additionalVector){var arrayValueToString=function(arrayFieldName,arrayVal){if(arrayVal!=null){if(arrayFieldName!=null){if(tipText.length>0){tipText.push(separator)}tipText.push(arrayFieldName)}if(arrayVal.toObject){tipText.push(" ");var obj=arrayVal.toObject();var keys=_.keys(obj);_.each(keys,function(key){var subVal=obj[key];if(subVal!=null&&subVal!=""){if(tipText.length>0){tipText.push(separator)}tipText.push(key);tipText.push(": <b>");tipText.push(morpheus.Util.toString(subVal));tipText.push("</b>")}})}else{tipText.push(": <b>");tipText.push(morpheus.Util.toString(arrayVal));tipText.push("</b>")}}};if(vector!=null){var primaryVal=vector.getValue(index);if(primaryVal!=null&&primaryVal!=""){var primaryFields=vector.getProperties().get(morpheus.VectorKeys.FIELDS);if(primaryFields!=null){var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);if(visibleFieldIndices===undefined){visibleFieldIndices=morpheus.Util.seq(primaryFields.length)}var additionalFieldNames=additionalVector!=null?additionalVector.getProperties().get(morpheus.VectorKeys.FIELDS):null;var additionalVal=additionalFieldNames!=null?additionalVector.getValue(index):null;if(tipText.length>0){tipText.push(separator)}tipText.push(vector.getName());for(var j=0;j<visibleFieldIndices.length;j++){arrayValueToString(primaryFields[visibleFieldIndices[j]],primaryVal[visibleFieldIndices[j]])}if(additionalVal!=null){if(tipText.length>0){tipText.push(separator)}tipText.push(additionalVector.getName());for(var j=0;j<visibleFieldIndices.length;j++){arrayValueToString(additionalFieldNames[visibleFieldIndices[j]],additionalVal[visibleFieldIndices[j]])}}}else if(primaryVal.summary){if(tipText.length>0){tipText.push(separator)}tipText.push(vector.getName());tipText.push(": ");var obj=primaryVal.summary;var keys=_.keys(obj);for(var i=0,nkeys=keys.length;i<nkeys;i++){var key=keys[i];if(key!=="__v"){var objVal=obj[key];var v;if(morpheus.Util.isArray(objVal)){v=morpheus.Util.arrayToString(objVal,", ")}else{v=morpheus.Util.toString(objVal)}if(tipText.length>0){tipText.push(separator)}tipText.push(key);tipText.push(": <b>");tipText.push(v);tipText.push("</b>")}}}else{if(tipText.length>0){tipText.push(separator)}tipText.push(vector.getName());tipText.push(": <b>");tipText.push(morpheus.Util.toString(primaryVal));tipText.push("</b>")}}}};morpheus.HeatMapTooltipProvider._tracksToString=function(tracks,metadata,index,tipText,separator){for(var i=0;i<tracks.length;i++){morpheus.HeatMapTooltipProvider.vectorToString(metadata.getByName(tracks[i].name),index,tipText,separator)}};morpheus.HeatMapTooltipProvider._metadataToString=function(options,tracks,metadata,index,tipText,separator){var filtered=[];for(var i=0,ntracks=tracks.length;i<ntracks;i++){var track=tracks[i];if(track.isVisible()&&track.isShowTooltip()){if(tracks[i].name===options.name){filtered.splice(0,0,track)}else{filtered.push(track)}}}morpheus.HeatMapTooltipProvider._tracksToString(filtered,metadata,index,tipText,separator)};morpheus.HeatMapTooltipProvider._nodesToString=function(tipText,nodes,color,separator){var renderField=function(name,value){if(value!=null){if(tipText.length>0){tipText.push(separator)}if(color){tipText.push('<span style="color:'+color+'">')}tipText.push(name);tipText.push(": <b>");if(_.isArray(value)){for(var i=0;i<value.length;i++){if(i>0){tipText.push(", ")}tipText.push(morpheus.Util.toString(value[i]))}}else{tipText.push(morpheus.Util.toString(value))}tipText.push("</b>");if(color){tipText.push("</span>")}}};_.each(nodes,function(node){if(node.info){for(var name in node.info){var value=node.info[name];renderField(name,value)}}renderField("height",node.height);renderField("depth",node.depth);var nLeafNodes=1+Math.abs(node.maxIndex-node.minIndex);if(nLeafNodes>0){renderField("# of leaf nodes",nLeafNodes)}})};morpheus.HeatMapTrackColorLegend=function(tracks,colorModel){morpheus.AbstractCanvas.call(this,false);this.tracks=tracks;this.colorModel=colorModel;this.canvas.style.position=""};morpheus.HeatMapTrackColorLegend.prototype={getPreferredSize:function(){var tracks=this.tracks;var colorModel=this.colorModel;var xpix=0;var ypix=0;var maxYPix=0;var canvas=this.canvas;var context=canvas.getContext("2d");context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector(tracks[i].settings.colorByField);if(vector.getProperties().get(morpheus.VectorKeys.DISCRETE)){var map=colorModel.getDiscreteColorScheme(vector);map.forEach(function(color,key){var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}ypix+=14})}else{maxWidth=220;ypix+=40}maxWidth=Math.max(maxWidth,context.measureText(vector.getName()).width);xpix+=maxWidth+10+14;maxYPix=Math.max(maxYPix,ypix)}return{width:xpix,height:maxYPix>0?maxYPix+12:0}},draw:function(clip,context){var tracks=this.tracks;var colorModel=this.colorModel;var xpix=0;for(var i=0;i<tracks.length;i++){var ypix=0;var vector=tracks[i].getVector(tracks[i].settings.colorByField);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);context.textAlign="left";context.textBaseline="top";context.fillText(vector.getName(),xpix,ypix);context.strokeStyle="LightGrey";var maxWidth=0;var textWidth=context.measureText(vector.getName()).width;if(!isNaN(textWidth)){maxWidth=Math.max(0,textWidth)}ypix+=14;if(vector.getProperties().get(morpheus.VectorKeys.DISCRETE)){var toStringFunction=morpheus.VectorTrack.vectorToString(vector);var map=colorModel.getDiscreteColorScheme(vector);var values=map.keys().sort(morpheus.SortKey.ASCENDING_COMPARATOR);values.forEach(function(key){if(key!=null){key=toStringFunction(key);var color=colorModel.getMappedValue(vector,key);var textWidth=context.measureText(key).width;if(!isNaN(textWidth)){maxWidth=Math.max(maxWidth,textWidth)}context.fillStyle=color;var xoffset=0;if(tracks[i].isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){context.fillRect(xpix,ypix,12,12);context.strokeRect(xpix,ypix,12,12);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;xoffset=16}context.fillText(key,xpix+xoffset,ypix);ypix+=14}})}else{var scheme=colorModel.getContinuousColorScheme(vector);context.save();context.translate(xpix,ypix);morpheus.HeatMapColorSchemeLegend.drawColorScheme(context,scheme,200);context.restore();maxWidth=Math.max(maxWidth,220);ypix+=40}xpix+=maxWidth+10+14}}};morpheus.Util.extend(morpheus.HeatMapTrackColorLegend,morpheus.AbstractCanvas);morpheus.HeatMapTrackFontLegend=function(tracks,model){morpheus.AbstractCanvas.call(this,false);this.tracks=tracks;this.model=model;this.canvas.style.position=""};morpheus.HeatMapTrackFontLegend.prototype={getPreferredSize:function(){var tracks=this.tracks;var model=this.model;var canvas=this.canvas;var context=canvas.getContext("2d");context.font="900 12px "+morpheus.CanvasUtil.getFontFamily(context);var xpix=0;var ypix=0;var maxYPix=0;for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector(tracks[i].settings.fontField);var map=model.getMap(vector.getName());map.forEach(function(font,key){if(font!=null&&font.weight!="400"){var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}ypix+=14}});xpix+=maxWidth+6;maxYPix=Math.max(maxYPix,ypix)}return{width:xpix,height:maxYPix>0?maxYPix+30:0}},draw:function(clip,context){var tracks=this.tracks;var model=this.model;var xpix=0;var ypix=0;context.textAlign="left";context.textBaseline="top";context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.strokeStyle="black";var font=context.font;for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var textVector=tracks[i].getVector();var fontVector=tracks[i].getVector(tracks[i].settings.fontField);context.font=font;context.fillText(textVector.getName(),xpix,ypix);maxWidth=Math.max(maxWidth,context.measureText(textVector.getName()).width);ypix+=14;var map=model.getMap(fontVector.getName());var values=map.keys().sort(morpheus.SortKey.ASCENDING_COMPARATOR);values.forEach(function(key){var mappedFont=model.getMappedValue(fontVector,key);if(mappedFont!=null&&mappedFont.weight!="400"){context.font=mappedFont.weight+" "+font;var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}context.fillText(key,xpix,ypix);ypix+=14}});xpix+=maxWidth+6}}};morpheus.Util.extend(morpheus.HeatMapTrackFontLegend,morpheus.AbstractCanvas);morpheus.HeatMapTrackShapeLegend=function(tracks,shapeModel){morpheus.AbstractCanvas.call(this,false);this.tracks=tracks;this.shapeModel=shapeModel;this.canvas.style.position=""};morpheus.HeatMapTrackShapeLegend.prototype={getPreferredSize:function(){var tracks=this.tracks;var shapeModel=this.shapeModel;var canvas=this.canvas;var context=canvas.getContext("2d");var xpix=0;var ypix=0;var maxYPix=0;for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector();var map=shapeModel.getMap(vector.getName());map.forEach(function(color,key){var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}ypix+=14});xpix+=maxWidth+24;maxYPix=Math.max(maxYPix,ypix)}return{width:xpix,height:maxYPix>0?maxYPix+30:0}},draw:function(clip,context){var tracks=this.tracks;var shapeModel=this.shapeModel;var xpix=0;var ypix=0;context.textAlign="left";context.textBaseline="top";context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.strokeStyle="black";for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector();context.fillText(vector.getName(),xpix,ypix);maxWidth=Math.max(maxWidth,context.measureText(vector.getName()).width);ypix+=14;var map=shapeModel.getMap(vector.getName());var values=map.keys().sort(morpheus.SortKey.ASCENDING_COMPARATOR);values.forEach(function(key){var shape=shapeModel.getMappedValue(vector,key);var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}morpheus.CanvasUtil.drawShape(context,shape,xpix+8,ypix+6,6);context.fillText(key,xpix+16,ypix);ypix+=14});xpix+=maxWidth+24}}};morpheus.Util.extend(morpheus.HeatMapTrackShapeLegend,morpheus.AbstractCanvas);morpheus.HeatMap=function(options){morpheus.Util.loadTrackingCode();var _this=this;var dontExtend=["parent","columnDendrogram","rowDendrogram"];var cache=[];for(var i=0;i<dontExtend.length;i++){var field=dontExtend[i];cache[i]=options[field];options[field]=null}options=$.extend(true,{},{el:null,dataset:undefined,rowAnnotations:undefined,columnAnnotations:undefined,columnGroupBy:undefined,rowGroupBy:undefined,colorScheme:undefined,rowSortBy:undefined,columnSortBy:undefined,rowDendrogram:undefined,columnDendrogram:undefined,columnDendrogramField:"id",rowDendrogramField:"id",rows:[],columns:[],tools:undefined,rowFilter:undefined,columnFilter:undefined,autohideTabBar:false,closeable:true,rename:true,rowSize:13,columnSize:13,rowGapSize:10,columnGapSize:10,drawGrid:true,gridColor:"#808080",showRowNumber:false,gridThickness:.1,height:"window",width:undefined,focus:true,tooltipMode:0,inheritFromParent:true,inheritFromParentOptions:{transpose:false},tooltip:undefined,structureUrlProvider:undefined,promises:undefined,renderReady:undefined,datasetReady:undefined,tabOpened:undefined,loadedCallback:undefined,name:undefined,rowsSortable:true,columnsSortable:true,popupEnabled:true,symmetric:false,keyboard:true,inlineTooltip:true,standalone:false,$loadingImage:morpheus.Util.createLoadingEl(),menu:{File:["Open",null,"Save Image","Save Dataset","Save Session",null,"Close Tab",null,"Rename"+" Tab"],Tools:["New Heat Map",null,"Hierarchical Clustering","KMeans Clustering",null,"Marker Selection","Nearest Neighbors","Create Calculated Annotation",null,"Adjust","Collapse","Similarity Matrix","Transpose",null,"Chart",null,"Sort/Group","Filter",null,"API"],View:["Zoom In","Zoom Out",null,"Fit To Window","Fit Rows To Window","Fit Columns To Window",null,"100%",null,"Options"],Edit:["Copy Image","Copy Selected Dataset",null,"Move Selected Rows To Top","Annotate Selected Rows","Copy Selected Rows","Invert"+" Selected Rows","Select All Rows","Clear Selected Rows",null,"Move Selected Columns To Top","Annotate Selected Columns","Copy Selected Columns","Invert"+" Selected Columns","Select All Columns","Clear Selected Columns"],Help:["Search Menus",null,"Contact","Configuration","Tutorial","Source Code",null,"Keyboard"+" Shortcuts"]},toolbar:{dimensions:true,zoom:true,searchRows:true,searchColumns:true,searchValues:false,options:true,saveImage:true,filter:true,colorKey:true}},options);for(var i=0;i<dontExtend.length;i++){var field=dontExtend[i];options[field]=cache[i]}if(options.menu==null){options.menu={}}if(options.toolbar==null){options.toolbar={}}this.options=options;this.tooltipProvider=morpheus.HeatMapTooltipProvider;if(!options.el){this.$el=$("<div></div>")}else{this.$el=$(options.el)}this.rowGapSize=options.rowGapSize;this.columnGapSize=options.columnGapSize;this.actionManager=new morpheus.ActionManager;this.actionManager.heatMap=this;this.$el.addClass("morpheus");if(this.options.dataset==null){var datasetFormBuilder=new morpheus.FormBuilder;datasetFormBuilder.append({name:"file",type:"file"});this.options.dataset=$.Deferred();morpheus.FormBuilder.showOkCancel({title:"Dataset",appendTo:this.getContentEl(),focus:this.getFocusEl(),content:datasetFormBuilder.$form,okCallback:function(){var file=datasetFormBuilder.getValue("file");morpheus.DatasetUtil.read(file).done(function(dataset){_this.options.dataset.resolve(dataset)}).fail(function(err){_this.options.dataset.reject(err)})},cancelCallback:function(){_this.options.dataset.reject("Session cancelled.")}})}if(this.options.name==null){this.options.name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(this.options.dataset.file?this.options.dataset.file:this.options.dataset))}var isPrimary=this.options.parent==null;if(this.options.parent==null){if(!morpheus.Util.isHeadless()){if(this.options.tabManager==null){this.tabManager=new morpheus.TabManager({landingPage:function(){if(_this.options.landingPage==null){_this.options.landingPage=new morpheus.LandingPage({tabManager:_this.tabManager});_this.options.landingPage.$el.prependTo(_this.$el)}return _this.options.landingPage},autohideTabBar:this.options.autohideTabBar})}else{this.tabManager=this.options.tabManager}if(this.options.tabManager==null){this.tabManager.appendTo(this.$el)}}}else{if(this.options.inheritFromParent){this.popupItems=this.options.parent.popupItems;if(!this.options.tabOpened){this.options.tabOpened=this.options.parent.options.tabOpened}this.options.drawCallback=this.options.parent.options.drawCallback}this.tabManager=this.options.parent.tabManager}this.$content=$("<div></div>");this.$content.css({width:"100%","user-select":"none","-webkit-user-select":"none","-webkit-user-drag":"none","-webkit-tap-highlight-color":"rgba(0, 0, 0, 0)","-moz-user-select":"none","-moz-user-drag":"none","-moz-tap-highlight-color":"rgba(0, 0, 0, 0)","-ms-user-select":"none","-ms-user-drag":"none","-ms-tap-highlight-color":"rgba(0, 0, 0, 0)","-o-user-select":"none","-o-user-drag":"none","-o-tap-highlight-color":"rgba(0, 0, 0, 0)","overflow-x":"visible","overflow-y":"visible"});this.$content.on("remove.morpheus",function(){_this.$content.off("remove.morpheus");_this.dispose()});if(!morpheus.Util.isHeadless()){var tab=this.tabManager.add({$el:this.$content,closeable:this.options.closeable,rename:this.options.rename,title:this.options.name,object:this,focus:this.options.focus});this.tabId=tab.id;this.$tabPanel=tab.$panel}if(options.$loadingImage){options.$loadingImage.appendTo(this.$content)}this.options.dataSource=!options.dataset?"":options.dataset.file?options.dataset.file:options.dataset;this._togglingInfoWindow=false;var promises=[];if(options.promises){for(var i=0;i<options.promises.length;i++){promises.push(options.promises[i])}}this.whenLoaded=[];if(options.rowAnnotations){var rowDef=morpheus.DatasetUtil.annotate({annotations:options.rowAnnotations,isColumns:false});rowDef.done(function(callbacks){_this.whenLoaded=_this.whenLoaded.concat(callbacks)});promises.push(rowDef)}if(options.columnAnnotations){var columnDef=morpheus.DatasetUtil.annotate({annotations:options.columnAnnotations,isColumns:true});columnDef.done(function(callbacks){_this.whenLoaded=_this.whenLoaded.concat(callbacks)});promises.push(columnDef)}if(options.rowDendrogram!=null&&_.isString(options.rowDendrogram)){if(options.rowDendrogram[0]==="("){_this.options.rowDendrogram=morpheus.DendrogramUtil.parseNewick(options.rowDendrogram)}else{var rowDendrogramDeferred=morpheus.Util.getText(options.rowDendrogram);rowDendrogramDeferred.done(function(text){_this.options.rowDendrogram=morpheus.DendrogramUtil.parseNewick(text)});promises.push(rowDendrogramDeferred)}}if(options.columnDendrogram!=null&&_.isString(options.columnDendrogram)){if(options.columnDendrogram[0]==="("){_this.options.columnDendrogram=morpheus.DendrogramUtil.parseNewick(options.columnDendrogram)}else{var columnDendrogramDeferred=morpheus.Util.getText(options.columnDendrogram);columnDendrogramDeferred.done(function(text){_this.options.columnDendrogram=morpheus.DendrogramUtil.parseNewick(text)});promises.push(columnDendrogramDeferred)}}var heatMapLoaded=function(){if(typeof window!=="undefined"){$(window).on("orientationchange.morpheus resize.morpheus",_this.resizeListener=function(){_this.revalidate()})}_this.revalidate();if(options.loadedCallback){options.loadedCallback(_this)}if(_this.tabManager){if(_this.options.focus){_this.tabManager.setActiveTab(tab.id);_this.focus()}else if(_this.tabManager.getTabCount()===1){_this.tabManager.setActiveTab(tab.id)}}_this.$el.trigger("heatMapLoaded",_this)};if(morpheus.Util.isArray(options.dataset)){var d=morpheus.DatasetUtil.readDatasetArray(options.dataset);d.fail(function(message){if(_this.options.$loadingImage){_this.options.$loadingImage.remove()}if(_this.options.error){_this.options.error(message)}morpheus.FormBuilder.showInModal({title:"Error",html:message,appendTo:_this.getContentEl(),focus:_this.getFocusEl()})});d.done(function(joined){if(_this.options.$loadingImage){_this.options.$loadingImage.remove()}_this.options.dataset=joined;_this._init();if(joined.getRowMetadata().getByName("Source")!=null&&!_this.options.colorScheme){_this.heatmap.getColorScheme().setSeparateColorSchemeForRowMetadataField("Source")}_.each(options.dataset,function(option){if(option.colorScheme){_this.heatmap.getColorScheme().setCurrentValue(morpheus.Util.getBaseFileName(morpheus.Util.getFileName(option.dataset)));_this.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(option.colorScheme))}else{try{_this.autoDisplay({extension:morpheus.Util.getExtension(morpheus.Util.getFileName(option.dataset)),filename:morpheus.Util.getBaseFileName(morpheus.Util.getFileName(option.dataset))})}catch(x){console.log("Autodisplay errror")}}});heatMapLoaded()})}else{var deferred=options.dataset.file?morpheus.DatasetUtil.read(options.dataset.file,options.dataset.options):morpheus.DatasetUtil.read(options.dataset);deferred.done(function(dataset){_this.options.dataset=dataset});deferred.fail(function(err){_this.options.$loadingImage.remove();var message=["Error opening "+(options.dataset.file?morpheus.Util.getFileName(options.dataset.file):morpheus.Util.getFileName(options.dataset))+"."];if(err.message){message.push("<br />Cause: ");message.push(err.message)}if(_this.options.error){_this.options.error(message)}morpheus.FormBuilder.showInModal({title:"Error",html:message.join(""),appendTo:_this.getContentEl(),focus:_this.getFocusEl()})});promises.push(deferred);var datasetOverlay=null;if(options.datasetOverlay){var d=options.datasetOverlay.file?morpheus.DatasetUtil.read(options.datasetOverlay.file,options.datasetOverlay.options):morpheus.DatasetUtil.read(options.datasetOverlay);d.done(function(dataset){datasetOverlay=dataset});promises.push(d)}$.when.apply($,promises).done(function(){if(_this.options.$loadingImage){_this.options.$loadingImage.remove()}if(_this.options.dataset==null){return _this.tabManager.remove(_this.tabId)}_this._init();if(datasetOverlay){morpheus.DatasetUtil.overlay({dataset:_this.options.dataset,newDataset:datasetOverlay,rowAnnotationName:"id",newRowAnnotationName:"id",columnAnnotationName:"id",newColumnAnnotationName:"id"})}heatMapLoaded()})}};morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS=6;morpheus.HeatMap.showTool=function(tool,heatMap,callback){if(tool.gui){var gui=tool.gui(heatMap.getProject());var formBuilder=new morpheus.FormBuilder;_.each(gui,function(item){formBuilder.append(item)});var tabId=heatMap.getTabManager().getActiveTabId();if(tool.init){tool.init(heatMap.getProject(),formBuilder,{heatMap:heatMap})}heatMap.trigger("beforeToolShown",{tool:tool,formBuilder:formBuilder});var okCallback=function(){var $dialogContent=$("<div><span>"+tool.toString()+'...</span><button class="btn'+' btn-xs btn-default" style="margin-left:6px;display: none;">Cancel</button></div>');var value=null;var $dialog=morpheus.FormBuilder.showInDraggableDiv({$content:$dialogContent,appendTo:heatMap.getContentEl(),width:"auto"});var input={};_.each(gui,function(item){input[item.name]=formBuilder.getValue(item.name)});setTimeout(function(){value=tool.execute({heatMap:heatMap,project:heatMap.getProject(),input:input});if(value instanceof Worker){$dialogContent.find("button").css("display","").on("click",function(){value.terminate()});value.onerror=function(e){value.terminate();morpheus.FormBuilder.showInModal({title:"Error",html:e,close:"Close",focus:heatMap.getFocusEl(),appendTo:heatMap.getContentEl()});if(e.stack){console.log(e.stack)}};var terminate=_.bind(value.terminate,value);value.terminate=function(){terminate();$dialog.remove();if(callback){callback(input)}}}else{if(value!=null&&typeof value.done==="function"){value.always(function(){if(callback){callback(input)}$dialog.remove()})}else{if(callback){callback(input)}$dialog.remove()}}},20);setTimeout(function(){if(!(value instanceof Worker)){$dialog.remove()}},5e3)};var $formDiv;tool.ok=function(){$formDiv.modal("hide");okCallback()};var guiOptions=$.extend({},{ok:true},gui.options);$formDiv=morpheus.FormBuilder.showOkCancel({title:tool.toString(),apply:tool.apply,ok:guiOptions.ok,cancel:guiOptions.cancel,size:guiOptions.size,draggable:true,content:formBuilder.$form,appendTo:heatMap.getContentEl(),align:"right",okCallback:okCallback,focus:heatMap.getFocusEl()})}else{tool.execute({heatMap:heatMap,project:heatMap.getProject(),input:{}});if(callback){callback({})}}};morpheus.HeatMap.getSpaces=function(groupByKeys,length,gapSize){var previousArray=[];var nkeys=groupByKeys.length;for(var keyIndex=0;keyIndex<nkeys;keyIndex++){var key=groupByKeys[keyIndex];previousArray.push(key.getValue(0))}var spaces=[];var sum=0;spaces.push(sum);for(var i=1;i<length;i++){var isEqual=true;for(var keyIndex=0;keyIndex<nkeys;keyIndex++){var key=groupByKeys[keyIndex];var comparator=key.getComparator();var val=key.getValue(i);var c=comparator(val,previousArray[keyIndex]);if(c!==0){isEqual=false;for(var keyIndex2=0;keyIndex2<nkeys;keyIndex2++){previousArray[keyIndex2]=groupByKeys[keyIndex2].getValue(i)}break}}if(!isEqual){sum+=gapSize}spaces.push(sum)}return spaces};morpheus.HeatMap.createGroupBySpaces=function(dataset,groupByKeys,gapSize,isColumns){if(groupByKeys.length>0){var nkeys=groupByKeys.length;for(var keyIndex=0;keyIndex<nkeys;keyIndex++){groupByKeys[keyIndex].init(groupByKeys[keyIndex].isColumns()?new morpheus.TransposedDatasetView(dataset):dataset)}return morpheus.HeatMap.getSpaces(groupByKeys,isColumns?dataset.getColumnCount():dataset.getRowCount(),gapSize)}};morpheus.HeatMap.isDendrogramVisible=function(project,isColumns){var sortKeys=isColumns?project.getColumnSortKeys():project.getRowSortKeys();if(sortKeys.length===0){return true}var size=isColumns?project.getSortedFilteredDataset().getColumnCount():project.getSortedFilteredDataset().getRowCount();for(var i=0;i<sortKeys.length;i++){if(!sortKeys[i].isPreservesDendrogram()||sortKeys[i].nvisible!==size){return false}}return true};morpheus.HeatMap.prototype={updatingScroll:false,getWhitespaceEl:function(){return this.$whitespace},getActionManager:function(){return this.actionManager},autoDisplay:function(options){if(options.filename==null){options.filename=""}var colorScheme;if(options.extension==="segtab"||options.extension==="seg"){colorScheme={scalingMode:"fixed",values:morpheus.HeatMapColorScheme.Predefined.CN().values.map(function(value){return Math.pow(2,1+value)}),colors:morpheus.HeatMapColorScheme.Predefined.CN().colors}}else if(options.extension==="maf"){colorScheme=morpheus.HeatMapColorScheme.Predefined.MAF();var rowMutProfile=this.project.getFullDataset().getRowMetadata().getByName("mutation_summary");var fieldNames=rowMutProfile.getProperties().get(morpheus.VectorKeys.FIELDS);var useMafColorMap=true;if(fieldNames.length!==morpheus.MafFileReader.FIELD_NAMES.length){useMafColorMap=false}else{for(var i=0;i<fieldNames.length;i++){if(fieldNames[i]!==morpheus.MafFileReader.FIELD_NAMES[i]){useMafColorMap=false;break}}}if(!useMafColorMap){colorScheme={scalingMode:"fixed",stepped:true,values:[0],colors:["rgb(255,255,255)"]};for(var i=0;i<fieldNames.length;i++){colorScheme.values.push(i+1);colorScheme.colors.push(morpheus.VectorColorModel.TWENTY_COLORS[i%morpheus.VectorColorModel.TWENTY_COLORS.length]);colorScheme.names.push(fieldNames[i])}}var columnMutationSummaryVectors=[];var columnMutationSummaryNames=["mutation_summary","mutation_summary_selection"];for(var i=0;i<columnMutationSummaryNames.length;i++){var name=columnMutationSummaryNames[i];if(this.project.getFullDataset().getColumnMetadata().getByName(name)){columnMutationSummaryVectors.push(this.project.getFullDataset().getColumnMetadata().getByName(name));track=this.getTrack(name,true);if(track){track.settingFromConfig("stacked_bar");if(name==="mutation_summary_selection"){track.settings.autoscaleAlways=true}}}}var track=this.getTrack("mutation_summary",false);if(track){track.settingFromConfig("stacked_bar")}for(var i=1;i<colorScheme.colors.length;i++){if(rowMutProfile){this.getProject().getRowColorModel().setMappedValue(rowMutProfile,i-1,colorScheme.colors[i])}for(var j=0;j<columnMutationSummaryVectors.length;j++){this.getProject().getColumnColorModel().setMappedValue(columnMutationSummaryVectors[j],i-1,colorScheme.colors[i])}}}else if(options.extension==="gmt"){colorScheme=morpheus.HeatMapColorScheme.Predefined.BINARY()}else if(options.filename==="all_lesions.conf_99"||options.filename==="all_data_by_genes.txt"||options.filename.toLowerCase().indexOf("gistic")!==-1){colorScheme={scalingMode:"fixed",values:[-.5,0,.5],colors:["blue","white","red"]}}else if(options.filename.toLowerCase().indexOf("copynumber")!==-1||options.filename.toLowerCase().indexOf("copy number")!==-1){colorScheme={scalingMode:"fixed",values:[-1.5,0,1.5],colors:["blue","white","red"]}}else if(options.filename.toLowerCase().indexOf("achilles")!==-1){colorScheme={scalingMode:"fixed",values:[-3,-1,1,3],colors:["blue","white","white","red"]}}if(colorScheme&&options.filename&&this.heatmap.getColorScheme()){this.heatmap.getColorScheme().setCurrentValue(options.filename);this.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(colorScheme))}return colorScheme},sortBasedOnSelection:function(sortOrder,isColumns,append){var project=this.project;var selectionModel=isColumns?project.getColumnSelectionModel():project.getRowSelectionModel();var modelIndices=selectionModel.toModelIndices();if(modelIndices.length===0){return}var priorSortKeyIndex=-1;if(sortOrder==null){var existingSortKeys=isColumns?project.getRowSortKeys():project.getColumnSortKeys();for(var i=0,length=existingSortKeys.length;i<length;i++){var key=existingSortKeys[i];if(key instanceof morpheus.SortByValuesKey&&morpheus.Util.arrayEquals(key.modelIndices,modelIndices)){priorSortKeyIndex=i;if(key.getSortOrder()===morpheus.SortKey.SortOrder.UNSORTED){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.DESCENDING){sortOrder=morpheus.SortKey.SortOrder.ASCENDING}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){sortOrder=morpheus.SortKey.SortOrder.TOP_N}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.TOP_N){sortOrder=morpheus.SortKey.SortOrder.UNSORTED}break}}}if(sortOrder==null){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}var sortKeys;if(append){sortKeys=!isColumns?project.getColumnSortKeys():project.getRowSortKeys();if(priorSortKeyIndex!==-1){if(sortOrder===morpheus.SortKey.SortOrder.UNSORTED){sortKeys.splice(priorSortKeyIndex,1)}else{sortKeys[priorSortKeyIndex].setSortOrder(sortOrder)}}else{if(sortOrder!==morpheus.SortKey.SortOrder.UNSORTED){sortKeys.push(new morpheus.SortByValuesKey(modelIndices,sortOrder,!isColumns))}}sortKeys=morpheus.SortKey.keepExistingSortKeys(sortKeys,!isColumns?project.getColumnSortKeys():project.getRowSortKeys())}else{var newSortKeys=sortOrder===morpheus.SortKey.SortOrder.UNSORTED?[]:[new morpheus.SortByValuesKey(modelIndices,sortOrder,!isColumns)];sortKeys=morpheus.SortKey.keepExistingSortKeys(newSortKeys,!isColumns?project.getColumnSortKeys():project.getRowSortKeys())}if(!isColumns){project.setColumnSortKeys(sortKeys,true);this.scrollLeft(0)}else{project.setRowSortKeys(sortKeys,true);this.scrollTop(0)}morpheus.Util.trackEvent({eventCategory:"Tool",eventAction:isColumns?"sortRowsBasedOnSelection":"sortColumnsBasedOnSelection"})},getToolbarElement:function(){return this.toolbar.$el},getToolbar:function(){return this.toolbar},setName:function(name){this.options.name=name},getName:function(){return this.options.name},showOptions:function(){new morpheus.HeatMapOptions(this)},getProject:function(){return this.project},getDendrogram:function(isColumns){return isColumns?this.columnDendrogram:this.rowDendrogram},toJSON:function(options){var _this=this;var json={};json.colorScheme=this.heatmap.getColorScheme().toJSON();json.name=this.options.name;json.showRowNumber=this.isShowRowNumber();json.rowShapeModel=this.getProject().getRowShapeModel().toJSON(this.getVisibleTracks(false));json.columnShapeModel=this.getProject().getColumnShapeModel().toJSON(this.getVisibleTracks(true));json.rowFontModel=this.getProject().getRowFontModel().toJSON(this.getVisibleTracks(false));json.columnFontModel=this.getProject().getColumnFontModel().toJSON(this.getVisibleTracks(true));json.rowColorModel=this.getProject().getRowColorModel().toJSON(this.getVisibleTracks(false));json.columnColorModel=this.getProject().getColumnColorModel().toJSON(this.getVisibleTracks(true));json.rows=this.getVisibleTracks(false).map(function(track){var size=morpheus.CanvasUtil.getPreferredSize(_this.getTrackHeaderByIndex(_this.getTrackIndex(track.getName(),false),false));var obj=track.settings;obj.field=track.getName();obj.size={width:size.widthSet?size.width:undefined};return obj});json.columns=this.getVisibleTracks(true).map(function(track){var size=morpheus.CanvasUtil.getPreferredSize(_this.getTrackHeaderByIndex(_this.getTrackIndex(track.getName(),true),true));var obj=track.settings;obj.field=track.getName();obj.size={width:size.widthSet?size.width:undefined,height:size.heightSet?size.height:undefined};return obj});json.rowSortBy=morpheus.SortKey.toJSON(this.getProject().getRowSortKeys());json.columnSortBy=morpheus.SortKey.toJSON(this.getProject().getColumnSortKeys());json.rowGroupBy=morpheus.SortKey.toJSON(this.getProject().getGroupRows());json.columnGroupBy=morpheus.SortKey.toJSON(this.getProject().getGroupColumns());json.rowFilter=morpheus.CombinedFilter.toJSON(this.getProject().getRowFilter());json.columnFilter=morpheus.CombinedFilter.toJSON(this.getProject().getColumnFilter());json.symmetric=this.options.symmetric;json.rowSize=this.heatmap.getRowPositions().getSize();json.columnSize=this.heatmap.getColumnPositions().getSize();json.rowGapSize=this.heatmap.rowGapSize;json.columnGapSize=this.heatmap.columnGapSize;json.drawGrid=this.heatmap.isDrawGrid();json.gridColor=this.heatmap.getGridColor();json.gridThickness=this.heatmap.getGridThickness();json.drawValues=this.heatmap.isDrawValues();json.rowSelection=this.getProject().getRowSelectionModel().toModelIndices();json.columnSelection=this.getProject().getColumnSelectionModel().toModelIndices();json.rowSearchTerm=this.toolbar.getSearchField(morpheus.HeatMapToolBar.ROW_SEARCH_FIELD).val();json.columnSearchTerm=this.toolbar.getSearchField(morpheus.HeatMapToolBar.COLUMN_SEARCH_FIELD).val();if(this.rowDendrogram!=null){var out=[];morpheus.DendrogramUtil.writeNewick(this.rowDendrogram.tree.rootNode,out,function(n){return n.index});json.rowDendrogram=out.join("");json.rowDendrogramField=null}if(this.columnDendrogram!=null){var out=[];morpheus.DendrogramUtil.writeNewick(this.columnDendrogram.tree.rootNode,out,function(n){return n.index});json.columnDendrogram=out.join("");json.columnDendrogramField=null}if(options.dataset){json.dataset=morpheus.Dataset.toJSON(this.getProject().getFullDataset())}return json},setDendrogram:function(tree,isColumns,modelOrder){var dendrogram=isColumns?this.columnDendrogram:this.rowDendrogram;if(dendrogram){dendrogram.dispose();dendrogram=null}if(tree!=null){var size=isColumns?this.project.getFullDataset().getColumnCount():this.project.getFullDataset().getRowCount();if(isColumns){dendrogram=new morpheus.ColumnDendrogram(this,tree,this.heatmap.getColumnPositions(),this.project);dendrogram.filter=this.project.getColumnFilter().shallowClone();this.columnDendrogram=dendrogram;var sortKey=new morpheus.SpecifiedModelSortOrder(modelOrder,modelOrder.length,"dendrogram",true);sortKey.setPreservesDendrogram(true);sortKey.setLockOrder(2);sortKey.setUnlockable(false);this.project.setColumnSortKeys([sortKey],true)}else{dendrogram=new morpheus.RowDendrogram(this,tree,this.heatmap.getRowPositions(),this.project);dendrogram.filter=this.project.getRowFilter().shallowClone();this.rowDendrogram=dendrogram;var sortKey=new morpheus.SpecifiedModelSortOrder(modelOrder,modelOrder.length,"dendrogram",false);sortKey.setPreservesDendrogram(true);sortKey.setLockOrder(2);sortKey.setUnlockable(false);this.project.setRowSortKeys([sortKey],true)}dendrogram.appendTo(this.$parent);dendrogram.$label.appendTo(this.$parent);dendrogram.$squishedLabel.appendTo(this.$parent)}else{var sortKeys=isColumns?this.project.getColumnSortKeys():this.project.getRowSortKeys();for(var i=0;i<sortKeys.length;i++){if(sortKeys[i].isPreservesDendrogram()){sortKeys.splice(i,1);i--}}if(isColumns){this.heatmap.getColumnPositions().setSquishedIndices(null);delete this.columnDendrogram;this.project.setColumnSortKeys(sortKeys,true)}else{delete this.rowDendrogram;this.project.setRowSortKeys(sortKeys,true);this.heatmap.getRowPositions().setSquishedIndices(null)}}this.trigger("dendrogramChanged",{isColumns:isColumns})},getTabManager:function(){return this.tabManager},getSelectedElementsText:function(){var _this=this;var project=this.project;var selectedViewIndices=project.getElementSelectionModel().getViewIndices();if(selectedViewIndices.size()>0){var tipText=[];var dataset=project.getSortedFilteredDataset();var rowTracks=_this.rowTracks.filter(function(t){return t.settings.inlineTooltip});var columnTracks=_this.columnTracks.filter(function(t){return t.settings.inlineTooltip});selectedViewIndices.forEach(function(id){var rowIndex=id.getArray()[0];var columnIndex=id.getArray()[1];tipText.push(morpheus.Util.nf(dataset.getValue(rowIndex,columnIndex)));rowTracks.forEach(function(track){tipText.push("\t");tipText.push(morpheus.Util.toString(dataset.getRowMetadata().getByName(track.name).getValue(rowIndex)))});columnTracks.forEach(function(track){tipText.push("\t");tipText.push(morpheus.Util.toString(dataset.getColumnMetadata().getByName(track.name).getValue(columnIndex)))});tipText.push("\n")});return tipText.join("")}},_init:function(){var _this=this;morpheus.MetadataUtil.renameFields(this.options.dataset,this.options);var dataset=this.options.dataset;var rowDendrogram=this.options.rowDendrogram;var columnDendrogram=this.options.columnDendrogram;_.each(this.whenLoaded,function(f){f(_this.options.dataset)});if(this.options.datasetReady){var updatedDataset=this.options.datasetReady(dataset);if(updatedDataset){dataset=updatedDataset}}this.project=new morpheus.Project(dataset);if(this.tabManager){this.tabManager.setTabTitle(this.tabId,this.project.getFullDataset().getRowCount()+" row"+morpheus.Util.s(this.project.getFullDataset().getRowCount())+" x "+this.project.getFullDataset().getColumnCount()+" column"+morpheus.Util.s(this.project.getFullDataset().getColumnCount()))}if(this.options.inheritFromParent&&this.options.parent!=null){morpheus.HeatMap.copyFromParent(this.project,this.options)}if(this.options.rowFilter){morpheus.CombinedFilter.fromJSON(_this.project.getRowFilter(),this.options.rowFilter);_this.project.setRowFilter(_this.project.getRowFilter(),true)}if(this.options.columnFilter){morpheus.CombinedFilter.fromJSON(_this.project.getColumnFilter(),this.options.columnFilter);_this.project.setColumnFilter(_this.project.getColumnFilter(),true)}this.whenLoaded=null;this.$parent=$("<div></div>").css("position","relative");this.$parent.appendTo(this.$content);if(!morpheus.Util.isHeadless()){this.toolbar=new morpheus.HeatMapToolBar(this)}this.vscroll=new morpheus.ScrollBar(true);this.vscroll.appendTo(this.$parent);this.vscroll.on("scroll",function(){if(_this.updatingScroll){return}_this.paintAll({paintRows:true,paintColumns:false,invalidateRows:true,invalidateColumns:false})});this.beforeColumnTrackDivider=new morpheus.Divider(false);this.beforeColumnTrackDivider.appendTo(this.$parent);var dragStartHeight=0;this.beforeColumnTrackDivider.on("resizeStart",function(e){dragStartHeight=_this.columnDendrogram.getUnscaledHeight()}).on("resize",function(e){var newHeight=Math.max(8,dragStartHeight+e.delta);_this.columnDendrogram.setPrefHeight(newHeight);_this.revalidate()}).on("resizeEnd",function(){dragStartHeight=0});this.afterRowDendrogramDivider=new morpheus.Divider(true);this.afterRowDendrogramDivider.appendTo(this.$parent);var rowDendrogramStartWidth=0;this.afterRowDendrogramDivider.on("resizeStart",function(e){rowDendrogramStartWidth=_this.rowDendrogram.getUnscaledWidth()}).on("resize",function(e){var newWidth=Math.max(8,rowDendrogramStartWidth+e.delta);_this.rowDendrogram.setPrefWidth(newWidth);_this.revalidate()}).on("resizeEnd",function(){rowDendrogramStartWidth=0});this.afterVerticalScrollBarDivider=new morpheus.Divider(true);this.afterVerticalScrollBarDivider.appendTo(this.$parent);var resizeStartHeatMapWidth=0;this.afterVerticalScrollBarDivider.on("resizeStart",function(e){resizeStartHeatMapWidth=_this.heatmap.getUnscaledWidth()}).on("resize",function(e){_this.heatmap.prefWidth=resizeStartHeatMapWidth+e.delta;_this.revalidate()});this.hscroll=new morpheus.ScrollBar(false);this.hscroll.appendTo(this.$parent);this.hscroll.on("scroll",function(){if(_this.updatingScroll){return}_this.paintAll({paintRows:false,paintColumns:true,invalidateRows:false,invalidateColumns:true})});this.$whitespace=$('<div style="position: absolute;"></div>');this.$whitespace.appendTo(this.$parent);var heatmap=new morpheus.HeatMapElementCanvas(this.project);if(this.options.drawCallback){heatmap.setDrawCallback(this.options.drawCallback)}$(heatmap.canvas).on("contextmenu",function(e){var items=[];morpheus.Popup.showPopup([{name:"Copy Image",class:"copy"},{name:"Save Image ("+morpheus.Util.COMMAND_KEY+"S)"},{separator:true},{name:"Show Inline Tooltip",checked:_this.options.inlineTooltip}],{x:e.pageX,y:e.pageY},e.target,function(event,item){if(item==="Show Inline Tooltip"){_this.options.inlineTooltip=!_this.options.inlineTooltip}else if(item==="Save Image ("+morpheus.Util.COMMAND_KEY+"S)"){_this.getActionManager().execute("Save Image")}else if(item==="Copy Selection"){var text=_this.getSelectedElementsText();if(text!==""){event.clipboardData.setData("text/plain",text)}}else if(item==="Copy Image"){_this.getActionManager().execute("Copy Image",{event:event})}else{console.log(item+" unknown.")}});e.preventDefault();e.stopPropagation();e.stopImmediatePropagation()});heatmap.appendTo(this.$parent);this.heatmap=heatmap;var rowDendrogramSortKey=null;if(rowDendrogram!=null){var tree=rowDendrogram;if(tree.leafNodes.length!==this.project.getSortedFilteredDataset().getRowCount()){throw"# leaf nodes in row dendrogram "+tree.leafNodes.length+" != "+this.project.getSortedFilteredDataset().getRowCount()}var rowIndices=null;if(this.options.rowDendrogramField!=null){var vector=dataset.getRowMetadata().getByName(this.options.rowDendrogramField);rowIndices=[];var map=new morpheus.Map;var re=/[,:]/g;for(var j=0,size=vector.size();j<size;j++){var key=vector.getValue(j);map.set(key.replace(re,""),j)}for(var i=0,length=tree.leafNodes.length;i<length;i++){var index=map.get(tree.leafNodes[i].name);if(index===undefined){throw"Unable to find row dendrogram id "+tree.leafNodes[i].name+" in row annotations"}rowIndices.push(index)}}else{}this.rowDendrogram=new morpheus.RowDendrogram(this,tree,heatmap.getRowPositions(),this.project,true);this.rowDendrogram.appendTo(this.$parent);this.rowDendrogram.$label.appendTo(this.$parent);this.rowDendrogram.$squishedLabel.appendTo(this.$parent);if(rowIndices!=null){rowDendrogramSortKey=new morpheus.SpecifiedModelSortOrder(rowIndices,rowIndices.length,"dendrogram");rowDendrogramSortKey.setLockOrder(2);rowDendrogramSortKey.setUnlockable(false);rowDendrogramSortKey.setPreservesDendrogram(true)}}var columnDendrogramSortKey=null;if(columnDendrogram!=null){var tree=columnDendrogram;if(tree.leafNodes.length!==this.project.getSortedFilteredDataset().getColumnCount()){throw"# leaf nodes "+tree.leafNodes.length+" != "+this.project.getSortedFilteredDataset().getColumnCount()}var columnIndices=null;if(this.options.columnDendrogramField!=null){columnIndices=[];var vector=dataset.getColumnMetadata().getByName(this.options.columnDendrogramField);var map=new morpheus.Map;var re=/[,:]/g;for(var j=0,size=vector.size();j<size;j++){var key=vector.getValue(j);map.set(key.replace(re,""),j)}for(var i=0,length=tree.leafNodes.length;i<length;i++){var index=map.get(tree.leafNodes[i].name);if(index===undefined){throw"Unable to find column dendrogram id "+tree.leafNodes[i].name+" in column annotations"}columnIndices.push(index)}}else{}this.columnDendrogram=new morpheus.ColumnDendrogram(this,tree,heatmap.getColumnPositions(),this.project,true);this.columnDendrogram.appendTo(this.$parent);this.columnDendrogram.$label.appendTo(this.$parent);this.columnDendrogram.$squishedLabel.appendTo(this.$parent);if(columnIndices!=null){columnDendrogramSortKey=new morpheus.SpecifiedModelSortOrder(columnIndices,columnIndices.length,"dendrogram");columnDendrogramSortKey.setLockOrder(2);columnDendrogramSortKey.setUnlockable(false);columnDendrogramSortKey.setPreservesDendrogram(true)}}if(this.options.drawGrid!=null){this.heatmap.setDrawGrid(this.options.drawGrid)}if(this.options.gridColor!=null){this.heatmap.setGridColor(this.options.gridColor)}if(this.options.gridThickness!=null){this.heatmap.setGridThickness(this.options.gridThickness)}if(this.options.drawValues!=null){this.heatmap.setDrawValues(this.options.drawValues)}if(rowDendrogramSortKey!=null){this.project.setRowSortKeys([rowDendrogramSortKey])}if(columnDendrogramSortKey!=null){this.project.setColumnSortKeys([columnDendrogramSortKey])}if(this.options.rowSortBy&&this.options.rowSortBy.length>0){this.project.setRowSortKeys(morpheus.SortKey.fromJSON(this.project,this.options.rowSortBy),false)}if(this.options.columnSortBy&&this.options.columnSortBy.length>0){this.project.setColumnSortKeys(morpheus.SortKey.fromJSON(this.project,this.options.columnSortBy),false)}if(this.options.rowGroupBy!=null&&this.options.rowGroupBy.length>0){var keys=morpheus.SortKey.fromJSON(this.project,this.options.rowGroupBy);for(var i=0;i<keys.length;i++){this.project.groupRows.push(keys[i])}}if(this.options.columnGroupBy!=null&&this.options.columnGroupBy.length>0){var keys=morpheus.SortKey.fromJSON(this.project,this.options.columnGroupBy);for(var i=0;i<keys.length;i++){this.project.groupColumns.push(keys[i])}}if(this.options.rowSelection!=null&&this.options.rowSelection.length>0){var indices=new morpheus.Set;for(var i=0,length=this.options.rowSelection.length;i<length;i++){indices.add(this.project.convertModelRowIndexToView(this.options.rowSelection[i]))}this.project.getRowSelectionModel().setViewIndices(indices,false)}if(this.options.columnSelection!=null&&this.options.columnSelection.length>0){var indices=new morpheus.Set;for(var i=0,length=this.options.columnSelection.length;i<length;i++){indices.add(this.project.convertModelColumnIndexToView(this.options.columnSelection[i]))}this.project.getColumnSelectionModel().setViewIndices(indices,false)}this.vSortByValuesIndicator=new morpheus.SortByValuesIndicator(this.project,true,heatmap.getRowPositions());this.vSortByValuesIndicator.appendTo(this.$parent);this.hSortByValuesIndicator=new morpheus.SortByValuesIndicator(this.project,false,heatmap.getColumnPositions());this.hSortByValuesIndicator.appendTo(this.$parent);this.verticalSearchBar=new morpheus.ScentedSearch(this.project.getRowSelectionModel(),heatmap.getRowPositions(),true,this.vscroll,this);this.horizontalSearchBar=new morpheus.ScentedSearch(this.project.getColumnSelectionModel(),heatmap.getColumnPositions(),false,this.hscroll,this);this.rowTracks=[];this.rowTrackHeaders=[];this.columnTracks=[];this.columnTrackHeaders=[];if(this.options.rowSize!=null&&this.options.rowSize!=="fit"){this.heatmap.getRowPositions().setSize(this.options.rowSize)}if(this.options.columnSize!=null&&this.options.columnSize!=="fit"){this.heatmap.getColumnPositions().setSize(this.options.columnSize)}var setInitialDisplay=function(isColumns,options){var nameToOption=new morpheus.Map;var displaySpecified=_this.options.parent!=null&&_this.options.inheritFromParent;if(options!=null&&options.length>0){displaySpecified=true;for(var i=0;i<options.length;i++){nameToOption.set(options[i].renameTo!=null?options[i].renameTo:options[i].field,options[i])}}var displayMetadata=isColumns?dataset.getColumnMetadata():dataset.getRowMetadata();if(!displaySpecified){var defaultFieldsToShow=new morpheus.Set;["pert_iname","moa","target","description","cell_id","pert_type"].forEach(function(field){defaultFieldsToShow.add(field)});for(var i=0,metadataCount=displayMetadata.getMetadataCount();i<metadataCount;i++){var v=displayMetadata.get(i);if(defaultFieldsToShow.has(v.getName())&&!nameToOption.has(v.getName())){nameToOption.set(v.getName(),{display:["text"]});displaySpecified=true}}}var isFirst=true;for(var i=0,metadataCount=displayMetadata.getMetadataCount();i<metadataCount;i++){var v=displayMetadata.get(i);var name=v.getName();var option=nameToOption.get(name);if(displaySpecified&&option==null){continue}if(morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS.has(name)&&option==null){continue}var count=isColumns?dataset.getColumnCount():dataset.getRowCount();if(option==null&&!displaySpecified&&count>1&&!morpheus.VectorUtil.containsMoreThanOneValue(v)){continue}if(option==null){option={}}if(option.title){v.getProperties().set(morpheus.VectorKeys.TITLE,option.title)}if(option.display==null){if(name==="pert_iname"||name==="id"||isFirst){option.inlineTooltip=true;option.display=["text"]}else{option.display=isColumns?"color,highlight":"text"}}isFirst=false;var track=_this.addTrack(name,isColumns,option);if(option.size){if(!isColumns&&option.size.width!=null){var header=_this.getTrackHeaderByIndex(_this.getTrackIndex(name,isColumns),isColumns);track.setPrefWidth(option.size.width);header.setPrefWidth(option.size.width)}else if(isColumns&&(option.size.width!=null||option.size.height!=null)){var header=_this.getTrackHeaderByIndex(_this.getTrackIndex(name,isColumns),isColumns);if(option.size.height){track.setPrefHeight(option.size.height);header.setPrefHeight(option.size.height)}if(option.size.width){track.setPrefWidth(option.size.width);header.setPrefWidth(option.size.width)}}}if(option.header&&option.header.font){var header=_this.getTrackHeaderByIndex(_this.getTrackIndex(name,isColumns),isColumns);header.font=option.header.font}if(option.formatter){v.getProperties().set(morpheus.VectorKeys.FORMATTER,morpheus.Util.createNumberFormat(option.formatter))}if(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)&&option.color){var m=isColumns?_this.project.getColumnColorModel():_this.project.getRowColorModel();if(track.getFullVector().getProperties.get(morpheus.VectorKeys.DISCRETE)){_.each(options.color,function(p){m.setMappedValue(v,p.value,p.color)})}else{var cs=m.createContinuousColorMap(v);var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;_.each(options.color,function(p){min=Math.min(min,p.value);max=Math.max(max,p.value)});cs.setMin(min);cs.setMax(max);var valueToFraction=d3.scale.linear().domain([cs.getMin(),cs.getMax()]).range([0,1]).clamp(true);var fractions=[];var colors=[];_.each(options.color,function(p){fractions.push(valueToFraction(p.value));colors.push(p.color)});cs.setFractions({fractions:fractions,colors:colors})}if(track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)&&option.shape){var m=isColumns?_this.project.getColumnShapeModel():_this.project.getRowShapeModel();_.each(options.shape,function(p){m.setMappedValue(v,p.value,p.shape)})}}}};setInitialDisplay(false,this.options.rows);setInitialDisplay(true,this.options.columns);function reorderTracks(array,isColumns){if(array==null||array.length<=1){return}var nameOrderPairs=[];var found=false;array.forEach(function(item,index){var name=item.renameTo||item.field;var order=index;if(item.order!=null){order=item.order;found=true}nameOrderPairs.push({name:name,order:order})});if(!found){array.forEach(function(item,index){var name=item.renameTo||item.field;nameOrderPairs.push({name:name,order:index})})}nameOrderPairs.sort(function(a,b){return a.order===b.order?0:a.order<b.order?-1:1});for(var i=0,counter=0;i<nameOrderPairs.length;i++){var index=_this.getTrackIndex(nameOrderPairs[i].name,isColumns);if(index!==-1){_this.moveTrack(index,counter,isColumns);counter++}}}reorderTracks(this.options.rows,false);reorderTracks(this.options.columns,true);if(this.options.showRowNumber){this.setShowRowNumber(true)}var colorSchemeSpecified=this.options.colorScheme!=null;if(this.options.colorScheme==null){var ext="";if(this.options.dataSource){ext=morpheus.Util.getExtension(morpheus.Util.getFileName(this.options.dataSource))}var colorScheme=this.autoDisplay({filename:morpheus.Util.getBaseFileName(morpheus.Util.getFileName(this.options.dataset)),extension:ext});if(colorScheme==null){colorScheme={type:"relative"}}this.options.colorScheme=colorScheme;var name=this.project.getFullDataset().getName();if(ext==="maf"&&!this.options.rowSortBy){var sortKeys=[];if(this.project.getFullDataset().getRowMetadata().getByName("order")){sortKeys.push(new morpheus.SortKey("order",morpheus.SortKey.SortOrder.ASCENDING))}sortKeys.push(new morpheus.SortKey("id",morpheus.SortKey.SortOrder.ASCENDING));this.project.setRowSortKeys(sortKeys,false)}if(morpheus.DatasetUtil.getSeriesIndex(this.project.getFullDataset(),"allelic_fraction")!==-1){this.options.sizeBy={seriesName:"allelic_fraction",min:0,max:1}}}if(this.options.parent&&this.options.inheritFromParent){this.heatmap.setPropertiesFromParent(this.options.parent.heatmap)}if(this.options.parent&&this.options.inheritFromParent&&!colorSchemeSpecified){heatmap.setColorScheme(this.options.parent.heatmap.getColorScheme().copy(this.project))}else{heatmap.setColorScheme(new morpheus.HeatMapColorScheme(this.project,this.options.colorScheme));if(this.options.dataset.getRowMetadata().getByName("Source")!=null){var sourcesSet=morpheus.VectorUtil.getSet(this.options.dataset.getRowMetadata().getByName("Source"));this.heatmap.getColorScheme().setSeparateColorSchemeForRowMetadataField("Source");sourcesSet.forEach(function(source){_this.autoDisplay({extension:morpheus.Util.getExtension(source),filename:""+source})})}}if(this.options.sizeBy){heatmap.getColorScheme().getSizer().setSeriesName(this.options.sizeBy.seriesName);heatmap.getColorScheme().getSizer().setMin(this.options.sizeBy.min);heatmap.getColorScheme().getSizer().setMax(this.options.sizeBy.max)}this.updateDataset();if(this.options.tabOpened){this.options.tabOpened(this);this.updateDataset()}if(this.options.renderReady){this.options.renderReady(this);this.updateDataset()}if(this.options.rowSize==="fit"){this.heatmap.getRowPositions().setSize(this.getFitRowSize());this.revalidate({paint:false})}if(this.options.columnSize==="fit"){this.heatmap.getColumnPositions().setSize(this.getFitColumnSize());this.revalidate({paint:false})}if(this.options.rowColorModel){this.getProject().getRowColorModel().fromJSON(this.options.rowColorModel)}if(this.options.columnColorModel){this.getProject().getColumnColorModel().fromJSON(this.options.columnColorModel)}if(this.options.rowShapeModel){this.getProject().getRowShapeModel().fromJSON(this.options.rowShapeModel)}if(this.options.columnShapeModel){this.getProject().getColumnShapeModel().fromJSON(this.options.columnShapeModel)}if(this.options.rowFontModel){this.getProject().getRowFontModel().fromJSON(this.options.rowFontModel)}if(this.options.columnFontModel){this.getProject().getColumnFontModel().fromJSON(this.options.columnFontModel)}if(this.options.rowSize==="fit"||this.options.columnSize==="fit"){if(this.options.columnSize==="fit"){this.heatmap.getColumnPositions().setSize(this.getFitColumnSize());this.revalidate({paint:false})}if(this.options.rowSize==="fit"){this.heatmap.getRowPositions().setSize(this.getFitRowSize());this.revalidate({paint:false})}this.paintAll({paintRows:true,paintColumns:true,invalidateRows:true,invalidateColumns:true})}this.options.parent=null;this.$tipFollow=$('<div style="display:none;"'+' class="morpheus-tip-inline"></div>');this.$tipFollow.appendTo(this.$parent);this.$tipInfoWindow=$('<div class="morpheus-tip-dialog"></div>');this.$tipInfoWindow.appendTo(this.$parent);if(!morpheus.Util.isHeadless()){this.$tipInfoWindow.dialog({close:function(event,ui){if(!_this._togglingInfoWindow){_this.toggleInfoWindow()}},autoOpen:false,width:220,height:280,minHeight:38,minWidth:10,collision:"fit",position:{my:"right-30 bottom",at:"right top",of:this.$parent},title:"Info"});this.setTooltipMode(this.options.tooltipMode)}this.getProject().on("rowFilterChanged columnFilterChanged rowGroupByChanged columnGroupByChanged rowSortOrderChanged columnSortOrderChanged datasetChanged",function(e){if(e.type==="datasetChanged"){var dataset=_this.getProject().getFullDataset();for(var i=0;i<_this.rowTracks.length;i++){var track=_this.rowTracks[i];if(!dataset.getRowMetadata().getByName(track.getName())){_this.removeTrack(track.getName(),false);i--}}for(var i=0;i<_this.columnTracks.length;i++){var track=_this.columnTracks[i];if(!dataset.getColumnMetadata().getByName(track.getName())){_this.removeTrack(track.getName(),true);i--}}}_this.updateDataset();_this.revalidate()});this.getProject().on("trackChanged",function(e){var columns=e.columns;_.each(e.vectors,function(v,i){var index=_this.getTrackIndex(v.getName(),columns);if(index===-1){_this.addTrack(v.getName(),columns,e.display[i])}else{var track=_this.getTrackByIndex(index,columns);var display=e.display[i];if(display){track.settingFromConfig(display)}track.setInvalid(true)}});_this.revalidate()});this.getProject().on("rowTrackRemoved",function(e){_this.removeTrack(e.vector.getName(),false);_this.revalidate()});this.getProject().on("columnTrackRemoved",function(e){_this.removeTrack(e.vector.getName(),true);_this.revalidate()});this.getProject().getRowSelectionModel().on("selectionChanged",function(){for(var i=0;i<_this.columnTracks.length;i++){var track=_this.columnTracks[i];if(track.getFullVector().getProperties().get(morpheus.VectorKeys.RECOMPUTE_FUNCTION_SELECTION)){var selectedDataset=_this.getProject().getSelectedDataset({selectedRows:true,selectedColumns:false,emptyToAll:false});var vector=selectedDataset.getColumnMetadata().getByName(track.getName());var f=morpheus.VectorUtil.jsonToFunction(vector,morpheus.VectorKeys.FUNCTION);if(typeof f==="function"){var view=new morpheus.DatasetColumnView(selectedDataset);for(var j=0,size=vector.size();j<size;j++){view.setIndex(j);vector.setValue(j,f(view,selectedDataset,j))}track.setInvalid(true);track.repaint()}}}_this.verticalSearchBar.update();_this.heatmap.updateRowSelectionCache();_this.paintAll({paintRows:true,paintColumns:false,invalidateRows:false,invalidateColumns:false})});this.getProject().getColumnSelectionModel().on("selectionChanged",function(){_this.horizontalSearchBar.update();_this.heatmap.updateColumnSelectionCache();_this.paintAll({paintRows:false,paintColumns:true,invalidateRows:false,invalidateColumns:false})});this.pasteListener=function(e){if(_this.isActiveComponent()){var text=e.originalEvent.clipboardData.getData("text/plain");if(text!=null&&text.length>0){e.preventDefault();e.stopPropagation();var url;if(text.indexOf("http")===0){url=text}else{var blob=new Blob([text],{type:"text/plain"});url=URL.createObjectURL(blob)}morpheus.HeatMap.showTool(new morpheus.OpenFileTool({file:url}),_this)}}};this.beforeCopyListener=function(e){if(_this.isActiveComponent()){e.preventDefault()}};this.copyListener=function(ev){if(_this.isActiveComponent()){var activeComponent=_this.getActiveComponent();var project=_this.project;if(activeComponent==="heatMap"||ev.shiftKey){var bounds=_this.getTotalSize();var height=bounds.height;var width=bounds.width;var canvas=$("<canvas></canvas>")[0];canvas.height=height;canvas.width=width;var context=canvas.getContext("2d");_this.snapshot(context);var url=canvas.toDataURL();ev.originalEvent.clipboardData.setData("text/html",'<img src="'+url+'">');ev.preventDefault();ev.stopImmediatePropagation();return}var dataset=project.getSelectedDataset({emptyToAll:false});var rowsSelected=dataset.getRowCount()>0;var columnsSelected=dataset.getColumnCount()>0;var columnMetadata=dataset.getColumnMetadata();var rowMetadata=dataset.getRowMetadata();var visibleColumnFields=_this.getVisibleTrackNames(true);var columnFieldIndices=[];_.each(visibleColumnFields,function(name){var index=morpheus.MetadataUtil.indexOf(columnMetadata,name);if(index!==-1){columnFieldIndices.push(index)}});columnMetadata=new morpheus.MetadataModelColumnView(columnMetadata,columnFieldIndices);var rowMetadata=dataset.getRowMetadata();var visibleRowFields=_this.getVisibleTrackNames(false);var rowFieldIndices=[];_.each(visibleRowFields,function(name){var index=morpheus.MetadataUtil.indexOf(rowMetadata,name);if(index!==-1){rowFieldIndices.push(index)}});rowMetadata=new morpheus.MetadataModelColumnView(rowMetadata,rowFieldIndices);var text=[];if(rowsSelected&&columnsSelected){text=(new morpheus.GctWriter).write(dataset)}else{var text=[];var model=rowsSelected?rowMetadata:columnMetadata;for(var i=0,count=model.getItemCount();i<count;i++){for(var j=0,nfields=model.getMetadataCount();j<nfields;j++){var v=model.get(j);if(j>0){text.push("\t")}text.push(morpheus.Util.toString(v.getValue(i)))}text.push("\n")}text=text.join("")}ev.originalEvent.clipboardData.setData("text/plain",text);ev.preventDefault();ev.stopImmediatePropagation()}};if(typeof window!=="undefined"){$(window).on("paste.morpheus",this.pasteListener).on("beforecopy.morpheus",this.beforeCopyListener).on("copy.morpheus",this.copyListener)}if(this.options.keyboard&&!morpheus.Util.isHeadless()){new morpheus.HeatMapKeyListener(this)}if(this.options.symmetric){this.getProject().setSymmetric(this)}var dragStartScrollTop;var dragStartScrollLeft;var panstartMousePosition;this.hammer=morpheus.Util.hammer(_this.heatmap.canvas,["pan","pinch","tap","swipe"]).on("swipe",this.swipe=function(event){event.preventDefault()}).on("panend",this.panend=function(event){_this.panning=false;if(panstartMousePosition){panstartMousePosition=null;_this.heatmap.setSelectionBox(null);_this.heatmap.repaint()}event.preventDefault()}).on("panmove",this.panmove=function(event){if(panstartMousePosition){var pos=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.scrollLeft(),_this.scrollTop());var rowIndex=_this.heatmap.getRowPositions().getIndex(pos.y,false);var columnIndex=_this.heatmap.getColumnPositions().getIndex(pos.x,false);_this.updatingScroll=false;_this.heatmap.setSelectionBox({y:[panstartMousePosition.rowIndex,rowIndex],x:[panstartMousePosition.columnIndex,columnIndex]});var rowIndices=new morpheus.Set;for(var i=Math.min(panstartMousePosition.rowIndex,rowIndex),end=Math.max(panstartMousePosition.rowIndex,rowIndex);i<=end;i++){rowIndices.add(i)}var columnIndices=new morpheus.Set;for(var i=Math.min(panstartMousePosition.columnIndex,columnIndex),end=Math.max(panstartMousePosition.columnIndex,columnIndex);i<=end;i++){columnIndices.add(i)}_this.project.getRowSelectionModel().setViewIndices(rowIndices,true);_this.project.getColumnSelectionModel().setViewIndices(columnIndices,true)}else{_this.updatingScroll=true;var rows=false;var columns=false;if(event.deltaY!==0){var pos=dragStartScrollTop+event.deltaY;_this.scrollTop(pos);rows=true}if(event.deltaX!==0){var pos=dragStartScrollLeft+event.deltaX;_this.scrollLeft(pos);columns=true}_this.updatingScroll=false;if(rows||columns){_this.paintAll({paintRows:rows,paintColumns:rows,invalidateRows:rows,invalidateColumns:columns})}}event.preventDefault()}).on("panstart",this.panstart=function(event){_this.panning=true;_this.project.setHoverRowIndex(-1);_this.project.setHoverColumnIndex(-1);if(event.srcEvent.shiftKey){var pos=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.scrollLeft(),_this.scrollTop());panstartMousePosition={rowIndex:_this.heatmap.getRowPositions().getIndex(pos.y,false),columnIndex:_this.heatmap.getColumnPositions().getIndex(pos.x,false)}}else{panstartMousePosition=null;dragStartScrollTop=_this.scrollTop();dragStartScrollLeft=_this.scrollLeft()}event.preventDefault()}).on("tap",this.tap=function(event){if(morpheus.Util.IS_MAC&&event.srcEvent.ctrlKey){return}_this.project.getRowSelectionModel().setViewIndices(new morpheus.Set,true);_this.project.getColumnSelectionModel().setViewIndices(new morpheus.Set,true)}).on("pinch",this.pinch=function(event){var scale=event.scale;_this.heatmap.getRowPositions().setSize(13*scale);_this.heatmap.getColumnPositions().setSize(13*scale);var reval={};if(_this.project.getHoverRowIndex()!==-1){reval.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}if(_this.project.getHoverColumnIndex()!==-1){reval.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}_this.revalidate(reval);event.preventDefault()});var heatMapMouseMoved=function(event){var mouseI,mouseJ;if(event.type==="mouseout"){mouseI=-1;mouseJ=-1}else{var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.scrollLeft(),_this.scrollTop());mouseI=_this.heatmap.getRowPositions().getIndex(position.y,false);mouseJ=_this.heatmap.getColumnPositions().getIndex(position.x,false)}_this.setMousePosition(mouseI,mouseJ,{event:event})};$(_this.heatmap.canvas).on("mouseout",heatMapMouseMoved).on("mousemove",heatMapMouseMoved);_.each(this.options.tools,function(item){var action=_this.getActionManager().getAction(item.name);if(action==null){console.log(item.name+" not found.")}else{var actionGui=action.gui();var gui=actionGui.gui(_this.getProject());var formBuilder=new morpheus.FormBuilder;_.each(gui,function(item){formBuilder.append(item)});var input={};_.each(gui,function(item){input[item.name]=formBuilder.getValue(item.name)});if(item.params){for(var key in item.params){input[key]=item.params[key]}}actionGui.execute({heatMap:_this,project:_this.getProject(),input:input})}})},setMousePosition:function(i,j,options){this.mousePositionOptions=options;var updateColumns=this.project.getHoverColumnIndex()!==j;var updateRows=this.project.getHoverRowIndex()!==i;if(updateColumns||updateRows){if(!this.panning){this.project.setHoverRowIndex(i);this.project.setHoverColumnIndex(j)}this.setToolTip(i,j,options);this.paintAll({paintRows:updateRows,paintColumns:updateColumns,invalidateRows:false,invalidateColumns:false})}else{this._updateTipFollowPosition(options)}this.trigger("change",{name:"setMousePosition",source:this,arguments:arguments})},getContentEl:function(){return this.$content},focus:function(){var scrollTop=document.body.scrollTop;this.$tabPanel.focus();document.body.scrollTop=scrollTop},getFocusEl:function(){return this.$tabPanel},setTooltipMode:function(mode){this._togglingInfoWindow=true;this.options.tooltipMode=mode;this.$tipInfoWindow.html("");this.toolbar.$tip.html("");this.$tipFollow.html("").css({display:"none"});this.toolbar.$tip.css("display",mode===0?"":"none");this.setToolTip(-1,-1);if(this.options.tooltipMode===1){this.$tipInfoWindow.dialog("open")}else{this.$tipInfoWindow.dialog("close")}this._togglingInfoWindow=false},toggleInfoWindow:function(){this.setTooltipMode(this.options.tooltipMode==1?0:1)},_setTipText:function(tipText,tipFollowText,options){if(this.options.tooltipMode===0){this.toolbar.$tip.html(tipText.join(""))}else if(this.options.tooltipMode===1){this.$tipInfoWindow.html(tipText.join(""))}if(tipFollowText!=null){this.tipFollowHidden=false;this.$tipFollow.html(tipFollowText);this._updateTipFollowPosition(options)}else{this.tipFollowHidden=true;this.$tipFollow.empty().css({display:"none"})}this.trigger("change",{name:"setToolTip",source:this,arguments:arguments})},setToolTip:function(rowIndex,columnIndex,options){options=options||{};if(this.options.showSeriesNameInTooltip){options.showSeriesNameInTooltip=true}if(this.options.tooltipSeriesIndices){options.tooltipSeriesIndices=this.options.tooltipSeriesIndices}if(options.heatMapLens){var maxSelectedCount=20;var $wrapper=$("<div></div>");var wrapperHeight=0;var wrapperWidth=0;var found=false;var inline=[];var indicesForLens=[];if(rowIndex!=null&&rowIndex.length>0){for(var hoverIndex=0;hoverIndex<rowIndex.length;hoverIndex++){var row=rowIndex[hoverIndex];if(row>=0&&(row>=this.heatmap.lastPosition.bottom||row<this.heatmap.lastPosition.top)){indicesForLens.push(row)}else{inline.push(row)}}if(indicesForLens.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<indicesForLens.length;hoverIndex++){var row=indicesForLens[hoverIndex];var heatMapWidth=this.heatmap.getUnscaledWidth();var top=row;var bottom=row+1;var startPix=this.heatmap.rowPositions.getPosition(top);var endPix=startPix+this.heatmap.rowPositions.getItemSize(top);var heatMapHeight=endPix-startPix;var canvas=morpheus.CanvasUtil.createCanvas();var trackWidth=0;for(var i=0,ntracks=this.rowTracks.length;i<ntracks;i++){var track=this.rowTracks[i];if(track.isVisible()){trackWidth+=track.getUnscaledWidth()}}var canvasWidth=trackWidth+heatMapWidth+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;canvas.width=canvasWidth*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.width=canvasWidth+"px";canvas.height=heatMapHeight*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.height=heatMapHeight+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);context.save();context.translate(-this.heatmap.lastClip.x,-startPix);context.rect(this.heatmap.lastClip.x,startPix,this.heatmap.lastClip.width,this.heatmap.lastClip.height);context.clip();this.heatmap._draw({left:this.heatmap.lastPosition.left,right:this.heatmap.lastPosition.right,top:top,bottom:bottom,context:context});context.restore();context.translate(heatMapWidth+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS,-startPix);trackWidth=0;for(var i=0,ntracks=this.rowTracks.length;i<ntracks;i++){var track=this.rowTracks[i];if(track.isVisible()){context.save();context.translate(trackWidth,0);context.rect(0,startPix,track.getUnscaledWidth(),track.lastClip.height);context.clip();track._draw({start:top,end:bottom,vector:track.getVector(),context:context,availableSpace:track.getUnscaledWidth()});context.restore();trackWidth+=track.getUnscaledWidth()}}$(canvas).appendTo($wrapper);canvas.style.top=wrapperHeight+"px";wrapperHeight+=parseFloat(canvas.style.height);wrapperWidth=parseFloat(canvas.style.width)}}if(indicesForLens.length>0){if(indicesForLens.length<maxSelectedCount){$wrapper.css({height:wrapperHeight,width:wrapperWidth});var rect=this.$parent[0].getBoundingClientRect();this.$tipFollow.html($wrapper).css({display:"",left:Math.round(parseFloat(this.heatmap.canvas.style.left)-1)+"px",top:options.event.clientY-rect.top-wrapperHeight/2+"px"})}else{this.$tipFollow.html("")}return}else{var tipText=[];var tipFollowText=[];if(inline.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<inline.length;hoverIndex++){this.tooltipProvider(this,inline[hoverIndex],-1,options,this.options.tooltipMode===0?"&nbsp;&nbsp;&nbsp;":"<br />",false,tipText);if(this.options.inlineTooltip){this.tooltipProvider(this,inline[hoverIndex],-1,options,"<br />",true,tipFollowText)}}}var text=tipFollowText.join("");this._setTipText(tipText,text.length===0?null:'<span style="max-width:400px;">'+text+"</span>",options)}}if(columnIndex!=null&&columnIndex.length>0){for(var hoverIndex=0;hoverIndex<columnIndex.length;hoverIndex++){var column=columnIndex[hoverIndex];if(column>=0&&(column>=this.heatmap.lastPosition.right||column<this.heatmap.lastPosition.left)){indicesForLens.push(column)}else{inline.push(column)}}if(indicesForLens.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<indicesForLens.length;hoverIndex++){var column=indicesForLens[hoverIndex];var heatMapHeight=this.heatmap.getUnscaledHeight();var left=column;var right=column+1;var startPix=this.heatmap.columnPositions.getPosition(left);var endPix=startPix+this.heatmap.columnPositions.getItemSize(left);var heatMapWidth=endPix-startPix;var canvas=morpheus.CanvasUtil.createCanvas();var trackHeight=0;for(var i=0,ntracks=this.columnTracks.length;i<ntracks;i++){var track=this.columnTracks[i];if(track.isVisible()){trackHeight+=track.getUnscaledHeight()}}var canvasHeight=trackHeight+heatMapHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;canvas.width=heatMapWidth*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.width=heatMapWidth+"px";canvas.height=canvasHeight*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.height=canvasHeight+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);context.translate(-startPix,0);context.save();context.rect(startPix,trackHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS,this.heatmap.lastClip.width,this.heatmap.lastClip.height+trackHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS);context.clip();context.translate(0,trackHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS-this.heatmap.lastClip.y);this.heatmap._draw({top:this.heatmap.lastPosition.top,bottom:this.heatmap.lastPosition.bottom,left:left,right:right,context:context});context.restore();trackHeight=0;for(var i=0,ntracks=this.columnTracks.length;i<ntracks;i++){var track=this.columnTracks[i];if(track.isVisible()){context.save();context.translate(0,trackHeight);context.rect(startPix,0,track.lastClip.width,track.getUnscaledHeight());context.clip();track._draw({start:left,end:right,vector:track.getVector(),context:context,availableSpace:track.getUnscaledHeight(),clip:{x:track.lastClip.x,y:track.lastClip.y}});context.restore();trackHeight+=track.getUnscaledHeight()}}canvas.style.left=wrapperWidth+"px";wrapperWidth+=parseFloat(canvas.style.width);wrapperHeight=parseFloat(canvas.style.height);$(canvas).appendTo($wrapper)}}if(indicesForLens.length>0){if(indicesForLens.length<maxSelectedCount){$wrapper.css({height:wrapperHeight,width:wrapperWidth});var rect=this.$parent[0].getBoundingClientRect();this.$tipFollow.html($wrapper).css({top:parseFloat(this.heatmap.canvas.style.top)-trackHeight-morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS-1,left:options.event.clientX-rect.left-wrapperWidth/2,display:""})}else{this.$tipFollow.html("")}return}else{var tipText=[];var tipFollowText=[];if(inline.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<inline.length;hoverIndex++){this.tooltipProvider(this,-1,inline[hoverIndex],options,this.options.tooltipMode===0?"&nbsp;&nbsp;&nbsp;":"<br />",false,tipText);if(this.options.inlineTooltip){this.tooltipProvider(this,-1,inline[hoverIndex],options,"<br />",true,tipFollowText)}}}var text=tipFollowText.join("");this._setTipText(tipText,text===""?null:'<span style="max-width:400px;">'+text+"</span>",options)}}}var tipText=[];this.tooltipProvider(this,rowIndex,columnIndex,options,this.options.tooltipMode===0?"&nbsp;&nbsp;&nbsp;":"<br />",false,tipText);var text=[];var customToolTip=false;var $tipFollowText;if(!this.panning){var tipFollowText=[];if(this.options.inlineTooltip){this.tooltipProvider(this,rowIndex,columnIndex,options,"<br />",true,tipFollowText);if(this.options.tooltip&&rowIndex!==-1&&columnIndex!==-1){tipFollowText.push('<div data-name="tip"></div>')}}text=tipFollowText.join("");$tipFollowText=$('<span style="max-width:400px;">'+text+"</span>");if(this.options.tooltip&&rowIndex!==-1&&columnIndex!==-1){this.options.tooltip(this,rowIndex,columnIndex,$tipFollowText.find("[data-name=tip]"));customToolTip=true}}this._setTipText(tipText,text.length>0||customToolTip?$tipFollowText:null,options)},_updateTipFollowPosition:function(options){if(this.tipFollowHidden){return}var parentRect=this.$parent[0].getBoundingClientRect();var tipRect=this.$tipFollow[0].getBoundingClientRect();var tipWidth=tipRect.width;var tipHeight=tipRect.height;var offset=10;var left=options.event.clientX-parentRect.left+offset;var top=options.event.clientY-parentRect.top+offset;var scrollBarSize=18;if(left+tipWidth>=parentRect.right-parentRect.left-scrollBarSize){left=options.event.clientX-parentRect.left-offset-tipWidth}if(top+tipHeight>=parentRect.bottom-parentRect.top-scrollBarSize){top=options.event.clientY-parentRect.top-offset-tipHeight}this.$tipFollow.css({left:left+"px",top:top+"px",display:""})},setTrackVisibility:function(tracks){var _this=this;_.each(tracks,function(track){var existingTrack=_this.getTrack(track.name,track.isColumns);if(track.visible&&existingTrack!=null&&_.keys(existingTrack.settings).length===0){existingTrack.settingFromConfig("Text")}_this.setTrackVisible(track.name,track.visible,track.isColumns)});this.revalidate();this.trigger("change",{name:"setTrackVisibility",source:this,arguments:arguments})},setTrackVisible:function(name,visible,isColumns){var trackIndex=this.getTrackIndex(name,isColumns);if(trackIndex===-1){if(!visible){return}this.addTrack(name,isColumns)}else{var track=isColumns?this.columnTracks[trackIndex]:this.rowTracks[trackIndex];var header=isColumns?this.columnTrackHeaders[trackIndex]:this.rowTrackHeaders[trackIndex];if(track.isVisible()!==visible){track.setVisible(visible);header.setVisible(visible)}else{return}}this.trigger("change",{name:"setTrackVisible",source:this,arguments:arguments})},addTrack:function(name,isColumns,renderSettings,trackIndex){if(name===undefined){throw"Name not specified"}var tracks=isColumns?this.columnTracks:this.rowTracks;var headers=isColumns?this.columnTrackHeaders:this.rowTrackHeaders;var existingIndex=this.getTrackIndex(name,isColumns);if(existingIndex!==-1){return tracks[existingIndex]}if(renderSettings==null){var metadata=isColumns?this.project.getFullDataset().getColumnMetadata():this.project.getFullDataset().getRowMetadata();renderSettings=morpheus.VectorUtil.getDataType(metadata.getByName(name))==="[number]"?{display:["bar"]}:{display:["text"]}}var positions=isColumns?this.heatmap.getColumnPositions():this.heatmap.getRowPositions();var track=new morpheus.VectorTrack(this.project,name,positions,isColumns,this);track.settingFromConfig(renderSettings);track.appendTo(this.$parent);var header=new morpheus.VectorTrackHeader(this.project,name,isColumns,this);header.appendTo(this.$parent);track._selection=new morpheus.TrackSelection(track,positions,isColumns?this.project.getColumnSelectionModel():this.project.getRowSelectionModel(),isColumns,this);if(trackIndex!=null&&trackIndex>=0){tracks.splice(trackIndex,0,track);headers.splice(trackIndex,0,header)}else{tracks.push(track);headers.push(header)}return track},addPopup:function(item){if(!this.popupItems){this.popupItems=[]}this.popupItems.push(item)},getPopupItems:function(){return this.popupItems||[]},removeTrack:function(name,isColumns){var index=this.getTrackIndex(name,isColumns);var tracks=isColumns?this.columnTracks:this.rowTracks;if(isNaN(index)||index<0||index>=tracks.length){console.log("removeTrack: "+name+" not found.");return}var headers=isColumns?this.columnTrackHeaders:this.rowTrackHeaders;var track=tracks[index];var header=headers[index];track.dispose();header.dispose();tracks.splice(index,1);headers.splice(index,1);this.trigger("change",{name:"removeTrack",source:this,arguments:arguments})},updateDataset:function(){var dataset=this.project.getSortedFilteredDataset();this.verticalSearchBar.update();this.horizontalSearchBar.update();this.heatmap.setDataset(dataset);this.heatmap.getRowPositions().setSpaces(morpheus.HeatMap.createGroupBySpaces(dataset,this.project.getGroupRows(),this.rowGapSize,false));this.heatmap.getColumnPositions().setSpaces(morpheus.HeatMap.createGroupBySpaces(dataset,this.project.getGroupColumns(),this.columnGapSize,true));this.trigger("change",{name:"updateDataset",source:this,arguments:arguments})},zoom:function(isZoomIn,options){options=$.extend({},{rows:true,columns:true},options);if(isZoomIn){if(options.rows){this.heatmap.getRowPositions().setSize(this.heatmap.getRowPositions().getSize()*1.5)}if(options.columns){this.heatmap.getColumnPositions().setSize(this.heatmap.getColumnPositions().getSize()*1.5)}}else{if(options.rows){this.heatmap.getRowPositions().setSize(this.heatmap.getRowPositions().getSize()/1.5)}if(options.columns){this.heatmap.getColumnPositions().setSize(this.heatmap.getColumnPositions().getSize()/1.5)}}var reval={};if(options.rows&&this.project.getHoverRowIndex()!==-1){reval.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}if(options.columns&&this.project.getHoverColumnIndex()!==-1){reval.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}this.revalidate(reval);this.trigger("change",{name:"zoom",source:this,arguments:arguments})},getTrackIndex:function(name,isColumns){var tracks=isColumns?this.columnTracks:this.rowTracks;for(var i=0,length=tracks.length;i<length;i++){if(tracks[i].name!==undefined&&tracks[i].name===name){return i}}return-1},getNumTracks:function(isColumns){return isColumns?this.columnTracks.length:this.rowTracks.length},moveTrack:function(index,newIndex,isColumns){var tracks=isColumns?this.columnTracks:this.rowTracks;var headers=isColumns?this.columnTrackHeaders:this.rowTrackHeaders;var track=tracks[index];tracks.splice(index,1);var header=headers[index];headers.splice(index,1);tracks.splice(newIndex,0,track);headers.splice(newIndex,0,header);this.trigger("change",{name:"moveTrack",source:this,arguments:arguments})},getTrackByIndex:function(index,isColumns){return isColumns?this.columnTracks[index]:this.rowTracks[index]},getTrackHeaderByIndex:function(index,isColumns){return isColumns?this.columnTrackHeaders[index]:this.rowTrackHeaders[index]},getTrack:function(name,isColumns){var index=this.getTrackIndex(name,isColumns);if(index===-1){return undefined}return isColumns?this.columnTracks[index]:this.rowTracks[index]},isActiveComponent:function(){var active=document.activeElement;var tagName=active.tagName;if(tagName=="INPUT"||tagName=="SELECT"||tagName=="TEXTAREA"){return false}return this.$tabPanel[0].contains(active)},getActiveComponent:function(){var active=document.activeElement;if(active.tagName==="CANVAS"){for(var i=0,ntracks=this.columnTracks.length;i<ntracks;i++){if(this.columnTracks[i].canvas===active){return"columnTrack"}}for(var i=0,ntracks=this.rowTracks.length;i<ntracks;i++){if(this.rowTracks[i].canvas===active){return"rowTrack"}}if(this.heatmap.canvas===active){return"heatMap"}}return""},dispose:function(){if(this.project==null){return}this.project.off();this.$tipInfoWindow.dialog("destroy");this.rowTrackHeaders.forEach(function(header){header.dispose()});this.columnTrackHeaders.forEach(function(header){header.dispose()});this.rowTracks.forEach(function(track){track.dispose()});this.columnTracks.forEach(function(track){track.dispose()});if(this.rowDendrogram!=null){this.rowDendrogram.dispose()}if(this.columnDendrogram!=null){this.columnDendrogram.dispose()}this.beforeColumnTrackDivider.dispose();this.afterRowDendrogramDivider.dispose();this.afterVerticalScrollBarDivider.dispose();this.hscroll.dispose();this.vscroll.dispose();this.hammer.off("swipe",this.swipe).off("panmove",this.panmove).off("panstart",this.panstart).off("tap",this.tap).off("pinch",this.pinch).off("panend",this.panend);this.hammer.destroy();if(typeof window!=="undefined"){$(window).off("paste.morpheus",this.pasteListener).off("beforecopy.morpheus",this.beforeCopyListener).off("copy.morpheus",this.copyListener).off("orientationchange.morpheus resize.morpheus",this.resizeListener)}},getVisibleTrackNames:function(isColumns){return this.getVisibleTracks(isColumns).map(function(track){return track.name})},getVisibleTracks:function(isColumns){var tracks=isColumns?this.columnTracks:this.rowTracks;return tracks.filter(function(track){return track.isVisible()&&!track.getFullVector().getProperties().has(morpheus.VectorKeys.IS_INDEX)})},isShowRowNumber:function(){return this.options.showRowNumber},setShowRowNumber:function(visible){this.options.showRowNumber=visible;if(!visible){this.removeTrack("#",false)}else{var track=this.addTrack("#",false,{popupEnabled:false,display:["text"]},0);track.getVector=function(name){var v=new morpheus.AbstractVector("#",this.project.getSortedFilteredDataset().getRowCount());v.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});v.getValue=function(index){return index+1};return v};track.getFullVector=function(){var v=new morpheus.AbstractVector("#",this.project.getFullDataset().getRowCount());v.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});v.getValue=function(index){return index+1};return v};track.showPopup=function(e,isHeader){if(e.preventDefault){e.preventDefault()}}}},resizeTrack:function(name,width,height,isColumns){var index=this.getTrackIndex(name,isColumns);if(index===-1){throw name+" not found in resize track"}var heatMapPrefWidth=null;if(!isColumns){var track=this.rowTracks[index];var header=this.rowTrackHeaders[index];track.setPrefWidth(width);header.setPrefWidth(width)}else{var track=this.columnTracks[index];var header=this.columnTrackHeaders[index];if(height){track.setPrefHeight(height);header.setPrefHeight(height)}if(width){for(var i=0;i<this.columnTracks.length;i++){this.columnTracks[i].setPrefWidth(width);this.columnTrackHeaders[i].setPrefWidth(width)}}}this.revalidate();this.trigger("change",{name:"resizeTrack",source:this,arguments:arguments})},isDendrogramVisible:function(isColumns){var dendrogram=isColumns?this.columnDendrogram:this.rowDendrogram;if(dendrogram!==undefined){return morpheus.HeatMap.isDendrogramVisible(this.project,isColumns)}},paintAll:function(options){var unscaledHeight=this.heatmap.getUnscaledHeight();var unscaledWidth=this.heatmap.getUnscaledWidth();var y=this.scrollTop();var x=this.scrollLeft();this.hscroll.paint();this.vscroll.paint();var rows=options.paintRows;var columns=options.paintColumns;var invalidateRows=options.invalidateRows;var invalidateColumns=options.invalidateColumns;this.hSortByValuesIndicator.setInvalid(invalidateRows||invalidateColumns);this.hSortByValuesIndicator.paint({x:x,y:0,width:unscaledWidth,height:this.hSortByValuesIndicator.getUnscaledHeight()});this.vSortByValuesIndicator.setInvalid(invalidateRows||invalidateColumns);this.vSortByValuesIndicator.paint({x:0,y:y,width:this.vSortByValuesIndicator.getUnscaledWidth(),height:unscaledHeight});if(rows){for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];track.setInvalid(invalidateRows);if(track.isVisible()){track.paint({x:0,y:y,height:unscaledHeight,width:unscaledWidth});this.rowTrackHeaders[i].paint()}}if(this.rowDendrogram!=null){this.rowDendrogram.setInvalid(invalidateRows);if(this.isDendrogramVisible(false)){this.rowDendrogram.setVisible(true);this.rowDendrogram.paint({x:0,y:y,height:unscaledHeight,width:this.rowDendrogram.getUnscaledWidth()})}else{this.rowDendrogram.setVisible(false)}}}if(columns){for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];track.setInvalid(invalidateColumns);track.paint({x:x,y:0,width:unscaledWidth,height:track.getUnscaledHeight()});this.columnTrackHeaders[i].paint()}if(this.columnDendrogram!=null){this.columnDendrogram.setInvalid(invalidateColumns);if(this.isDendrogramVisible(true)){this.columnDendrogram.setVisible(true);this.columnDendrogram.paint({x:x,y:0,width:unscaledWidth,height:this.columnDendrogram.getUnscaledHeight()})}else{this.columnDendrogram.setVisible(false)}}}if(invalidateRows||invalidateColumns){this.heatmap.setInvalid(true)}this.heatmap.paint({x:x,y:y,width:unscaledWidth,height:unscaledHeight});this.trigger("change",{name:"paintAll",source:this,arguments:arguments})},scrollTop:function(pos){if(pos===undefined){return this.vscroll.getValue()}if(isNaN(pos)){pos=0}if(this.vscroll.getVisibleExtent()===this.vscroll.getTotalExtent()){pos=0}pos=Math.max(pos,0);pos=Math.min(this.vscroll.getMaxValue(),pos);if(pos!==this.vscroll.getValue()){this.vscroll.setValue(pos,true);this.trigger("change",{name:"scrollTop",source:this,arguments:arguments})}return pos},scrollLeft:function(pos){if(pos===undefined){return this.hscroll.getValue()}if(isNaN(pos)){pos=0}if(this.hscroll.getVisibleExtent()===this.hscroll.getTotalExtent()){pos=0}pos=Math.max(pos,0);pos=Math.min(this.hscroll.getMaxValue(),pos);if(pos!==this.hscroll.getValue()){this.trigger("change",{name:"scrollLeft",source:this,arguments:arguments});this.hscroll.setValue(pos,true)}return pos},getSelectedTrackName:function(isColumns){return isColumns?this.selectedColumnTrackName:this.selectedRowTrackName},getLastSelectedTrackInfo:function(){return this.selectedTrackInfo},setSelectedTrack:function(name,isColumns){var previousName=isColumns?this.selectedColumnTrackName:this.selectedRowTrackName;if(name!==previousName){var index=this.getTrackIndex(previousName,isColumns);if(index!==-1){this.getTrackHeaderByIndex(index,isColumns).setSelected(false)}if(isColumns){this.selectedColumnTrackName=name;this.selectedTrackInfo={name:name,isColumns:true}}else{this.selectedRowTrackName=name;this.selectedTrackInfo={name:name,isColumns:false}}var index=this.getTrackIndex(name,isColumns);if(index!==-1){this.getTrackHeaderByIndex(index,isColumns).setSelected(true)}this.trigger("change",{name:"setSelected",source:this,arguments:arguments})}},saveImage:function(file,format){var _this=this;var bounds=this.getTotalSize();if(format==="pdf"){var context=new canvas2pdf.PdfContext(blobStream(),{size:[bounds.width,bounds.height]});this.snapshot(context);context.stream.on("finish",function(){var blob=context.stream.toBlob("application/pdf");saveAs(blob,file,true)});context.end()}else if(format==="svg"){var context=new C2S(bounds.width,bounds.height);this.snapshot(context);var svg=context.getSerializedSvg();var prefix=[];prefix.push('<?xml version="1.0" encoding="utf-8"?>\n');prefix.push('<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"'+' "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n');svg=prefix.join("")+svg;var blob=new Blob([svg],{type:"text/plain;charset=utf-8"});saveAs(blob,file,true)}else{var canvas=$("<canvas></canvas>")[0];var height=bounds.height;var width=bounds.width;var backingScale=morpheus.CanvasUtil.BACKING_SCALE;canvas.height=backingScale*height;canvas.style.height=height+"px";canvas.width=backingScale*width;canvas.style.width=width+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);this.snapshot(context);var toBlob=canvas.toBlobHD?["toBlobHD"]:"toBlob";canvas[toBlob](function(blob){if(blob==null||blob.size===0){morpheus.FormBuilder.showInModal({title:"Save Image",html:"Image is too large to save.",appendTo:_this.getContentEl(),focus:_this.getFocusEl()});return}saveAs(blob,file,true)})}},getTotalSize:function(options){options=$.extend({},{legend:true},options);var _this=this;var heatmapPrefSize=this.heatmap.getPreferredSize();var totalSize={width:heatmapPrefSize.width,height:heatmapPrefSize.height};if(this.isDendrogramVisible(false)){totalSize.width+=this.rowDendrogram.getUnscaledWidth()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}if(this.isDendrogramVisible(true)){totalSize.height+=this.columnDendrogram.getUnscaledHeight()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}var maxRowHeaderHeight=0;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){var headerSize=this.rowTrackHeaders[i].getPrintSize();totalSize.width+=Math.max(headerSize.width,track.getPrintSize().width);maxRowHeaderHeight=Math.max(maxRowHeaderHeight,headerSize.height)}}var maxColumnHeaderWidth=0;var columnTrackHeightSum=0;for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){columnTrackHeightSum+=track.getPrintSize().height;maxColumnHeaderWidth=Math.max(maxColumnHeaderWidth,this.columnTrackHeaders[i].getPrintSize().width)}}totalSize.height+=Math.max(columnTrackHeightSum,maxRowHeaderHeight)+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;totalSize.width+=maxColumnHeaderWidth+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;if(options.legend){var totalLegendWidth=15;var maxLegendHeight=0;var colorByValues=this.heatmap.getColorScheme().getColorByValues();var ntracks=colorByValues.length;for(var i=0;i<ntracks;i++){var value=colorByValues[i];if(value!=null||ntracks===1){this.heatmap.getColorScheme().setCurrentValue(value);var names=this.heatmap.getColorScheme().getNames();maxLegendHeight=Math.max(maxLegendHeight,names!=null?names.length*14:30);totalLegendWidth+=250}}maxLegendHeight+=10;totalSize.height=totalSize.height+maxLegendHeight;totalSize.width=Math.max(totalSize.width,totalLegendWidth)}var trackLegendSize=new morpheus.HeatMapTrackColorLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getColumnColorModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackColorLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getRowColorModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getColumnShapeModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getRowShapeModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getColumnFontModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getRowFontModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);return totalSize},getHeatMapElementComponent:function(){return this.heatmap},snapshot:function(context,options){options=$.extend({},{legend:true},options);var heatmapPrefSize=this.heatmap.getPreferredSize();var totalSize=this.getTotalSize(options);var legendHeight=0;if(options.legend){var colorByValues=this.heatmap.getColorScheme().getColorByValues();context.save();context.translate(15,0);var ntracks=colorByValues.length;for(var i=0,ntracks=colorByValues.length;i<ntracks;i++){var value=colorByValues[i];if(value!=null||ntracks===1){if(value!="null"){}var trackLegend=new morpheus.ColorSupplierLegend(this.heatmap.getColorScheme(),value);trackLegend.draw({},context);legendHeight=Math.max(legendHeight,trackLegend.getUnscaledHeight());var legendWidth=trackLegend.getUnscaledWidth();context.translate(legendWidth,0)}}legendHeight+=10;context.restore()}var legendOffset=15;var maxLegendHeight=0;context.save();context.translate(legendOffset,legendHeight);var trackLegend=new morpheus.HeatMapTrackColorLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getColumnColorModel());trackLegend.draw({},context);var legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackShapeLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getColumnShapeModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackFontLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getColumnFontModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackColorLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getRowColorModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackShapeLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getRowShapeModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackFontLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getRowFontModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();legendHeight+=maxLegendHeight;var heatmapY=this.isDendrogramVisible(true)?this.columnDendrogram.getUnscaledHeight()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS:0;heatmapY+=legendHeight;var columnTrackY=heatmapY;var heatmapX=this.isDendrogramVisible(false)?this.rowDendrogram.getUnscaledWidth()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS:0;var isColumnTrackVisible=false;for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){var header=this.columnTrackHeaders[i];heatmapX=Math.max(heatmapX,header.getPrintSize().width);heatmapY+=track.getPrintSize().height;isColumnTrackVisible=true}}if(isColumnTrackVisible){heatmapY+=morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){var header=this.rowTrackHeaders[i];heatmapY=Math.max(heatmapY,header.getPrintSize().height)}}if(this.isDendrogramVisible(true)){var columnDendrogramClip={x:0,y:0,height:this.columnDendrogram.getUnscaledHeight(),width:heatmapPrefSize.width};context.save();context.translate(heatmapX,legendHeight);this.columnDendrogram.prePaint(columnDendrogramClip,context);this.columnDendrogram.draw(columnDendrogramClip,context);context.restore()}if(this.isDendrogramVisible(false)){var rowDendrogramClip={x:0,y:0,width:this.rowDendrogram.getUnscaledWidth(),height:heatmapPrefSize.height};context.save();context.translate(0,heatmapY);this.rowDendrogram.prePaint(rowDendrogramClip,context);this.rowDendrogram.draw(rowDendrogramClip,context);context.restore()}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){context.save();context.translate(heatmapX,columnTrackY);var trackClip={x:0,y:0,width:heatmapPrefSize.width,height:track.getPrintSize().height};track.print(trackClip,context);context.restore();var header=this.columnTrackHeaders[i];context.save();var headerSize=header.getPrintSize();var headerClip={x:0,y:0,width:headerSize.width,height:trackClip.height};context.translate(heatmapX-2,columnTrackY+trackClip.height);header.print(headerClip,context);context.restore();columnTrackY+=Math.max(headerClip.height,trackClip.height)}}context.save();context.translate(heatmapX,heatmapY);this.heatmap.draw({x:0,y:0,width:heatmapPrefSize.width,height:heatmapPrefSize.height},context);context.restore();var rowTrackWidthSum=0;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){context.save();var tx=morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS+heatmapX+heatmapPrefSize.width+rowTrackWidthSum;var ty=heatmapY;var trackClip={x:0,y:0,width:track.getPrintSize().width,height:heatmapPrefSize.height};context.translate(tx,ty);context.strokeStyle="white";context.rect(0,0,trackClip.width,trackClip.height);context.stroke();context.clip();track.print(trackClip,context);context.restore();var header=this.rowTrackHeaders[i];context.save();var headerSize=header.getPrintSize();var headerClip={x:0,y:0,width:headerSize.width,height:headerSize.height};context.translate(tx,ty-4);header.print(headerClip,context);context.restore();rowTrackWidthSum+=Math.max(headerSize.width,trackClip.width)}}},resetZoom:function(){var heatmap=this.heatmap;var rowSizes=heatmap.getRowPositions();var columnSizes=heatmap.getColumnPositions();rowSizes.setSize(13);columnSizes.setSize(13);var reval={};if(this.project.getHoverRowIndex()!==-1){reval.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}if(this.project.getHoverColumnIndex()!==-1){reval.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}this.revalidate(reval)},getFitColumnSize:function(){var heatmap=this.heatmap;var availablePixels=this.getAvailableWidth();if(availablePixels===-1){return 13}if(this.rowDendrogram){availablePixels-=this.rowDendrogram.getUnscaledWidth()}var trackPixels=12;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){trackPixels+=track.getUnscaledWidth()}}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){trackPixels+=this.columnTrackHeaders[i].getUnscaledWidth();break}}availablePixels-=trackPixels;var positions=heatmap.getColumnPositions();var totalCurrent=positions.getItemSize(positions.getLength()-1)+positions.getPosition(positions.getLength()-1);var size=positions.getSize();size=size*(availablePixels/totalCurrent);size=Math.min(13,size);return size},getFitRowSize:function(){var heatmap=this.heatmap;var availablePixels=this.getAvailableHeight();if(availablePixels===-1){return 13}if(this.columnDendrogram){availablePixels-=this.columnDendrogram.getUnscaledHeight()}var trackPixels=12;for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){trackPixels+=track.getUnscaledHeight()}}availablePixels-=trackPixels;var positions=heatmap.getRowPositions();var totalCurrent=positions.getItemSize(positions.getLength()-1)+positions.getPosition(positions.getLength()-1);var size=positions.getSize();size=size*(availablePixels/totalCurrent);size=Math.min(13,size);return size},fitToWindow:function(options){if(options.fitRows){this.heatmap.getRowPositions().setSize(this.getFitRowSize())}if(options.fitColumns){this.heatmap.getColumnPositions().setSize(this.getFitColumnSize())}if(options.repaint){var revalOptions={};if(options.fitRows){if(this.project.getHoverRowIndex()!==-1){revalOptions.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}}if(options.fitColumns){if(this.project.getHoverColumnIndex()!==-1){revalOptions.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}}this.revalidate(revalOptions)}},getAvailableHeight:function(){if(_.isNumber(this.options.height)){return this.options.height}var height=$(window).height()-this.$parent.offset().top-24;if(this.options.height==="window"){return height}return Math.max(Math.round(screen.height*.7),height)},getAvailableWidth:function(){if(this.options.width){return this.options.width}return this.tabManager.getWidth()-30},revalidate:function(options){if(morpheus.Util.isHeadless()){for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];track.setInvalid(true);if(track.isVisible()){track.paint({x:0,y:0,height:10,width:10})}}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];track.setInvalid(true);if(track.isVisible()){track.paint({x:0,y:0,height:10,width:10})}}return}options=$.extend({},{paint:true},options);this.updatingScroll=true;var availableHeight=this.getAvailableHeight();var availableWidth=this.getAvailableWidth();var heatmapPrefSize=this.heatmap.getPreferredSize();var columnDendrogramHeight=0;var rowDendrogramWidth=0;if(this.columnDendrogram){columnDendrogramHeight=morpheus.CanvasUtil.getPreferredSize(this.columnDendrogram).height}if(this.rowDendrogram){rowDendrogramWidth=morpheus.CanvasUtil.getPreferredSize(this.rowDendrogram).width}var rowTrackWidthSum=0;for(var i=0,length=this.rowTracks.length;i<length;i++){if(this.rowTracks[i].isVisible()){if(this.rowTracks[i].getPrefWidth()!==undefined){this.rowTrackHeaders[i].setPrefWidth(this.rowTracks[i].getPrefWidth())}rowTrackWidthSum+=Math.max(morpheus.CanvasUtil.getPreferredSize(this.rowTrackHeaders[i]).width,morpheus.CanvasUtil.getPreferredSize(this.rowTracks[i]).width)}}if(availableWidth!==-1&&rowTrackWidthSum+rowDendrogramWidth+heatmapPrefSize.width>availableWidth){rowTrackWidthSum=0;for(var i=0,length=this.rowTracks.length;i<length;i++){if(this.rowTracks[i].isVisible()){var rowTrackHeaderSize=morpheus.CanvasUtil.getPreferredSize(this.rowTrackHeaders[i]);var width=Math.max(rowTrackHeaderSize.width,morpheus.CanvasUtil.getPreferredSize(this.rowTracks[i]).width);if(!rowTrackHeaderSize.widthSet){width=Math.min(400,width);this.rowTracks[i].setPrefWidth(width);this.rowTrackHeaders[i].setPrefWidth(width)}rowTrackWidthSum+=width}}}var ypos=columnDendrogramHeight;var maxHeaderWidth=0;for(var i=0,length=this.columnTracks.length;i<length;i++){if(this.columnTracks[i].isVisible()){if(this.columnTracks[i].getPrefHeight()!==undefined){this.columnTrackHeaders[i].setPrefHeight(this.columnTracks[i].getPrefHeight())}var width=morpheus.CanvasUtil.getPreferredSize(this.columnTrackHeaders[i]).width;maxHeaderWidth=Math.max(maxHeaderWidth,width)}}var xpos=Math.max(rowDendrogramWidth,maxHeaderWidth);var heatMapWidth=heatmapPrefSize.width;var maxHeatMapWidth=Math.max(50,availableWidth===-1?Number.MAX_VALUE:availableWidth-rowTrackWidthSum-xpos-morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS);if(maxHeatMapWidth>0&&heatMapWidth>maxHeatMapWidth){heatMapWidth=maxHeatMapWidth;heatMapWidth=Math.min(heatMapWidth,heatmapPrefSize.width)}if(this.heatmap.prefWidth!==undefined){heatMapWidth=Math.min(heatmapPrefSize.width,this.heatmap.prefWidth)}if(this.columnDendrogram!==undefined){this.columnDendrogram.setBounds({width:heatMapWidth,height:columnDendrogramHeight,left:xpos,top:0});this.columnDendrogram.$label.css("left",xpos+this.columnDendrogram.getUnscaledWidth()+10).css("top",2);this.columnDendrogram.$squishedLabel.css("left",xpos+this.columnDendrogram.getUnscaledWidth()+10).css("top",18);this.beforeColumnTrackDivider.setVisible(true);this.beforeColumnTrackDivider.setBounds({left:xpos-maxHeaderWidth,top:ypos,width:maxHeaderWidth});ypos++}else{this.beforeColumnTrackDivider.setVisible(false)}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){var size=morpheus.CanvasUtil.getPreferredSize(track);var headerSize=morpheus.CanvasUtil.getPreferredSize(this.columnTrackHeaders[i]);size.height=Math.max(size.height,headerSize.height);track.setBounds({width:heatMapWidth,height:size.height,left:xpos,top:ypos});this.columnTrackHeaders[i].setBounds({width:maxHeaderWidth,height:size.height,left:xpos-maxHeaderWidth,top:ypos});ypos+=size.height}}this.$whitespace[0].style.left=Math.ceil(xpos+heatMapWidth+10)+"px";this.$whitespace[0].style.top="0px";ypos+=morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;var heatMapHeight=heatmapPrefSize.height;if(availableHeight!==-1&&heatMapHeight>availableHeight-ypos){heatMapHeight=Math.max(100,Math.min(heatmapPrefSize.height,availableHeight-ypos))}if(ypos<0){ypos=0}if(this.rowDendrogram){this.rowDendrogram.setBounds({width:Math.max(rowDendrogramWidth,maxHeaderWidth),height:heatMapHeight,left:0,top:ypos});this.rowDendrogram.$label.css("left",0).css("top",2);this.afterRowDendrogramDivider.setVisible(true);this.afterRowDendrogramDivider.setBounds({height:heatMapHeight,left:this.rowDendrogram.getUnscaledWidth(),top:ypos});xpos++}else{this.afterRowDendrogramDivider.setVisible(false)}this.heatmap.setBounds({width:heatMapWidth,height:heatMapHeight,left:xpos,top:ypos});this.hSortByValuesIndicator.setBounds({height:4,width:heatMapWidth,left:xpos,top:ypos-4});this.hscroll.setVisible(heatMapWidth<heatmapPrefSize.width);this.hscroll.setExtent(heatMapWidth,heatmapPrefSize.width,options.scrollLeft!==undefined?options.scrollLeft:heatmapPrefSize.width===this.hscroll.getTotalExtent()?this.hscroll.getValue():heatmapPrefSize.width*this.hscroll.getValue()/this.hscroll.getMaxValue());this.hscroll.setBounds({left:xpos,top:ypos+heatMapHeight+2});xpos+=heatMapWidth;var nvisibleRowTracks=0;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){nvisibleRowTracks++;break}}this.vSortByValuesIndicator.setBounds({width:4,height:heatMapHeight,left:xpos,top:ypos});if(nvisibleRowTracks>0){xpos=xpos+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}var rowAnnotationXStart=xpos;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){var size=morpheus.CanvasUtil.getPreferredSize(track);var headerSize=morpheus.CanvasUtil.getPreferredSize(this.rowTrackHeaders[i]);size.width=Math.max(headerSize.width,size.width);size.height=heatMapHeight;track.setBounds({width:size.width,height:size.height,left:xpos,top:ypos});this.rowTrackHeaders[i].setBounds({width:size.width,left:xpos,top:ypos-headerSize.height-5,height:headerSize.height});xpos+=size.width}}this.afterVerticalScrollBarDivider.setVisible(nvisibleRowTracks>0?true:false);this.afterVerticalScrollBarDivider.setBounds({left:rowAnnotationXStart-2,top:ypos-18});this.vscroll.setVisible(heatMapHeight<heatmapPrefSize.height);this.vscroll.setExtent(heatMapHeight,heatmapPrefSize.height,options.scrollTop!==undefined?options.scrollTop:heatmapPrefSize.height===this.vscroll.getTotalExtent()?this.vscroll.getValue():heatmapPrefSize.height*this.vscroll.getValue()/this.vscroll.getMaxValue());xpos+=2;this.vscroll.setBounds({left:xpos,top:ypos});xpos+=this.vscroll.getUnscaledWidth();if(this.hscroll.isVisible()){ypos+=this.hscroll.getUnscaledHeight()+2}var totalHeight=2+ypos+heatMapHeight;if(options.paint){this.paintAll({paintRows:true,paintColumns:true,invalidateRows:true,invalidateColumns:true})}this.$parent.css({height:Math.ceil(totalHeight)+"px",width:availableWidth===-1?Math.ceil(xpos+2)+"px":""});this.updatingScroll=false;this.trigger("change",{name:"revalidate",source:this,arguments:arguments})}};morpheus.HeatMap.copyFromParent=function(project,options){project.rowColorModel=options.parent.getProject().getRowColorModel().copy();project.columnColorModel=options.parent.getProject().getColumnColorModel().copy();project.rowShapeModel=options.parent.getProject().getRowShapeModel().copy();project.columnShapeModel=options.parent.getProject().getColumnShapeModel().copy();project.rowFontModel=options.parent.getProject().getRowFontModel().copy();project.columnFontModel=options.parent.getProject().getColumnFontModel().copy();var parentRowTracks=options.parent.rowTracks||[];var parentColumnTracks=options.parent.columnTracks||[];if(options.inheritFromParentOptions.rows){project.columnShapeModel=project.rowShapeModel;project.columnColorModel=project.rowColorModel;project.columnFontModel=project.rowFontModel;parentColumnTracks=parentRowTracks.slice().reverse()}if(options.inheritFromParentOptions.columns){project.rowShapeModel=project.columnShapeModel;project.rowColorModel=project.columnColorModel;project.rowFontModel=project.columnFontModel;parentRowTracks=parentColumnTracks.slice().reverse()}if(options.inheritFromParentOptions.transpose){var tmp=project.rowShapeModel;project.rowShapeModel=project.columnShapeModel;project.columnShapeModel=tmp;tmp=project.rowColorModel;project.rowColorModel=project.columnColorModel;project.columnColorModel=tmp;tmp=project.rowFontModel;project.rowFontModel=project.columnFontModel;project.columnFontModel=tmp;tmp=parentRowTracks.slice().reverse();parentRowTracks=parentColumnTracks.slice().reverse();parentColumnTracks=tmp}options.rows=options.rows||[];for(var i=0;i<parentRowTracks.length;i++){var track=parentRowTracks[i];if(track.isVisible()){options.rows.push({order:options.rows.length,field:track.getName(),display:$.extend(true,{},track.settings),force:true})}}options.columns=options.columns||[];for(var i=0;i<parentColumnTracks.length;i++){var track=parentColumnTracks[i];if(track.isVisible()){options.columns.push({order:options.columns.length,field:track.getName(),display:$.extend(true,{},track.settings),force:true})}}};morpheus.Util.extend(morpheus.HeatMap,morpheus.Events);morpheus.HelpMenu=function(){var html=[];html.push('<ul class="morpheus-footer-links">');html.push('<li><a href="index.html">Home</a></li>');html.push('<li><a data-name="contact" href="#">Contact</a></li>');html.push('<li><a href="documentation.html">Documentation</a></li>');html.push('<li><a href="tutorial.html">Tutorial</a></li>');html.push('<li><a href="configuration.html">Configuration</a></li>');html.push('<li><a href="https://github.com/cmap/morpheus.js">Source Code</a></li>');html.push('<li><a href="https://github.com/cmap/morpheus.R">R Interface</a></li>');html.push('<li><a href="https://github.com/cmap/morpheus-export">Command Line</a></li>');html.push("</ul>");this.$el=$(html.join(""));this.$el.find("[data-name=contact]").on("click",function(e){morpheus.FormBuilder.showInModal({title:"Contact",html:"Please email us at morpheus@broadinstitute.org",focus:document.activeElement});e.preventDefault()})};morpheus.HistogramLegend=function(dataset,colorScheme,metadataValue){morpheus.AbstractCanvas.call(this,true);this.colorScheme=colorScheme;this.metadataValue=metadataValue;this.dataset=dataset;this.binNumberToOccurences=null;this.setBounds({width:250,height:70});this.name=null;this.canvas.style.position="";this.canvas.style.border="1px solid LightGrey"};morpheus.HistogramLegend.prototype={binSize:0,maxCount:0,total:0,setName:function(name){this.name=name},setBinSize:function(binSize){this.binSize=binSize},buildHistogram:function(){var binSize=this.binSize;var dataset=this.dataset;var metadataValue=this.metadataValue;var colorScheme=this.colorScheme;var min=colorScheme.getMin();var max=colorScheme.getMax();if(min===max){min-=.5;max+=.5}var vector=dataset.getRowMetadata().getByName(colorScheme.getSeparateColorSchemeForRowMetadataField());var numberOfBins=Math.ceil((max-min)/binSize);var binNumberToOccurences=new Uint32Array(numberOfBins);this.binNumberToOccurences=binNumberToOccurences;var index=0;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){if(vector==null||vector.getValue(i)===metadataValue){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(isNaN(value)){continue}var bin=Math.floor((value-min)/binSize);if(bin<0){bin=0}else if(bin>=numberOfBins){bin=numberOfBins-1}binNumberToOccurences[bin]++}}}var maxCount=0;var total=0;for(var i=0;i<numberOfBins;i++){var count=binNumberToOccurences[i];maxCount=count>=maxCount?count:maxCount;total+=count}this.maxCount=maxCount;this.total=total},draw:function(clip,context){this.buildHistogram();var colorScheme=this.colorScheme;var canvasWidth=this.getUnscaledWidth()-50;var valueToPosition=d3.scale.linear().domain([colorScheme.getMin(),colorScheme.getMax()]).range([0,canvasWidth]).clamp(true);var histogramHeight=30;var countToPosition=d3.scale.linear().domain([0,this.maxCount/this.total]).range([histogramHeight,0]).clamp(true);var binNumberToOccurences=this.binNumberToOccurences;var min=colorScheme.getMin();var binSize=this.binSize;var y0=countToPosition(0);if(this.name!=null){context.font="11px "+morpheus.CanvasUtil.getFontFamily(context);context.fillStyle="black";context.lineWidth=1;context.fillText(this.name,.5,12);context.translate(0,14)}context.lineWidth=.2;context.strokeStyle="#D3D2C2";context.fillStyle="#D3D2C2";context.translate(25,0);context.beginPath();context.moveTo(0,y0);context.lineTo(canvasWidth,y0);context.stroke();context.lineWidth=1;context.strokeStyle="white";for(var i=0,numberOfBins=binNumberToOccurences.length;i<numberOfBins;i++){var count=binNumberToOccurences[i];if(count>0){count/=this.total;var start=min+i*binSize;var end=start+binSize;var x=valueToPosition(start);var width=valueToPosition(end)-x;var y=countToPosition(count);context.rect(x,y0,width,y-y0);context.fill();context.stroke()}}context.translate(0,histogramHeight+1);context.fillStyle="black";morpheus.HeatMapColorSchemeLegend.drawColorScheme(context,this.colorScheme,canvasWidth,false,false,6)}};morpheus.Util.extend(morpheus.HistogramLegend,morpheus.AbstractCanvas);morpheus.LegendWithStops=function(){var _this=this;morpheus.AbstractCanvas.call(this,false);this.setBounds({width:300,height:40});$(this.canvas).on("mousedown",function(event){var position=morpheus.CanvasUtil.getMousePos(event.target,event);_this.selectedIndex=_this.findIndexForPosition(position);_this.trigger("selectedIndex",{selectedIndex:_this.selectedIndex})});this.hammer=morpheus.Util.hammer(this.canvas,["pan"]).on("panmove",this.panmove=function(event){if(_this.selectedIndex!==-1){var position=morpheus.CanvasUtil.getMousePos(event.target,event);var fraction=_this.fractionToStopPix.invert(position.x);fraction=Math.max(0,fraction);fraction=Math.min(1,fraction);_this.trigger("moved",{fraction:fraction})}}).on("panstart",this.panstart=function(event){}).on("panend",this.panend=function(event){_this.selectedIndex=-1});$(this.canvas).on("keydown",function(e){if((e.which==8||e.which==46)&&_this.selectedIndex!==-1){_this.trigger("delete");e.preventDefault();e.stopPropagation();e.stopImmediatePropagation()}})};morpheus.LegendWithStops.prototype={border:7,stopHalfSize:5,selectedIndex:-1,destroy:function(){$(this.canvas).off("keyup").off("mousedown");this.hammer.off("panstart",this.panstart).off("panmove",this.panmove);this.hammer.destroy()},setSelectedIndex:function(index){this.selectedIndex=index},findIndexForPosition:function(position){if(position.y>=22){for(var i=0,length=this.fractions.length;i<length;i++){var pix=this.fractionToStopPix(this.fractions[i]);var start=pix-this.stopHalfSize;var end=pix+this.stopHalfSize;if(position.x>=start&&position.x<=end){return i}}}return-1},draw:function(fractions,colors,stepped,fractionToStopPix){this.fractions=fractions;this.colors=colors;this.stepped=stepped;this.fractionToStopPix=fractionToStopPix;var context=this.canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);context.clearRect(0,0,this.getUnscaledWidth(),this.getUnscaledHeight());context.translate(this.border,0);morpheus.HeatMapColorSchemeLegend.draw(context,fractions,colors,this.getUnscaledWidth()-2*this.border,this.getUnscaledHeight()-20,stepped);context.translate(-this.border,0);context.lineWidth=1;context.strokeStyle="Grey";context.strokeRect(this.border,0,this.getUnscaledWidth()-2*this.border,this.getUnscaledHeight()-20);for(var i=0;i<fractions.length;i++){if(i>0&&fractions[i]===fractions[i-1]){continue}context.fillStyle=colors[i];var pix=fractionToStopPix(fractions[i]);context.fillRect(pix-this.stopHalfSize,22,this.stopHalfSize*2,this.stopHalfSize*2);if(this.selectedIndex===i){context.lineWidth=2;context.strokeStyle="black"}else{context.lineWidth=1;context.strokeStyle="Grey"}context.strokeRect(pix-this.stopHalfSize,22,this.stopHalfSize*2,this.stopHalfSize*2)}}};morpheus.Util.extend(morpheus.LegendWithStops,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.LegendWithStops,morpheus.Events);morpheus.Popup={};morpheus.Popup.initted=false;morpheus.Popup.init=function(){if(morpheus.Popup.initted){return}morpheus.Popup.initted=true;morpheus.Popup.$popupDiv=$(document.createElement("div"));morpheus.Popup.$popupDiv.css("position","absolute").css("zIndex",1050).css("overflow","auto").addClass("dropdown clearfix");morpheus.Popup.$contextMenu=$(document.createElement("ul"));morpheus.Popup.$contextMenu.addClass("dropdown-menu").css("display","block").css("position","static").css("margin-bottom","5px");morpheus.Popup.$contextMenu.appendTo(morpheus.Popup.$popupDiv);morpheus.Popup.$contextMenu.on("click","a",function(e){e.preventDefault();var $this=$(this);morpheus.Popup.popupCallback(e,$this.data("name"));morpheus.Popup.hide()})};morpheus.Popup.popupInDom=false;morpheus.Popup.hidePopupMenu=function(e){if(morpheus.Popup.component==e.target){e.preventDefault();e.stopPropagation()}morpheus.Popup.hide()};morpheus.Popup.hide=function(){morpheus.Popup.$popupDiv.hide();$(document.body).off("mousedown",morpheus.Popup.hidePopupMenu);morpheus.Popup.popupCallback=null;morpheus.Popup.component=null};morpheus.Popup.showPopup=function(menuItems,position,component,callback){morpheus.Popup.init();if(morpheus.Popup.component==component){morpheus.Popup.hide();return}morpheus.Popup.popupCallback=callback;morpheus.Popup.component=component;var html=[];for(var i=0,length=menuItems.length;i<length;i++){var item=menuItems[i];if(item.header){html.push('<li role="presentation" class="dropdown-header">'+item.name+"</li>")}else if(item.separator){html.push('<li class="divider"></li>')}else{html.push('<li role="presentation"');if(item.disabled){html.push('class="disabled"')}html.push('><a data-name="'+item.name+'" data-type="popup-item" tabindex="-1" href="#"');if(item.class){html.push(' class="'+item.class+'"')}html.push(">");if(item.checked){html.push('<span class="dropdown-checkbox fa fa-check"></span>')}html.push(item.name);if(item.icon){html.push('<span class="pull-right '+item.icon+'"></span>')}html.push("</a>");html.push("</li>")}}morpheus.Popup.$contextMenu.html(html.join(""));if(!morpheus.Popup.popupInDom){morpheus.Popup.popupInDom=true;morpheus.Popup.$popupDiv.appendTo($(document.body))}var $body=$(document.body);var $window=$(window);var windowWidth=$window.width();var windowHeight=$window.height();var popupWidth=morpheus.Popup.$popupDiv.width();var popupHeight=morpheus.Popup.$popupDiv.height();var left=position.x;var top=position.y;if(left+popupWidth>=windowWidth){left-=popupWidth;left=Math.max(4,left)}if(top+popupHeight>=windowHeight){top-=popupHeight;top=Math.max(4,top)}morpheus.Popup.$popupDiv.css({display:"block",left:left,top:top});morpheus.Popup.$popupDiv.show();$body.off("mousedown",morpheus.Popup.hidePopupMenu);window.setTimeout(function(){$body.on("mousedown",function(e){var $target=$(e.target);if($target[0]!==morpheus.Popup.$popupDiv[0]&&$target.data("type")!=="popup-item"){morpheus.Popup.hidePopupMenu(e)}})},1)};morpheus.RowDendrogram=function(heatMap,tree,positions,project){morpheus.AbstractDendrogram.call(this,heatMap,tree,positions,project,morpheus.AbstractDendrogram.Type.ROW)};morpheus.RowDendrogram.prototype={drawNode:function(context,node){var radius=this.getNodeRadius(node);var pix=this.toPix(node);context.beginPath();context.arc(pix[0],pix[1],radius,Math.PI*2,false);context.fill()},isDragHotSpot:function(p){return Math.abs(this.scale(this.cutHeight)-p.x)<=2},drawCutSlider:function(clip,context){if(context.setLineDash){context.setLineDash([5])}context.strokeStyle="black";var nx=this.scale(this.cutHeight);context.beginPath();context.moveTo(nx,clip.y);context.lineTo(nx,this.getUnscaledHeight());context.stroke();if(context.setLineDash){context.setLineDash([])}},getPreferredSize:function(){return{width:100,height:Math.ceil(this.positions.getPosition(this.positions.getLength()-1)+this.positions.getItemSize(this.positions.getLength()-1))}},paintMouseOver:function(clip,context){if(this.project.getHoverRowIndex()!==-1){morpheus.CanvasUtil.resetTransform(context);context.translate(0,-clip.y);this.drawRowBorder(context,this.positions,this.project.getHoverRowIndex(),this.getUnscaledWidth())}},drawRowBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(0,pix+size);context.lineTo(gridSize,pix+size);context.stroke();context.beginPath();context.moveTo(0,pix);context.lineTo(gridSize,pix);context.stroke()},createScale:function(){return d3.scale.linear().domain([0,this.tree.maxHeight]).range([this.getUnscaledWidth(),0])},getMaxIndex:function(clip){return morpheus.Positions.getBottom(clip,this.positions)},getMinIndex:function(clip){return morpheus.Positions.getTop(clip,this.positions)},toPix:function(node){var min=this.positions.getPosition(node.minIndex)+this.positions.getItemSize(node.minIndex)/2;var max=this.positions.getPosition(node.maxIndex)+this.positions.getItemSize(node.maxIndex)/2;return[this.scale(node.height),(min+max)/2]},drawPathFromNodeToParent:function(context,node){var pix=this.toPix(node);var parentPix=this.toPix(node.parent);context.beginPath();context.moveTo(pix[0],pix[1]);context.lineTo(parentPix[0],pix[1]);context.lineTo(parentPix[0],parentPix[1]);context.stroke()},drawNodePath:function(context,node,minIndex,maxIndex){var children=node.children;var left=children[0];var right=children[1];var ry=this.toPix(right)[1];var rx=this.scale(right.height);var ly=this.toPix(left)[1];var lx=this.scale(left.height);var nx=this.scale(node.height);var x;var y;if(!this.drawLeafNodes){var leftIsLeaf=left.children!==undefined;var rightIsLeaf=right.children!==undefined;if(leftIsLeaf){lx=nx+4}if(rightIsLeaf){rx=nx+4}x=[rx,nx,nx,lx];y=[ry,ry,ly,ly]}else{x=[rx,nx,nx,lx];y=[ry,ry,ly,ly]}context.beginPath();context.moveTo(x[0],y[0]);for(var i=1,length=x.length;i<length;i++){context.lineTo(x[i],y[i])}context.stroke()}};morpheus.Util.extend(morpheus.RowDendrogram,morpheus.AbstractDendrogram);morpheus.ScentedSearch=function(model,positions,isVertical,scrollbar,heatMap){morpheus.AbstractCanvas.call(this,false);this.model=model;this.positions=positions;this.isVertical=isVertical;this.scrollbar=scrollbar;this.heatMap=heatMap;this.searchIndices=[];scrollbar.decorator=this;var _this=this;var mouseMove=function(e){var indices=_this.getSearchIndices(e);document.body.style.cursor=indices.length===0?"default":"pointer";scrollbar.canvas.style.cursor=indices.length===0?"default":"pointer";var tipOptions={event:e,heatMapLens:indices.length>=0};if(isVertical){heatMap.setToolTip(indices.length>=0?indices:null,-1,tipOptions)}else{heatMap.setToolTip(-1,indices.length>=0?indices:null,tipOptions)}};var mouseExit=function(e){document.body.style.cursor="default";scrollbar.canvas.style.cursor="default";heatMap.setToolTip(-1,-1,{event:e})};$(scrollbar.canvas).on("mousemove.morpheus",mouseMove).on("mouseout.morpheus",mouseExit)};morpheus.ScentedSearch.LINE_HEIGHT=3.5;morpheus.ScentedSearch.prototype={mouseMovedIndex:-1,getIndex:function(event){var pix=morpheus.CanvasUtil.getMousePos(event.target,event);var val=pix[this.isVertical?"y":"x"];return this.getIndexForPix(val)},getSearchIndices:function(event){var pix=morpheus.CanvasUtil.getMousePos(event.target,event);var val=pix[this.isVertical?"y":"x"];return this.getSearchIndicesForPix(val)},getSearchIndicesForPix:function(pix){var indices=this.searchIndices;if(indices==null){return[]}var scale=this.scale;var tolerance=morpheus.ScentedSearch.LINE_HEIGHT;var matches=[];for(var i=0,length=indices.length;i<length;i++){var midVal=this.positions.getPosition(indices[i])*scale;if(Math.abs(midVal-pix)<=tolerance){matches.push(indices[i])}}return matches},getIndexForPix:function(pix){var indices=this.searchIndices;if(indices==null){return-1}var tolerance=morpheus.ScentedSearch.LINE_HEIGHT;if(this.mouseMovedIndex>0){var midVal=this.positions.getPosition(indices[this.mouseMovedIndex])*scale;if(Math.abs(midVal-pix)<=tolerance){return this.mouseMovedIndex}}var low=0;var scale=this.scale;var high=indices.length-1;while(low<=high){var mid=low+high>>1;var midVal=this.positions.getPosition(indices[mid])*scale;var cmp=0;if(Math.abs(midVal-pix)<=tolerance){cmp=0}else if(midVal<pix){cmp=-1}else if(midVal>pix){cmp=1}if(cmp<0)low=mid+1;else if(cmp>0)high=mid-1;else return mid}return-1},tap:function(position){var val=position[this.isVertical?"y":"x"];var index=this.getIndexForPix(val);this.scrollbar.canvas.style.cursor=index<0?"default":"pointer";if(index>=0){if(this.isVertical){this.heatMap.scrollTop(this.positions.getPosition(this.searchIndices[index]))}else{this.heatMap.scrollLeft(this.positions.getPosition(this.searchIndices[index]))}return true}return false},update:function(){this.searchIndices=this.model.getViewIndices().values().sort(function(a,b){return a<b?-1:1})},draw:function(clip,context){var width=this.scrollbar.getUnscaledWidth();var height=this.scrollbar.getUnscaledHeight();var availableLength=(this.isVertical?height:width)-morpheus.ScentedSearch.LINE_HEIGHT;this.scale=availableLength/(this.positions.getPosition(this.positions.getLength()-1)+this.positions.getItemSize(this.positions.getLength()-1));context.fillStyle=morpheus.ScentedSearch.TICK_COLOR;context.lineWidth=1;this.drawIndices(context,this.searchIndices);this.drawHoverMatchingValues(context)},drawHoverMatchingValues:function(context){var heatmap=this.heatMap;context.fillStyle=morpheus.ScentedSearch.MATCHING_VALUES_TICK_COLOR;if(heatmap.mousePositionOptions&&heatmap.mousePositionOptions.name!=null){var isColumns=!this.isVertical;var track=heatmap.getTrack(heatmap.mousePositionOptions.name,isColumns);if(track==null){return}if(track.settings.highlightMatchingValues){var hoverIndex=isColumns?heatmap.getProject().getHoverColumnIndex():heatmap.getProject().getHoverRowIndex();if(hoverIndex===-1){return}var vector=track.getVector();var value=vector.getValue(hoverIndex);var valueToModelIndices=track.getFullVector().getProperties().get(morpheus.VectorKeys.VALUE_TO_INDICES);if(!valueToModelIndices){var fullVector=track.getFullVector();valueToModelIndices=morpheus.VectorUtil.createValueToIndicesMap(fullVector);fullVector.getProperties().set(morpheus.VectorKeys.VALUE_TO_INDICES,valueToModelIndices)}var modelIndices=valueToModelIndices.get(value);if(modelIndices==null){console.log("valueToModelIndices error");return}var scale=this.scale;var lineLength=!this.isVertical?this.scrollbar.getUnscaledHeight():this.scrollbar.getUnscaledWidth();var isVertical=this.isVertical;var positions=this.positions;var project=heatmap.getProject();for(var i=0,length=modelIndices.length;i<length;i++){var modelIndex=modelIndices[i];var index=isVertical?project.convertModelRowIndexToView(modelIndex):project.convertModelColumnIndexToView(modelIndex);if(index===-1){continue}var pix=positions.getPosition(index)*scale;if(isVertical){context.fillRect(0,pix,lineLength,morpheus.ScentedSearch.LINE_HEIGHT)}else{context.fillRect(pix,0,morpheus.ScentedSearch.LINE_HEIGHT,lineLength)}}}}},drawIndices:function(context,highlightedIndices){var scale=this.scale;var lineLength=!this.isVertical?this.scrollbar.getUnscaledHeight():this.scrollbar.getUnscaledWidth();var isVertical=this.isVertical;var positions=this.positions;for(var i=0,length=highlightedIndices.length;i<length;i++){var index=highlightedIndices[i];var pix=positions.getPosition(index)*scale;if(isVertical){context.beginPath();context.rect(0,pix,lineLength,morpheus.ScentedSearch.LINE_HEIGHT);context.fill()}else{context.beginPath();context.rect(pix,0,morpheus.ScentedSearch.LINE_HEIGHT,lineLength);context.fill()}}}};morpheus.Util.extend(morpheus.ScentedSearch,morpheus.AbstractCanvas);morpheus.ScentedSearch.MATCHING_VALUES_TICK_COLOR="black";morpheus.ScentedSearch.TICK_COLOR="#3182bd";morpheus.ScrollBar=function(isVertical){morpheus.AbstractCanvas.call(this);this.isVertical=isVertical;$(this.canvas).css("border","1px solid #d8d8d8");if(isVertical){this.setBounds({width:12})}else{this.setBounds({height:12})}this.field=this.isVertical?"y":"x";var that=this;var mouseMove=function(event){if(!morpheus.CanvasUtil.dragging){var position=morpheus.CanvasUtil.getMousePos(event.target,event,true);var mouseOver=position[that.field]>=that.thumbPos&&position[that.field]<=that.thumbPos+that.thumbExtent;if(that.thumbMouseOver!==mouseOver){that.thumbMouseOver=mouseOver;that.repaint()}}};var mouseExit=function(e){if(!morpheus.CanvasUtil.dragging&&that.thumbMouseOver){that.thumbMouseOver=false;that.repaint()}};$(this.canvas).on("mousemove",mouseMove).on("mouseout",mouseExit).on("mouseenter",mouseMove);this.hammer=morpheus.Util.hammer(this.canvas,[this.isVertical?"panv":"panh","tap"]).on("panstart",this.panstart=function(event){var position=morpheus.CanvasUtil.getMousePos(event.target,event,true);if(position[that.field]>=that.thumbPos&&position[that.field]<=that.thumbPos+that.thumbExtent){that.draggingThumb=true;that.dragStartThumbPos=that.thumbPos}else{that.draggingThumb=false}}).on("panend",this.panend=function(event){that.draggingThumb=false}).on("panmove",this.panmove=function(event){if(that.draggingThumb){var position=morpheus.CanvasUtil.getMousePos(event.target,event);var thumbPosPix=that.dragStartThumbPos+(that.isVertical?event.deltaY:event.deltaX);var f=thumbPosPix/(that.visibleExtent-that.thumbExtent);var value=f*that.maxValue;that.setValue(value,true);event.preventDefault();event.srcEvent.stopPropagation();event.srcEvent.stopImmediatePropagation()}}).on("tap doubletap",this.tap=function(event){if(!that.draggingThumb){var position=morpheus.CanvasUtil.getMousePos(event.target,event);if(!that.decorator.tap(position)){var thumbExtentToValue=that.thumbExtent/that.totalExtent*that.totalExtent;that.scrollToTop=position[that.field]<that.thumbPos;that.setValue(that.scrollToTop?that.value-thumbExtentToValue:that.value+thumbExtentToValue,true)}}})};morpheus.ScrollBar.prototype={thumbPos:0,thumbExtent:0,extent:0,value:0,maxValue:0,totalExtent:0,visibleExtent:0,dragStartThumbPos:0,draggingThumb:false,thumbMouseOver:false,dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.hammer.off("panend",this.panend).off("panstart",this.panstart).off("panmove",this.panmove).off("tap",this.tap).off("doubletap",this.tap);this.hammer.destroy()},draw:function(clip,context){var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();if(this.visibleExtent===this.totalExtent){context.clearRect(0,0,width,height)}else{context.fillStyle="rgb(241,241,241)";context.fillRect(0,0,width,height);context.fillStyle=!this.thumbMouseOver?"rgb(137,137,137)":"rgb(100,100,100)";if(this.isVertical){context.fillRect(0,this.thumbPos,width,this.thumbExtent)}else{context.fillRect(this.thumbPos,0,this.thumbExtent,height)}}this.decorator.draw(clip,context)},setThumbPosFromValue:function(){var f=this.maxValue==0?0:this.value/this.maxValue;this.thumbPos=f*(this.visibleExtent-this.thumbExtent);this.thumbPos=Math.max(0,this.thumbPos)},getValue:function(){return this.value},getMaxValue:function(){return this.maxValue},setValue:function(value,trigger){if(isNaN(value)){value=0}if(this.visibleExtent===this.totalExtent){value=0}value=Math.max(value,0);value=Math.min(this.maxValue,value);this.value=value;this.setThumbPosFromValue();if(trigger){this.trigger("scroll",{value:this.value});this.repaint()}return this.value},setTotalExtent:function(totalExtent){this.totalExtent=totalExtent;this._setRange()},getTotalExtent:function(){return this.totalExtent},getVisibleExtent:function(){return this.visibleExtent},_setRange:function(){this.thumbExtent=Math.max(10,this.visibleExtent*(this.visibleExtent/this.totalExtent));this.maxValue=this.totalExtent-this.visibleExtent;this.maxValue=Math.max(0,this.maxValue);if(this.isVertical){this.setBounds({height:this.visibleExtent})}else{this.setBounds({width:this.visibleExtent})}},setExtent:function(visibleExtent,totalExtent,value){this.visibleExtent=visibleExtent;this.totalExtent=totalExtent;this._setRange();this.setValue(value,false)}};morpheus.Util.extend(morpheus.ScrollBar,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.ScrollBar,morpheus.Events);morpheus.ShapeChooser=function(options){var formBuilder=new morpheus.FormBuilder;var map=options.map;var html=['<select name="valuePicker" class="selectpicker" data-live-search="true">'];map.forEach(function(val,key){html.push("<option");html.push(' value="');html.push(key);html.push('">');html.push(key);html.push("</option>")});html.push("</select>");formBuilder.append({name:"selected_value",type:"custom",value:html.join("")});var shapeField=new morpheus.ShapeField({showNone:true});formBuilder.append({style:"max-width:50px;",name:"selected_shape",type:"custom",value:'<div data-name="shape"></div>'});shapeField.$el.appendTo(formBuilder.$form.find("[data-name=shape]"));var $valuePicker=formBuilder.$form.find("[name=valuePicker]");var selectedVal=$valuePicker.val();var _this=this;shapeField.setShapeValue(map.get(selectedVal));shapeField.on("change",function(e){map.set(selectedVal,e.shape);_this.trigger("change",{value:selectedVal,shape:e.shape})});$valuePicker.selectpicker().change(function(){selectedVal=$valuePicker.val();shapeField.setShapeValue(map.get(selectedVal))});this.$div=formBuilder.$form};morpheus.ShapeChooser.prototype={};morpheus.Util.extend(morpheus.ShapeChooser,morpheus.Events);morpheus.ShapeField=function(options){var shapes=options.shapes||morpheus.VectorShapeModel.SHAPES;var _this=this;var html=[];var size2=8;var x=4;var y=4;html.push('<div style="margin-bottom:1em;" class="btn-group">');html.push('<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown" aria-expanded="false"><span data-name="selection"></span> <span class="fa fa-caret-down"></span></button>');html.push('<ul class="dropdown-menu" role="menu">');if(options.showNone){html.push('<li><a data-name="none" href="#">(None)</a></li>')}for(var i=0;i<shapes.length;i++){var context=new C2S(size2*2,size2*2);context.translate(4,4);morpheus.CanvasUtil.drawShape(context,shapes[i],x,y,size2);var svg=context.getSerializedSvg();html.push('<li><a data-name="'+shapes[i]+'" href="#">'+svg+"</a></li>")}html.push("</ul></div>");var $el=$(html.join(""));var $header=$el.find("[data-name=selection]");$el.on("click","li > a",function(e){e.preventDefault();var shape=$(this).data("name");setShapeValue(shape);_this.trigger("change",{shape:shape})});var setShapeValue=function(val){if(val==="none"){$header.html("(None)")}else{var context=new C2S(size2*2,size2*2);context.translate(4,4);morpheus.CanvasUtil.drawShape(context,val,x,y,size2);$header.html(context.getSerializedSvg())}};this.setShapeValue=setShapeValue;this.$el=$el};morpheus.ShapeField.prototype={};morpheus.Util.extend(morpheus.ShapeField,morpheus.Events);morpheus.SortByValuesIndicator=function(project,isVertical,positions){morpheus.AbstractCanvas.call(this,true);this.project=project;this.isVertical=isVertical;this.positions=positions;this.lastPosition={start:-1,end:-1}};morpheus.SortByValuesIndicator.prototype={prePaint:function(clip,context){var positions=this.positions;var start=0;var end=positions.getLength();if(!this.isVertical){start=morpheus.Positions.getLeft(clip,positions);end=morpheus.Positions.getRight(clip,positions)}else{start=morpheus.Positions.getTop(clip,positions);end=morpheus.Positions.getBottom(clip,positions)}if(this.invalid||start!==this.lastPosition.start||end!==this.lastPosition.end){this.lastPosition.start=start;this.lastPosition.end=end;this.invalid=true}},draw:function(clip,context){var project=this.project;var isVertical=this.isVertical;var positions=this.positions;var sortKeys=isVertical?project.getColumnSortKeys():project.getRowSortKeys();context.translate(-clip.x,-clip.y);context.fillStyle="black";context.textBaseline="top";context.textAlign="left";context.font="8px "+morpheus.CanvasUtil.getFontFamily(context);var start=0;var end=positions.getLength();if(!isVertical){start=morpheus.Positions.getLeft(clip,positions);end=morpheus.Positions.getRight(clip,positions)}else{start=morpheus.Positions.getTop(clip,positions);end=morpheus.Positions.getBottom(clip,positions)}var arrowWidth=3;var arrowHeight=4;for(var i=0;i<sortKeys.length;i++){var key=sortKeys[i];if(key instanceof morpheus.SortByValuesKey){var modelIndices=key.modelIndices;for(var j=0;j<modelIndices.length;j++){var modelIndex=modelIndices[j];var view=isVertical?project.convertModelRowIndexToView(modelIndex):project.convertModelColumnIndexToView(modelIndex);if(view!==-1&&view>=start&&view<end){context.save();var pix=positions.getPosition(view);var size=positions.getItemSize(view);if(!isVertical){context.translate(pix+size/2,0)}else{context.translate(2,pix+size/2)}context.beginPath();if(key.getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight);context.lineTo(-arrowWidth,arrowHeight)}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.DESCENDING){context.moveTo(0,arrowHeight);context.lineTo(arrowWidth,0);context.lineTo(-arrowWidth,0)}else{context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight/2);context.lineTo(0,arrowHeight);context.lineTo(-arrowWidth,arrowHeight/2)}context.fill();context.restore()}}}}}};morpheus.Util.extend(morpheus.SortByValuesIndicator,morpheus.AbstractCanvas);morpheus.SortDialog=function(project){var _this=this;var $chooserDiv=$('<div class="container-fluid"></div>');var $div=$('<div class="container-fluid"></div>');var html=[];html.push('<div style="border-bottom:1px solid LightGrey;margin-bottom:20px;" class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-2"><label class="control-label">Sort</label></div>');html.push('<div class="col-xs-5">');html.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="rows" checked>Rows</label></div>');html.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="columns">Columns</label></div>');html.push("</div>");html.push("</form>");html.push("</div>");$chooserDiv.html(html.join(""));function toggle(isColumns){_this.isColumns=isColumns;var $element=_this.build(project,isColumns);$div.empty().html($element);$div.on("click","[data-name=delete]",function(e){var $this=$(this);e.preventDefault();$this.closest("div.row").remove()});$div.on("click","[data-name=add]",function(e){var $this=$(this);var level=[];var $sibling=$this.closest("div.row");_this.createLevel(level,new morpheus.SortKey("",morpheus.SortKey.SortOrder.ASCENDING),_this.fields);$sibling.after($(level.join("")));e.preventDefault()})}$chooserDiv.on("change","[name=rowsOrColumns]",function(e){var $this=$(this);toggle($this.val()==="columns")});toggle(false);var $outer=$("<div></div>");$chooserDiv.appendTo($outer);$div.appendTo($outer);morpheus.FormBuilder.showOkCancel({title:"Sort",content:$outer,okCallback:function(){var $forms=$div.find("form");var sortBy=$forms.find("[name=sortBy]").map(function(){return $(this).val()});var lockOrder=$forms.find("[name=lockOrder]").map(function(){return $(this).prop("checked")});var sortOrder=$forms.find("[name=sortOrder]:checked").map(function(){return $(this).val()});var groupBy=$div.find("[name=groupBy]").val();var newSortKeys=[];var modelIndices=_this.isColumns?project.getRowSelectionModel().toModelIndices():project.getColumnSelectionModel().toModelIndices();var existingSortKeys=_this.isColumns?project.getColumnSortKeys():project.getRowSortKeys();for(var i=0;i<existingSortKeys.length;i++){if(existingSortKeys[i].isUnlockable()){existingSortKeys.splice(i,1);i--}}var newSortKeyFields=new morpheus.Set;for(var i=0;i<sortBy.length;i++){if(!newSortKeyFields.has(sortBy[i])){newSortKeyFields.add(sortBy[i]);var key=null;if(sortBy[i]==="selection"){key=new morpheus.SortByValuesKey(modelIndices,sortOrder[i],_this.isColumns)}else if(sortBy[i]!==""){key=new morpheus.SortKey(sortBy[i],sortOrder[i])}if(key!=null){newSortKeys.push(key);if(lockOrder[i]){key.setLockOrder(1)}}}}var newGroupKeys=[];if(groupBy!=null){for(var i=0;i<groupBy.length;i++){newGroupKeys.push(new morpheus.SortKey(groupBy[i],morpheus.SortKey.SortOrder.UNSORTED))}}if(_this.isColumns){project.setGroupColumns(newGroupKeys,true);project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys(newSortKeys,existingSortKeys),true)}else{project.setGroupRows(newGroupKeys,true);project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys(newSortKeys,existingSortKeys),true)}}})};morpheus.SortDialog.prototype={isColumns:false,build:function(project,isColumns){var fields=morpheus.MetadataUtil.getMetadataNames(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata());this.fields=fields;var html=[];var sortKeys=isColumns?project.getColumnSortKeys():project.getRowSortKeys();this.createLevel0(html);for(var i=0;i<sortKeys.length;i++){if(sortKeys[i].isUnlockable()){this.createLevel(html,sortKeys[i],fields)}}html.push('<div class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-2"><label>Group by</label></div>');html.push('<div class="col-xs-4">');var groupByKeys=(isColumns?project.getGroupColumns():project.getGroupRows()).map(function(key){return key.field});html.push('<select multiple name="groupBy" class="selectpicker form-control">');_.each(fields,function(field){html.push('<option value="'+field+'"');if(_.indexOf(groupByKeys,field)!==-1){html.push(" selected")}html.push(">");html.push(field);html.push("</option>")});html.push("</select>");html.push("</div>");html.push("</div>");var $div=$(html.join(""));$div.find(".selectpicker").selectpicker({iconBase:"fa",tickIcon:"fa-check",style:"btn-default btn-sm"});return $div},createLevel0:function(html){html.push('<div style="border-bottom:1px solid LightGrey;margin-bottom:20px;" class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-8">');html.push('<a data-name="add" href="#">Add sort level</a>');html.push("</div>");html.push("</form>");html.push("</div>")},createLevel:function(html,key,fields){html.push('<div style="border-bottom:1px solid LightGrey;margin-bottom:20px;" class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-2"><label class="control-label">Sort by</label></div>');html.push('<div class="col-xs-4">');html.push('<select name="sortBy" class="form-control">');html.push('<option value=""></option>');html.push('<option value="selection"'+(key instanceof morpheus.SortByValuesKey?" selected":"")+">selection</option>");_.each(fields,function(field){html.push('<option value="'+field+'"');if(field==key.toString()){html.push(" selected")}html.push(">");html.push(field);html.push("</option>")});html.push("</select>");html.push("</div>");html.push('<div class="col-xs-5">');html.push('<div class="radio"><label><input type="radio" name="sortOrder" value="ascending"'+(morpheus.SortKey.SortOrder.ASCENDING==key.getSortOrder()?" checked":"")+">Ascending</label></div>");html.push('<div class="radio"><label><input type="radio" name="sortOrder" value="descending"'+(morpheus.SortKey.SortOrder.DESCENDING==key.getSortOrder()?" checked":"")+">Descending</label></div>");html.push("</div>");html.push('<div class="col-xs-1">');html.push('<a data-name="delete">Delete</a>');html.push("</div>");html.push('<div class="col-xs-12">');html.push('<div class="checkbox"><label><input name="lockOrder" type="checkbox"'+(key.getLockOrder()!==0?" checked":"")+"> Lock sort level</label></div>");html.push("</div>");html.push('<div class="col-xs-12">');html.push("<br />");html.push('<a data-name="add" href="#">Add sort level</a>');html.push("</div>");html.push("</form>");html.push("</div>")}};morpheus.SteppedColorSupplier=function(){morpheus.AbstractColorSupplier.call(this);this.hiddenValue=0;this.hiddenValues=new morpheus.Set;this.stepped=true};morpheus.SteppedColorSupplier.linearScale=function(value,input0,input1,pix0,pix1){return(value-input0)/(input1-input0)*(pix1-pix0)+pix0};morpheus.SteppedColorSupplier.prototype={createInstance:function(){return new morpheus.SteppedColorSupplier},isStepped:function(){return true},getHiddenValues:function(){return this.hiddenValues},getIndexForFraction:function(f){var fractions=this.fractions;if(f<=fractions[0]){return 0}if(f>=fractions[fractions.length-1]){return fractions.length-1}for(var i=0;i<fractions.length-1;i++){var left=fractions[i];var right=fractions[i+1];if(f>=left&&f<right){return i}}return fractions.length-1},getColor:function(row,column,value){if(this.hiddenValues.has(value)){value=this.hiddenValue}if(isNaN(value)){return this.missingColor}var min=this.min;var max=this.max;var colors=this.colors;if(value<=min){return colors[0]}else if(value>=max){return colors[colors.length-1]}var fraction=morpheus.SteppedColorSupplier.linearScale(value,min,max,0,100)/100;return colors[this.getIndexForFraction(fraction)]}};morpheus.Util.extend(morpheus.SteppedColorSupplier,morpheus.AbstractColorSupplier);morpheus.TabManager=function(options){this.options=$.extend({},{autohideTabBar:false,rename:true},options);var _this=this;this.activeTabObject=null;this.activeTabId=null;this.idToTabObject=new morpheus.Map;this.$nav=$('<ul class="nav nav-tabs compact morpheus-nav"></ul>');this.$nav.sortable({containment:"parent",axis:"x",helper:"clone",cancel:"li:not(.morpheus-sortable)",items:"li.morpheus-sortable"});this.$nav.sortable("disable");this.$nav.on("click","li > a",function(e){var tabId=$(this).data("link");if(tabId!=null){e.preventDefault();if(_this.activeTabId!==tabId){$(this).tab("show")}}});if(this.options.autohideTabBar){this.$nav.css("display","none")}if(options.dropTab){var html=[];html.push('<li class="morpheus-tab-addon dropdown pull-right tabdrop">');html.push('<div class="btn-group">');html.push('<button type="button" class="morpheus-drop-tab-toggle btn btn-link'+' dropdown-toggle"'+' data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">');html.push(' <span class="fa fa-angle-double-down"></span>');html.push("</button>");html.push('<ul class="dropdown-menu dropdown-menu-right" role="menu">');html.push("</ul>");html.push("</div>");html.push("</li>");var $tabDrop=$(html.join(""));var $tabDropMenu=$tabDrop.find(".dropdown-menu");$tabDrop.appendTo(this.$nav);var updateDropTab=function(){var totalWith=_this.$nav.width()-17;var sum=0;var tabDropItems=[];_this.$nav.find("> li").each(function(){var $li=$(this);var $a=$li.find("a");if(!$li.hasClass("morpheus-tab-addon")){var title=$a.contents().first().text();var isActive=$li.hasClass("active");var href=$a.attr("href");tabDropItems.push('<li class="'+(isActive?"active":"")+'"><a data-link="'+href.substring(1)+'" data-toggle="tab"'+' href="'+href+'">'+title+"</a></li>");sum+=$li.outerWidth();if(sum>=totalWith){$li.css("display","none")}else{$li.css("display","")}}});$tabDrop.css("display",tabDropItems.length>0?"":"none");$tabDropMenu.html(tabDropItems.join(""))};$tabDrop.css("display","none");this.$nav.on("sortstop",function(event,ui){updateDropTab()});$(window).on("resize",updateDropTab);this.$nav.on("remove",function(){$(window).off("resize",updateDropTab)});this.on("add remove rename reorder change",function(){updateDropTab()})}this.$nav.on("dblclick","li > a",function(e){e.preventDefault();var $a=$(this);var $li=$a.parent("li");if($li.hasClass("morpheus-tab-addon")){return}_this.rename($a.data("link"))});this.$nav.on("contextmenu.morpheus","li > a",function(e){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();var $a=$(this);var $li=$a.parent("li");if($li.hasClass("morpheus-tab-addon")){return}var menuItems=[];if($a.data("morpheus-rename")&&_this.options.rename){menuItems.push({name:"Rename"})}if($a.data("morpheus-pin")){menuItems.push({name:"Unpin tab"})}else{menuItems.push({name:"Pin tab"})}if(menuItems.length>0){morpheus.Popup.showPopup(menuItems,{x:e.pageX,y:e.pageY},e.target,function(event,item){if(item==="Rename"){_this.rename($a.data("link"))}else if(item==="Pin tab"){$a.data("morpheus-pin",true);$li.removeClass("morpheus-sortable");$li.detach();_this.$nav.prepend($li);$a.find(".close").hide();_this.$nav.sortable("option","items","li.morpheus-sortable");_this.$nav.sortable("refresh")}else if(item==="Unpin tab"){$a.data("morpheus-pin",false);$li.addClass("morpheus-sortable");$a.find(".close").show();_this.$nav.sortable("option","items","li.morpheus-sortable");_this.$nav.sortable("refresh")}})}return false});this.$nav.on("click","button",function(e){e.preventDefault();var target=$(this).attr("data-target");if(target!=null){target=target.substring(1);_this.remove(target)}});this.$tabContent=$('<div class="tab-content"></div>');this.$nav.on("shown.bs.tab",'a[data-toggle="tab"]',function(e){var previous=_this.activeTabId;_this.activeTabId=$(e.target).data("link");_this.activeTabObject=_this.idToTabObject.get(_this.activeTabId);_this.$nav.find("li").removeClass("active");_this.$nav.find("[data-link="+_this.activeTabId+"]").each(function(){$(this).parent().addClass("active")});var scrollTop=document.body.scrollTop;$("#"+_this.activeTabId).focus();document.body.scrollTop=scrollTop;if(_this.adding){return}_this.trigger("change",{tab:_this.activeTabId,previous:previous})})};morpheus.TabManager.prototype={getTabText:function(id){return this.$nav.find("> li > a").filter("a[data-link="+id+"]").contents().first().text()},getTabCount:function(){return this.idToTabObject.size()},setTabText:function(id,text){this.$nav.find("> li > a").filter("[data-link="+id+"]").contents().first().replaceWith(text+"&nbsp;");this.idToTabObject.get(id).setName(name)},addTask:function(task){},removeTask:function(task){},getWidth:function(){return this.$tabContent.outerWidth()||$(window).width()},getActiveTab:function(){return this.activeTabObject},getActiveTabId:function(){return this.activeTabId},add:function(options){this.adding=true;var id=_.uniqueId("morpheus-tab");this.idToTabObject.set(id,options.object);var li=[];li.push('<li class="morpheus-sortable" role="presentation">');li.push('<a data-morpheus-rename="'+options.rename+'" data-toggle="tab" data-link="'+id+'" href="#'+id+'">');li.push(options.title);li.push('&nbsp;<i style="color:black;"></i>');if(options.closeable){li.push('&nbsp<button style="font-size: 18px;" type="button" class="close"'+' aria-label="Close"'+' data-target="#'+id+'"><span aria-hidden="true">×</span></button>')}li.push("</a></li>");var $link=$(li.join(""));$link.appendTo(this.$nav);var $panel=$('<div tabIndex="0" style="outline:0;cursor:default;" role="tabpanel"'+' class="tab-pane" id="'+id+'"></div>');options.$el.appendTo($panel);$panel.appendTo(this.$tabContent);if(options.enabled===false){$link.addClass("disabled");$link.find("a").addClass("btn disabled")}if(options.focus){this.$nav.find('> li > a[data-toggle="tab"]:last').tab("show");this.activeTabId=id;this.activeTabObject=options.object;$panel.focus()}if(this.options.autohideTabBar){this.$nav.css("display",this.idToTabObject.size()>1?"":"none")}this.getTabCount()<=1?this.$nav.sortable("disable"):this.$nav.sortable("enable");this.adding=false;this.trigger("add");return{$panel:$panel,id:id}},appendTo:function($target){this.$nav.appendTo($target);this.$tabContent.appendTo($target)},remove:function(target){if(target===undefined){target=this.activeTabId}var obj=this.idToTabObject.remove(target);$("#"+target).remove();this.activeTabObject=null;this._getA(target).parent().remove();this.$tabContent.find(target).remove();var $a=this.$nav.find('> li > a[data-toggle="tab"]:last');if($a.length===0){if(this.options.landingPage){if(typeof this.options.landingPage==="function"){this.options.landingPage().show()}else{this.options.landingPage.show()}}}$a.tab("show");if(this.options.autohideTabBar){this.$nav.css("display",this.idToTabObject.size()>1?"":"none")}this.getTabCount()<=1?this.$nav.sortable("disable"):this.$nav.sortable("enable");if(this.idToTabObject.size()>0){$($a.attr("href")).focus()}if(obj!=null&&obj.onRemove){obj.onRemove()}this.trigger("remove",{tab:target})},setOptions:function(options){this.options=options;if(this.options.autohideTabBar){this.$nav.css("display",this.idToTabObject.size()>1?"":"none")}},getOptions:function(){return this.options},setActiveTab:function(id){if(id!==this.activeTabId){var $a=this._getA(id);$a.parent().removeClass("disabled");$a.removeClass("btn disabled");$a.tab("show");var previous=this.activeTabId;this.activeTabId=id;this.activeTabObject=this.idToTabObject.get(this.activeTabId);this.trigger("change",{tab:this.activeTabId,previous:previous})}},setTabTitle:function(id,title){this._getA(id).attr("title",title)},_getA:function(id){if(id[0]==="#"){id=id.substring(1)}return this.$nav.find("> li > a[data-link="+id+"]:first")},setTabEnabled:function(id,enabled){var $a=this._getA(id);if(enabled){$a.parent().removeClass("disabled");$a.removeClass("btn disabled")}else{$a.parent().addClass("disabled");$a.addClass("btn disabled")}},getIdToTabObject:function(){return this.idToTabObject},getTabObject:function(id){return this.idToTabObject.get(id)},rename:function(id){var $a=this._getA(id);var $li=$a.parent();if($li.hasClass("morpheus-tab-addon")){return}if(!$a.data("morpheus-rename")||!this.options.rename){return}var _this=this;var builder=new morpheus.FormBuilder;builder.append({name:"name",type:"text",value:$.trim($a.contents().first().text())});morpheus.FormBuilder.showOkCancel({title:"Rename Tab",content:builder.$form,focus:document.activeElement,okCallback:function(){var name=$.trim(builder.getValue("name"));if(name!==""){if(_this.activeTabObject!=null&&_this.activeTabObject.setName){_this.activeTabObject.setName(name)}$a.contents().first().replaceWith(name+"&nbsp;");_this.trigger("rename")}}})}};morpheus.Util.extend(morpheus.TabManager,morpheus.Events);morpheus.Table=function(options){options=morpheus.Table.createOptions(options);this.options=options;if(!options.width){options.width=options.$el.attr("class")}var _this=this;var height=options.height;var $gridDiv=$('<div class="slick-table'+(options.tableClass?" "+options.tableClass:"")+'" style="width:'+options.fixedWidth+";height:"+height+'"></div>');this.$gridDiv=$gridDiv;$gridDiv.appendTo(options.$el);var columns=options.columns;this.columns=columns;var visibleColumns=columns.filter(function(c){return c.visible});var grid=new morpheus.Grid({gridOptions:{select:options.select,rowHeight:options.rowHeight,autoEdit:false,editable:false,autoHeight:options.height==="auto",enableTextSelectionOnCells:true},$el:$gridDiv,items:options.items,columns:visibleColumns});this.grid=grid;this.searchFunction=null;var searchFilter={isEmpty:function(){return _this.searchFunction==null},init:function(){},accept:function(item){return _this.searchFunction(item)}};this.grid.getFilter().add(searchFilter);var $header=$('<div class="slick-table-header"><div name="top"></div><div style="display: inline-block;" name="left" class="pad-bottom-8 pad-top-8"></div><div name="right" class="pull-right pad-bottom-8'+' pad-top-8"></div></div>');this.$header=$header;var $right=$header.find(".pull-right");if(options.search){var tableSearch=new morpheus.TableSearchUI({$el:$header.find("[name=top]"),$right:$right});tableSearch.setTable(this);this.tableSearch=tableSearch}if(options.columnPicker&&visibleColumns.length!==this.columns.length){var select=[];select.push('<select data-width="90px" data-selected-text-format="static" title="Columns..." multiple class="pad-left-4 selectpicker show-tick">');var sortedColumns=this.columns.slice().sort(function(a,b){a=a.name.toLowerCase();b=b.name.toLowerCase();return a===b?0:a<b?-1:1});sortedColumns.forEach(function(c,i){select.push('<option value="'+i+'"');if(c.visible){select.push(" selected")}select.push(">");select.push(c.name);select.push("</option>")});select.push("</select>");var $select=$(select.join(""));$select.appendTo($right);$select.selectpicker({iconBase:"fa",tickIcon:"fa-check",style:"btn-default btn-xs"});$select.on("change",function(){var oldColumns=grid.getColumns().map(function(c){return c.id});var selectedColumnIndices=$select.val();visibleColumns=[];for(var i=0;i<selectedColumnIndices.length;i++){visibleColumns.push(sortedColumns[parseInt(selectedColumnIndices[i])])}var newColumns=visibleColumns.map(function(c){return c.id});grid.setColumns(visibleColumns);if(newColumns.length>oldColumns.length){var set=new morpheus.Set;for(var i=0;i<newColumns.length;i++){set.add(newColumns[i])}for(var i=0;i<oldColumns.length;i++){set.remove(oldColumns[i])}var added=set.values();grid.setSortColumns([{columnId:added[0],sortAsc:true}])}_this.resize();_this.redraw()})}$header.prependTo(options.$el);var collapsed=false;var lastWidth=-1;var resize=function(){if(!_this.options.responsive){return}var gridWidth=options.$el.width();if(gridWidth===lastWidth){return}lastWidth=gridWidth;$gridDiv.css("width",gridWidth+"px");if(!collapsed&&gridWidth<options.collapseBreakpoint&&visibleColumns.length>1){collapsed=true;$gridDiv.addClass("slick-stacked");_this.grid.grid.getOptions().rowHeight=(options.collapsedRowHeight?options.collapsedRowHeight:options.rowHeight)*visibleColumns.length;_this.grid.grid.setColumns([{id:0,tooltip:function(item,value){var html=[];for(var i=0;i<visibleColumns.length;i++){var text=visibleColumns[i].tooltip(item,visibleColumns[i].getter(item));if(text!=null&&text!==""){html.push(text)}}return html.join("<br />")},collapsed:true,getter:function(item){return item},formatter:function(row,cell,value,columnDef,dataContext){var html=[];html.push('<div class="slick-table-wrapper"><div class="slick-cell-wrapper">');if(options.rowHeader){html.push(options.rowHeader(dataContext));html.push('<div style="height:4px;"></div>')}for(var i=0;i<visibleColumns.length;i++){if(i>0){html.push('<div style="height:4px;"></div>')}var c=visibleColumns[i];html.push(c.name);html.push(":");var s=c.renderer(dataContext,c.getter(dataContext));html.push(s)}html.push("</div></div>");return html.join("")},sortable:false,name:""}]);$gridDiv.find(".slick-header").hide();_this.grid.grid.resizeCanvas();_this.grid.grid.invalidate()}else if(collapsed&&gridWidth>=options.collapseBreakpoint){$gridDiv.removeClass("slick-stacked");collapsed=false;if(options.showHeader){$gridDiv.find(".slick-header").show()}_this.grid.grid.getOptions().rowHeight=options.rowHeight;_this.grid.grid.setColumns(visibleColumns);_this.grid.grid.resizeCanvas();if(options.select){_this.grid.grid.setSelectedRows(_this.grid.grid.getSelectedRows())}_this.grid.grid.invalidate()}else{_this.grid.grid.resizeCanvas();_this.grid.grid.invalidate()}_this.grid.maybeAutoResizeColumns()};if(!options.showHeader){$gridDiv.find(".slick-header").hide()}if(options.responsive){$(window).on("resize orientationchange",resize);$gridDiv.on("remove",function(){$(window).off("resize",resize)});resize()}this.resize=resize;if(visibleColumns.length>1&&options.items!=null&&options.items.length>0){this.setItems(options.items)}if(!$gridDiv.is(":visible")){var $parent=$gridDiv;var observer=new MutationObserver(function(mutations){if(window.getComputedStyle($parent[0]).display!=="none"){observer.disconnect();resize()}});while($parent.length>0){if(window.getComputedStyle($parent[0]).display==="none"){break}$parent=$parent.parent()}if($parent.length>0){observer.observe($parent[0],{attributes:true,childList:false,characterData:false})}}};morpheus.Table.defaultRenderer=function(item,value){if(value==null){return""}else if(_.isNumber(value)){return morpheus.Util.nf(value)}else if(morpheus.Util.isArray(value)){var s=[];for(var i=0,length=value.length;i<length;i++){if(i>0){s.push(", ")}var val=value[i];s.push(value[i])}return s.join("")}else{return""+value}};morpheus.Table.prototype={toText:function(){var text=[];var items=this.getItems();var columns=this.columns.filter(function(c){return c.visible});for(var j=0;j<columns.length;j++){if(j>0){text.push("\t")}text.push(columns[j].name)}text.push("\n");for(var i=0;i<items.length;i++){var item=items[i];for(var j=0;j<columns.length;j++){if(j>0){text.push("\t")}var value=columns[j].getter(item);text.push(morpheus.Util.toString(value))}text.push("\n")}return text.join("")},setHeight:function(height){this.options.height=height;if(height==="auto"){this.$gridDiv.css("height","");this.grid.grid.getOptions().autoHeight=true;this.grid.grid.setOptions(this.grid.grid.getOptions())}else{this.$gridDiv.css("height",height)}this.grid.grid.resizeCanvas();if(height==="auto"){var height=this.getItems().length*this.options.rowHeight+this.options.rowHeight;this.$gridDiv.find(".slick-viewport").css("height",height+"px")}this.grid.grid.invalidate()},setSearchVisible:function(visible){this.$header.find("[name=search]").css("display",visible?"":"none")},autocomplete:function(tokens,response){var matches=[];var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);var columns=this.columns.filter(function(c){return c.searchable&&c.visible||c.alwaysSearch});var ncolumns=columns.length;var showField=ncolumns>1;if(token===""){if(ncolumns<=1){return response(matches)}for(var i=0;i<ncolumns;i++){var field=columns[i].name;matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})}matches.sort(function(a,b){return a.value===b.value?0:a.value<b.value?-1:1});return response(matches)}var field=null;var semi=token.indexOf(":");var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");if(semi>0){if(token.charCodeAt(semi-1)!==92){var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[token.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}var columnNameToColumn=new morpheus.Map;var columnNames=columns.map(function(c){return c.name});for(var i=0;i<columnNames.length;i++){columnNameToColumn.set(columnNames[i],columns[i])}var c=columnNameToColumn.get(possibleField);if(c!==undefined){token=$.trim(token.substring(semi+1));columns=[c];ncolumns=1}}}else if(ncolumns>1){var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");for(var j=0;j<ncolumns;j++){var field=columns[j].name;if(regex.test(field)){matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})}}}var set=new morpheus.Set;var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");var items=this.getItems();var dataTypes=[];var filteredColumns=[];columns.forEach(function(c){var dataType=null;for(var i=0,nitems=items.length;i<nitems;i++){var value=c.getter(items[i]);if(value!=null){dataType=morpheus.Util.getDataType(value);break}}if(dataType==="string"||dataType==="[string]"){dataTypes.push(dataType);filteredColumns.push(c)}});columns=filteredColumns;ncolumns=columns.length;var maxSize=matches.length+10;for(var i=0,nitems=items.length;i<nitems;i++){var item=items[i];for(var j=0;j<ncolumns;j++){var field=columns[j].name;var value=columns[j].getter(item);var dataType=dataTypes[j];if(dataType==="[string]"){var nvalues=value==null?0:value.length;for(var k=0;k<nvalues;k++){var val=value[k];if(regex.test(val)&&!set.has(val)){set.add(val);matches.push({value:showField?field+":"+val:val,label:showField?'<span style="font-weight:300;">'+field+":</span>"+'<span style="font-weight:900;">'+val+"</span>":'<span style="font-weight:900;">'+val+"</span>"})}if(matches.length===maxSize){return response(matches)}}}else{if(regex.test(value)&&!set.has(value)){set.add(value);matches.push({value:showField?field+":"+value:value,label:showField?'<span style="font-weight:300;">'+field+":</span>"+'<span style="font-weight:900;">'+value+"</span>":'<span style="font-weight:900;">'+value+"</span>"});if(matches.length===maxSize){return response(matches)}}}}}return response(matches)},searchWithPredicates:function(predicates){if(predicates==null||predicates.length===0){this.searchFunction=null;this.grid.setFilter(this.grid.getFilter());return}var columns=this.columns.filter(function(c){return c.searchable&&c.visible||c.alwaysSearch});var columnNameToColumn=new morpheus.Map;var columnNames=columns.map(function(c){return c.name});for(var i=0;i<columnNames.length;i++){columnNameToColumn.set(columnNames[i],columns[i])}var filteredPredicates=[];var npredicates=predicates.length;for(var i=0;i<npredicates;i++){var predicate=predicates[i];var filterColumnName=predicate.getField();if(filterColumnName!=null){var column=columnNameToColumn.get(filterColumnName);if(column){predicate.column=column;filteredPredicates.push(predicate)}}else{filteredPredicates.push(predicate)}}predicates=filteredPredicates;npredicates=predicates.length;var f=function(item){for(var p=0;p<npredicates;p++){var predicate=predicates[p];var searchColumns;if(predicate.column){searchColumns=[predicate.column]}else{searchColumns=columns}for(var j=0,ncolumns=searchColumns.length;j<ncolumns;j++){var value=searchColumns[j].getter(item);if(morpheus.Util.isArray(value)){var nvalues=value.length;for(var i=0;i<nvalues;i++){if(predicate.accept(value[i])){return true}}}else{var predicate=predicates[p];if(predicate.accept(value)){return true}}}}return false};this.searchFunction=f;this.grid.setFilter(this.grid.getFilter())},search:function(text){if(text===""){this.searchFunction=null;this.grid.setFilter(this.grid.getFilter())}else{var tokens=morpheus.Util.getAutocompleteTokens(text);var columns=this.columns.filter(function(c){return c.searchable&&c.visible||c.alwaysSearch});var columnNames=columns.map(function(c){return c.name});var predicates=morpheus.Util.createSearchPredicates({tokens:tokens,fields:columnNames});this.searchWithPredicates(predicates)}},getSelectedRows:function(){return this.grid.getSelectedRows()},getSelectedItems:function(){return this.grid.getSelectedItems()},getSelectedItem:function(){return this.grid.getSelectedItem()},setSelectedRows:function(rows){this.grid.setSelectedRows(rows)},getItems:function(items){return this.grid.getItems()},getAllItemCount:function(){return this.grid.getAllItemCount()},getFilteredItemCount:function(){return this.grid.getFilteredItemCount()},setFilter:function(f){this.grid.setFilter(f)},getFilter:function(){return this.grid.getFilter()},setItems:function(items){this.grid.setItems(items);this.grid.redraw()},redraw:function(){this.grid.redraw()},on:function(evtStr,handler){this.grid.on(evtStr,handler);return this},off:function(evtStr,handler){this.grid.off(evtStr,handler);return this},trigger:function(evtStr){this.grid.trigger(evtStr)}};morpheus.Table.createOptions=function(options){options=$.extend(true,{},{items:[],height:"564px",collapseBreakpoint:400,showHeader:true,select:true,rowHeader:null,responsive:true,fixedWidth:"320px",columnPicker:true},options);if(!options.columns){options.columns=[{name:""}]}var columns=[];options.columns.forEach(function(c,i){var column=$.extend(true,{},{id:i,tooltip:function(dataContext,value){return morpheus.Table.defaultRenderer(dataContext,value)},formatter:function(row,cell,value,columnDef,dataContext){var html=[];html.push('<div class="slick-table-wrapper"><div class="slick-cell-wrapper">');if(options.rowHeader&&cell===0){html.push(options.rowHeader(dataContext))}html.push(column.renderer(dataContext,value));html.push("</div></div>");return html.join("")},comparator:function(a,b){var aNaN=a==null||_.isNumber(a)&&isNaN(a);var bNaN=b==null||_.isNumber(b)&&isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}if(a.toLowerCase){a=a.toLowerCase()}if(b.toLowerCase){b=b.toLowerCase()}return a===b?0:a<b?-1:1},sortable:true,searchable:true,width:null,name:c.name,renderer:morpheus.Table.defaultRenderer},c);if(column.visible===undefined){column.visible=true}if(!column.getter){column.getter=column.field==null?function(item){return item}:function(item){return item[c.field]}}columns.push(column)});options.columns=columns;if(options.columns.length===1){options.tableClass="slick-table-compact"}else{options.tableClass="slick-bordered-table"}if(!options.rowHeight){options.rowHeight=22}return options};morpheus.TableSearchUI=function(options){var _this=this;var $search=$('<input name="search" type="text" class="form-control input-sm"'+' placeholder="Search" autocomplete="off">');$search.appendTo(options.$el);this.$search=$search;this.$searchResults=$('<span class="pad-top-2 tableview-rowcount" name="search"></span>');this.$showAll=$('<div style="display:inline-block;min-width:60px;" name="search" class="pad-left-8 text-button-copy tableview-rowcount">Show'+" all</div>");this.$searchResults.appendTo(options.$right);this.$showAll.appendTo(options.$right);this.$showAll.on("click",function(e){e.preventDefault();$search.val("");_this.table.search("");_this.table.trigger("showAll",{table:_this.table})});$search.on("keyup",_.debounce(function(){_this.table.search($.trim($(this).val()))},100));morpheus.Util.autosuggest({$el:$search,suggestWhenEmpty:true,filter:function(tokens,response){_this.table.autocomplete(tokens,response)},select:function(){_this.table.search($.trim($search.val()))}})};morpheus.TableSearchUI.prototype={updateSearchLabel:function(){var text="Showing: "+morpheus.Util.intFormat(this.table.getFilteredItemCount())+" / "+morpheus.Util.intFormat(this.table.getAllItemCount());this.$searchResults.html(text)},setTable:function(table){this.table=table;var _this=this;table.on("filter",function(){_this.updateSearchLabel()})}};morpheus.TrackSelection=function(track,positions,selectionModel,isColumns,heatMap){var canvas=track.canvas;var startIndex=-1;var coord=isColumns?"x":"y";function getPosition(event,useDelta){if(track.settings.squished){var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);var squishFactor=total/(isColumns?track.getUnscaledWidth():track.getUnscaledHeight());var clientXY=morpheus.CanvasUtil.getClientXY(event,useDelta);var p=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,0,0,useDelta);p[coord]*=squishFactor;return p}else{return morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,heatMap.scrollLeft(),heatMap.scrollTop(),useDelta)}}var panning=false;var scrollIntervalId;var lastScrollTime=(new Date).getTime();var _this=this;var throttlePanMove=50;function mouseleave(e){var scroll=function(){var now=(new Date).getTime();var rect=canvas.getBoundingClientRect();var doPan=false;if(!isColumns){if(e.clientY>rect.bottom||e.clientY<rect.top){doPan=true}}else{if(e.clientX>rect.right||e.clientX<rect.left){doPan=true}}if(doPan){_this.panmove(e);scrollIntervalId=setTimeout(scroll,throttlePanMove)}};scrollIntervalId=setTimeout(scroll,throttlePanMove);$(canvas).one("mouseover",mouseover)}function mouseover(){clearTimeout(scrollIntervalId);$(canvas).one("mouseleave",mouseleave)}this.hammer=morpheus.Util.hammer(canvas,["pan","tap","longpress"]).on("longpress",this.longpress=function(event){event.preventDefault();event.srcEvent.stopImmediatePropagation();event.srcEvent.stopPropagation();heatMap.setSelectedTrack(track.name,isColumns);track.showPopup(event.srcEvent)}).on("panend",this.panend=function(event){panning=false;clearInterval(scrollIntervalId);$(canvas).off("mouseover mouseleave")}).on("panmove",this.panmove=function(event){var now=(new Date).getTime();var elapsed=now-lastScrollTime;if(elapsed<throttlePanMove){return}var position=getPosition(event);var endIndex=positions.getIndex(position[coord],false);var commandKey=event.srcEvent==null?false:morpheus.Util.IS_MAC?event.srcEvent.metaKey:event.srcEvent.ctrlKey;var viewIndices=commandKey?selectionModel.getViewIndices():new morpheus.Set;var _startIndex=startIndex;if(startIndex>endIndex){var tmp=endIndex;endIndex=_startIndex;_startIndex=tmp}for(var i=_startIndex;i<=endIndex;i++){viewIndices.add(i)}selectionModel.setViewIndices(viewIndices,true);if(!isColumns){var scrollTop=heatMap.scrollTop();var heatMapHeight=heatMap.heatmap.getUnscaledHeight();var scrollBottom=scrollTop+heatMapHeight;if(position.y>scrollBottom){heatMap.scrollTop(position.y+8-heatMapHeight)}else if(position.y<scrollTop){heatMap.scrollTop(position.y-8)}}else{var scrollLeft=heatMap.scrollLeft();var heatMapWidth=heatMap.heatmap.getUnscaledWidth();var scrollRight=scrollLeft+heatMapWidth;if(position.x>scrollRight){heatMap.scrollLeft(position.x+8-heatMapWidth)}else if(position.x<scrollLeft){heatMap.scrollLeft(position.x-8)}}event.preventDefault();if(event.srcEvent!=null){event.srcEvent.stopPropagation();event.srcEvent.stopImmediatePropagation()}lastScrollTime=(new Date).getTime()}).on("panstart",this.panstart=function(event){heatMap.setSelectedTrack(track.name,isColumns);var position=getPosition(event,true);startIndex=positions.getIndex(position[coord],false);panning=true;$(canvas).one("mouseleave.morpheus",mouseleave)}).on("tap doubletap",this.tap=function(event){var position=getPosition(event);var index=positions.getIndex(position[coord],false);if(event.tapCount>1){if(isColumns&&!heatMap.options.columnsSortable||!isColumns&&!heatMap.options.rowsSortable){return}heatMap.sortBasedOnSelection(null,isColumns,event.srcEvent.shiftKey)}else{heatMap.setSelectedTrack(track.name,isColumns);var commandKey=morpheus.Util.IS_MAC?event.srcEvent.metaKey:event.srcEvent.ctrlKey;if(morpheus.Util.IS_MAC&&event.srcEvent.ctrlKey){return}var viewIndices;if(commandKey){viewIndices=selectionModel.getViewIndices();if(viewIndices.has(index)){viewIndices.remove(index)}else{viewIndices.add(index)}}else if(event.srcEvent.shiftKey){viewIndices=selectionModel.getViewIndices();var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;viewIndices.forEach(function(viewIndex){min=Math.min(viewIndex,min);max=Math.max(viewIndex,max)});if(index>=max){for(var i=max;i<=index;i++){viewIndices.add(i)}}else{for(var i=Math.min(index,min),max=Math.max(index,min);i<=max;i++){viewIndices.add(i)}}}else{viewIndices=new morpheus.Set;viewIndices.add(index)}selectionModel.setViewIndices(viewIndices,true)}})};morpheus.TrackSelection.prototype={dispose:function(){this.hammer.off("longpress",this.longpress).off("panstart",this.panstart).off("panmove",this.panmove).off("panend",this.panend).off("tap",this.tap).off("doubletap",this.tap);this.hammer.destroy()}};morpheus.VectorTrackHeader=function(project,name,isColumns,heatMap){morpheus.AbstractCanvas.call(this);this.font={weight:"400"};this.project=project;this.name=name;this.isColumns=isColumns;var canvas=this.canvas;this.heatMap=heatMap;this.selectedBackgroundColor="#c8c8c8";this.backgroundColor="rgb(255,255,255)";var vector=(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata()).getByName(name);if(vector&&vector.getProperties().has(morpheus.VectorKeys.TITLE)){this.canvas.setAttribute("title",vector.getProperties().get(morpheus.VectorKeys.TITLE));$(this.canvas).tooltip()}var _this=this;this.setBounds({height:this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET});function getResizeCursor(pos){if(isColumns){if(pos.y<3){return{cursor:"ns-resize",isPrevious:true}}if(pos.y>=_this.getUnscaledHeight()-3){return{cursor:"ns-resize",isPrevious:false}}if(pos.x>=_this.getUnscaledWidth()-3){return{isPrevious:false,cursor:"ew-resize"}}}else{if(pos.x<3&&heatMap.getTrackIndex(name,isColumns)>0){return{cursor:"ew-resize",isPrevious:true}}if(pos.x>=_this.getUnscaledWidth()-3){return{cursor:"ew-resize",isPrevious:false}}}}var mouseMove=function(event){if(!morpheus.CanvasUtil.dragging){var pos=morpheus.CanvasUtil.getMousePos(event.target,event);var resizeCursor=getResizeCursor(pos);canvas.style.cursor=resizeCursor==null?"default":resizeCursor.cursor;_this.isMouseOver=true;_this.repaint()}};var mouseExit=function(e){if(!morpheus.CanvasUtil.dragging){canvas.style.cursor="default"}_this.isMouseOver=false;_this.repaint()};var showPopup=function(e){heatMap.setSelectedTrack(_this.name,isColumns);var track=heatMap.getTrack(_this.name,isColumns);if(!track){throw _this.name+" track not found"}e.preventDefault();if(e.stopPropagation){e.stopPropagation()}if(e.stopImmediatePropagation){e.stopImmediatePropagation()}track.showPopup(e,true);return false};$(this.canvas).css({"background-color":this.backgroundColor}).on("mousemove.morpheus",mouseMove).on("mouseout.morpheus",mouseExit).on("mouseenter.morpheus",mouseMove).on("contextmenu.morpheus",showPopup).addClass("morpheus-track-header "+(isColumns?"morpheus-columns":"morpheus-rows"));var resizeCursor;var dragStartWidth=0;var dragStartHeight=0;var reorderingTrack=false;var dragStartPosition;var resizeTrackName;this.hammer=morpheus.Util.hammer(canvas,["pan","tap","longpress"]).on("longpress",this.longpress=function(event){event.preventDefault();heatMap.setSelectedTrack(_this.name,isColumns);var track=heatMap.getTrack(_this.name,isColumns);track.showPopup(event.srcEvent,true)}).on("panend",this.panend=function(event){_this.isMouseOver=false;morpheus.CanvasUtil.dragging=false;canvas.style.cursor="default";var index=heatMap.getTrackIndex(_this.name,isColumns);var header=heatMap.getTrackHeaderByIndex(index,isColumns);var track=heatMap.getTrackByIndex(index,isColumns);var $canvas=$(track.canvas);$canvas.css("z-index","0");$(header.canvas).css("z-index","0");heatMap.revalidate()}).on("panstart",this.panstart=function(event){_this.isMouseOver=false;if(morpheus.CanvasUtil.dragging){return}if(resizeCursor!=null){morpheus.CanvasUtil.dragging=true;canvas.style.cursor=resizeCursor.cursor;if(resizeCursor.isPrevious){var index=heatMap.getTrackIndex(_this.name,isColumns);index--;if(index===-1){index=0}var header=heatMap.getTrackHeaderByIndex(index,isColumns);dragStartWidth=header.getUnscaledWidth();dragStartHeight=header.getUnscaledHeight();resizeTrackName=header.name}else{resizeTrackName=null;dragStartWidth=_this.getUnscaledWidth();dragStartHeight=_this.getUnscaledHeight()}event.preventDefault();reorderingTrack=false}else{var index=heatMap.getTrackIndex(_this.name,isColumns);if(index==-1){throw _this.name+" not found"}var header=heatMap.getTrackHeaderByIndex(index,isColumns);var track=heatMap.getTrackByIndex(index,isColumns);heatMap.setSelectedTrack(_this.name,isColumns);var $canvas=$(track.canvas);dragStartPosition=$canvas.position();$canvas.css("z-index","100");$(header.canvas).css("z-index","100");morpheus.CanvasUtil.dragging=true;resizeCursor=undefined;reorderingTrack=true}}).on("panmove",this.panmove=function(event){_this.isMouseOver=false;if(resizeCursor!=null){var width;var height;if(resizeCursor.cursor==="ew-resize"){var dx=event.deltaX;width=Math.max(8,dragStartWidth+dx)}if(resizeCursor.cursor==="ns-resize"){var dy=event.deltaY;height=Math.max(8,dragStartHeight+dy)}heatMap.resizeTrack(resizeTrackName==null?_this.name:resizeTrackName,width,height,isColumns)}else if(reorderingTrack){var index=heatMap.getTrackIndex(_this.name,isColumns);var header=heatMap.getTrackHeaderByIndex(index,isColumns);var track=heatMap.getTrackByIndex(index,isColumns);var ntracks=heatMap.getNumTracks(isColumns);var delta=isColumns?event.deltaY:event.deltaX;var newIndex=index+(delta>0?1:-1);newIndex=Math.min(Math.max(0,newIndex),ntracks-1);var prop=isColumns?"top":"left";var w=isColumns?"getUnscaledHeight":"getUnscaledWidth";var trackBounds={};trackBounds[prop]=dragStartPosition[prop]+delta;track.setBounds(trackBounds);header.setBounds(trackBounds);var dragOverTrack=heatMap.getTrackByIndex(newIndex,isColumns);var dragOverWidth=dragOverTrack[w]();var dragOverLeft=$(dragOverTrack.canvas).position()[prop];var dragleft=dragStartPosition[prop]+delta;var dragright=dragleft+track[w]();if(delta>0&&dragright>=dragOverLeft+dragOverWidth/2||delta<0&&dragleft<=dragOverLeft+dragOverWidth/2){if(index!==newIndex){heatMap.moveTrack(index,newIndex,isColumns);var otherHeader=heatMap.getTrackHeaderByIndex(index,isColumns);var otherTrack=heatMap.getTrackByIndex(index,isColumns);var $movedCanvas=$(otherTrack.canvas);var newLeft=$movedCanvas.position()[prop];if(delta<0){newLeft+=track[w]()}else{newLeft-=track[w]()}var otherBounds={};otherBounds[prop]=newLeft;otherTrack.setBounds(otherBounds);otherHeader.setBounds(otherBounds)}}}}).on("tap",this.tap=function(event){if(morpheus.Util.IS_MAC&&event.srcEvent.ctrlKey){return}_this.isMouseOver=false;heatMap.setSelectedTrack(_this.name,isColumns);var vector=(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata()).getByName(name);if(isColumns&&!heatMap.options.columnsSortable||vector==null){return}if(!isColumns&&!heatMap.options.rowsSortable||vector==null){return}var additionalSort=event.srcEvent.shiftKey;var isGroupBy=false;var existingSortKeyIndex=_this.getSortKeyIndexForColumnName(_this.getSortKeys(),_this.name);var sortOrder;var sortKey;var dataType=morpheus.VectorUtil.getDataType(vector);if(existingSortKeyIndex!=null){sortKey=_this.getSortKeys()[existingSortKeyIndex.index];if(sortKey.getSortOrder()===morpheus.SortKey.SortOrder.UNSORTED){sortOrder=morpheus.SortKey.SortOrder.ASCENDING}else if(sortKey.getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}else if(sortKey.getSortOrder()===morpheus.SortKey.SortOrder.TOP_N){sortOrder=morpheus.SortKey.SortOrder.UNSORTED}else{sortOrder=dataType==="number"||dataType==="[number]"?morpheus.SortKey.SortOrder.TOP_N:morpheus.SortKey.SortOrder.UNSORTED}}else{sortKey=new morpheus.SortKey(_this.name,morpheus.SortKey.SortOrder.ASCENDING);sortOrder=morpheus.SortKey.SortOrder.ASCENDING}if(sortKey!=null){sortKey.setSortOrder(sortOrder);_this.setSortingStatus(_this.getSortKeys(),sortKey,additionalSort,isGroupBy)}});$(this.canvas).on("mousedown",function(event){resizeCursor=getResizeCursor(morpheus.CanvasUtil.getMousePos(event.target,event,true))})};morpheus.VectorTrackHeader.FONT_OFFSET=2;morpheus.VectorTrackHeader.prototype={selected:false,isMouseOver:false,defaultFontHeight:11,dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.hammer.off("longpress",this.longpress).off("panend",this.panend).off("panstart",this.panstart).off("panmove",this.panmove).off("tap",this.tap);this.hammer.destroy()},getPreferredSize:function(){var size=this.getPrintSize();size.width+=24;if(!this.isColumns){size.height=this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET}return size},getPrintSize:function(){var context=this.canvas.getContext("2d");context.font=this.fontWeight+" "+this.defaultFontHeight+"px "+morpheus.CanvasUtil.getFontFamily(context);var textWidth=4+context.measureText(this.name).width;return{width:textWidth,height:this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET}},getSortKeys:function(){return this.isColumns?this.project.getColumnSortKeys():this.project.getRowSortKeys()},setOrder:function(sortKeys){if(this.isColumns){this.project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,this.project.getColumnSortKeys()),false)}else{this.project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,this.project.getRowSortKeys()),false)}},setGroupBy:function(groupBy){var existingGroupBy=this.isColumns?this.project.groupColumns:this.project.groupRows;var index=-1;for(var i=0,length=existingGroupBy.length;i<length;i++){if(existingGroupBy[i].toString()===groupBy.toString()){index=i;break}}var newGroupBy=[groupBy];if(index!==-1){newGroupBy=existingGroupBy;newGroupBy.splice(index,1)}if(this.isColumns){this.project.setGroupColumns(newGroupBy,true)}else{this.project.setGroupRows(newGroupBy,true)}},setSelected:function(selected){if(selected!=this.selected){this.selected=selected;$(this.canvas).css({"background-color":this.selected?this.selectedBackgroundColor:this.backgroundColor})}},setSortingStatus:function(sortKeys,sortKey,additionalSort,isGroupBy){if(!isGroupBy){if(sortKey.getSortOrder()==morpheus.SortKey.SortOrder.UNSORTED&&!additionalSort){this.setOrder([])}else{if(additionalSort&&sortKeys.length==0){additionalSort=false}if(!additionalSort){sortKeys=[sortKey]}else{var sortKeyIndex=this.getSortKeyIndexForColumnName(sortKeys,sortKey.toString());if(sortKeyIndex===null){sortKeys.push(sortKey)}else{sortKeys[sortKeyIndex.index]=sortKey}}this.setOrder(sortKeys)}}if(isGroupBy){this.setGroupBy(sortKey)}else{if(this.isColumns){this.project.trigger("columnSortOrderChanged")}else{this.project.trigger("rowSortOrderChanged")}}},getSortKeyIndexForColumnName:function(sortKeys,columnName){if(sortKeys!=null){var counter=0;for(var i=0,size=sortKeys.length;i<size;i++){if(sortKeys[i].isUnlockable()){counter++}if(sortKeys[i]instanceof morpheus.SortKey&&columnName===sortKeys[i].toString()){return{index:i,number:counter}}}}return null},print:function(clip,context){if(clip.height<=6){return}context.textBaseline="bottom";if(this.isColumns){context.textAlign="right";context.font=this.font.weight+" "+Math.min(this.defaultFontHeight,clip.height-morpheus.VectorTrackHeader.FONT_OFFSET)+"px "+morpheus.CanvasUtil.getFontFamily(context)}else{context.textAlign="left";context.font=clip.height-morpheus.VectorTrackHeader.FONT_OFFSET+"px "+morpheus.CanvasUtil.getFontFamily(context)}context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.fillText(this.name,0,0)},draw:function(clip,context){var sortKeys=this.getSortKeys();var name=this.name;var existingSortKeyIndex=this.getSortKeyIndexForColumnName(sortKeys,name);var unlockableSortKeys=sortKeys.filter(function(key){return key.isUnlockable()});morpheus.CanvasUtil.resetTransform(context);context.clearRect(0,0,this.getUnscaledWidth(),this.getUnscaledHeight());if(this.getUnscaledHeight()<5){return}context.strokeStyle="#ddd";if(this.isColumns){context.beginPath();context.moveTo(0,this.getUnscaledHeight());context.lineTo(this.getUnscaledWidth(),this.getUnscaledHeight());context.stroke();context.textAlign="right"}else{context.beginPath();context.moveTo(this.getUnscaledWidth(),0);context.lineTo(this.getUnscaledWidth(),this.getUnscaledHeight());context.stroke();context.textAlign="left"}var textWidth=context.measureText(name).width;var isColumns=this.isColumns;var xpix=this.isColumns?this.getUnscaledWidth()-2:10;if(isColumns){if(existingSortKeyIndex!=null){xpix-=6;if(sortKeys[existingSortKeyIndex.index].getLockOrder()!==0){xpix-=10}}if(sortKeys.length>1){xpix-=6}}context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;var ypix=this.isColumns?this.getUnscaledHeight()/2:this.getUnscaledHeight()-(this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET)/2;context.textBaseline="middle";if(this.isMouseOver){var xdot=xpix-(isColumns?textWidth+4:4);var ydot=ypix-3;for(var i=0;i<2;i++){for(var j=0;j<3;j++){context.fillRect(xdot-i*3,ydot+j*3,1.5,1.5)}}}var fontHeight=Math.min(this.defaultFontHeight,this.getUnscaledHeight()-morpheus.VectorTrackHeader.FONT_OFFSET);fontHeight=Math.min(fontHeight,morpheus.VectorTrack.MAX_FONT_SIZE);context.font=this.font.weight+" "+fontHeight+"px "+morpheus.CanvasUtil.getFontFamily(context);context.fillText(name,xpix,ypix);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;if(existingSortKeyIndex!==null){context.beginPath();var x=this.isColumns?xpix+4:xpix+textWidth+6;var arrowHeight=Math.min(8,this.getUnscaledHeight()/2-1);var arrowWidth=3;if(sortKeys[existingSortKeyIndex.index].getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){context.translate(x,ypix-arrowHeight);context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight);context.lineTo(-arrowWidth,arrowHeight)}else if(sortKeys[existingSortKeyIndex.index].getSortOrder()===morpheus.SortKey.SortOrder.DESCENDING){context.translate(x,ypix);context.moveTo(0,arrowHeight);context.lineTo(arrowWidth,0);context.lineTo(-arrowWidth,0)}else{context.translate(x,ypix-arrowHeight/2);context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight/2);context.lineTo(0,arrowHeight);context.lineTo(-arrowWidth,arrowHeight/2)}context.fill();morpheus.CanvasUtil.resetTransform(context);context.textAlign="left";if(unlockableSortKeys.length>1){context.font="8px "+morpheus.CanvasUtil.getFontFamily(context);var sortIndex=""+existingSortKeyIndex.number;context.fillText(sortIndex,x+4,ypix-2);x+=context.measureText(sortIndex).width}if(sortKeys[existingSortKeyIndex.index].getLockOrder()!==0){context.font=fontHeight+"px FontAwesome";context.fillText("",x+arrowWidth+2,ypix)}}}};morpheus.Util.extend(morpheus.VectorTrackHeader,morpheus.AbstractCanvas);morpheus.VectorTrack=function(project,name,positions,isColumns,heatmap){morpheus.AbstractCanvas.call(this,true);this.preferredSize={width:0,height:0};this.project=project;this.positions=positions;this.isColumns=isColumns;this.name=name;this.visible=true;this.heatmap=heatmap;this.id=_.uniqueId();var _this=this;this.updateSpanMapFunction=function(){_this.spanMap=morpheus.VectorUtil.createSpanMap(_this.getVector())};this.lastPosition={start:-1,end:-1};this.events="rowSortOrderChanged rowFilterChanged datasetChanged";var mouseMoved=function(event){var index=-1;if(event.type!=="mouseout"){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,heatmap.scrollLeft(),heatmap.scrollTop());if(_this.settings.squished){var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);var squishFactor=total/(isColumns?_this.getUnscaledWidth():_this.getUnscaledHeight());position[isColumns?"x":"y"]*=squishFactor}index=!isColumns?_this.positions.getIndex(position.y,false):_this.positions.getIndex(position.x,false)}if(isColumns){heatmap.setMousePosition(-1,index,{name:_this.name,event:event})}else{heatmap.setMousePosition(index,-1,{name:_this.name,event:event})}};$(this.canvas).on("contextmenu.morpheus",function(e){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();heatmap.setSelectedTrack(_this.name,isColumns);_this.showPopup(e);return false});this.settings={maxTextWidth:undefined,squished:false,inlineTooltip:false,tooltip:true,highlightMatchingValues:false,colorBarSize:12,stackedBar:false,display:[],selectionColor:"rgb(182,213,253)",colorByField:null,fontField:null,barColor:"#bdbdbd",barSize:40,min:undefined,mid:undefined,max:undefined,autoscaleAlways:false,minMaxReversed:false};$(this.canvas).on("mousemove.morpheus mouseout.morpheus",mouseMoved)};morpheus.VectorTrack.RENDER={TEXT:"text",COLOR:"color",BAR:"bar",MOLECULE:"molecule",TEXT_AND_COLOR:"text_and_color",TEXT_AND_FONT:"text_and_font",SHAPE:"shape",ARC:"arc",BOX_PLOT:"box_plot",HEAT_MAP:"heat_map"};morpheus.VectorTrack.vectorToString=function(vector){var dataType=morpheus.VectorUtil.getDataType(vector);var formatter=vector.getProperties().get(morpheus.VectorKeys.FORMATTER);if(formatter!=null){if(typeof formatter==="object"){formatter=morpheus.Util.createNumberFormat(formatter.pattern);if(dataType==="[number]"){var nf=formatter;formatter=function(v){var s=[];if(v!=null){for(var i=0,arrayLength=v.length;i<arrayLength;i++){s.push(nf(v[i]))}}return s.join(", ")}}vector.getProperties().set(morpheus.VectorKeys.FORMATTER,formatter)}}else if(dataType==="number"){formatter=morpheus.Util.nf}else if(dataType==="[number]"){formatter=function(v){var s=[];if(v!=null){for(var i=0,arrayLength=v.length;i<arrayLength;i++){s.push(morpheus.Util.nf(v[i]))}}return s.join(", ")}}else if(dataType==="[string]"){formatter=function(v){var s=[];if(v!=null){for(var i=0,arrayLength=v.length;i<arrayLength;i++){s.push(v[i])}}return s.join(", ")}}else{formatter=function(v){return""+v}}return formatter};morpheus.VectorTrack.prototype={settingFromConfig:function(conf){var _this=this;var settings=this.settings;var fromString=function(s){settings.display=[];var tokens=s.split(",");for(var i=0,length=tokens.length;i<length;i++){var method=$.trim(tokens[i]);method=method.toUpperCase();var mapped=morpheus.VectorTrack.RENDER[method];if(mapped!==undefined){settings.display.push(mapped)}else if(method==="DISCRETE"){_this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE,true)}else if(method==="CONTINUOUS"){_this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,false)}else if(method==="HIGHLIGHT"){settings.highlightMatchingValues=true}else if(method==="STACKED_BAR"){settings.stackedBar=true;settings.display.push(morpheus.VectorTrack.RENDER.BAR)}else if(method==="TOOLTIP"){settings.inlineTooltip=true}else{console.log(method+" not found.")}}};var fromArray=function(array){settings.display=[];for(var i=0;i<array.length;i++){var method=array[i].toUpperCase();var mapped=morpheus.VectorTrack.RENDER[method];if(mapped!==undefined){settings.display.push(mapped)}else{console.log(method+" not found.")}}};var fromObject=function(obj){settings.display=[];for(var key in obj){if(obj[key]){var method=key.toUpperCase();var mapped=morpheus.VectorTrack.RENDER[method];if(mapped!==undefined){settings.display.push(mapped)}}}};if(conf!=null){if(_.isString(conf)){fromString(conf)}else if(_.isArray(conf)){fromArray(conf)}else{var userSuppliedSettings=conf;if(!_.isArray(conf.display)&&_.isObject(conf.display)){userSuppliedSettings=conf.display}settings=$.extend({},settings,userSuppliedSettings);settings.maxTextWidth=undefined;if(userSuppliedSettings.discrete!=null){_this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE,userSuppliedSettings.discrete)}if(_.isArray(userSuppliedSettings.display)){settings.display=userSuppliedSettings.display}else if(_.isString(userSuppliedSettings.display)){fromString(userSuppliedSettings.display)}if(!_.isArray(settings.render)&&_.isObject(settings.render)){fromObject(settings.render);delete settings.render}}this.settings=settings}if(!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT))){settings.display.push(morpheus.VectorTrack.RENDER.TEXT)}this._update()},setShowTooltip:function(value){this.settings.tooltip=value},isShowTooltip:function(){return this.settings.tooltip},isRenderAs:function(value){return this.settings.display.indexOf(value)!==-1},dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);$(this.canvas).off();this._selection.dispose();this.project.off(this.events,this.updateSpanMapFunction)},getName:function(){return this.name},getVector:function(name){name=name==null?this.name:name;var vector=this.isColumns?this.project.getSortedFilteredDataset().getColumnMetadata().getByName(name):this.project.getSortedFilteredDataset().getRowMetadata().getByName(name);return!vector?new morpheus.Vector(name,0):vector},getFullVector:function(){var vector=this.isColumns?this.project.getFullDataset().getColumnMetadata().getByName(this.name):this.project.getFullDataset().getRowMetadata().getByName(this.name);return!vector?new morpheus.Vector(this.name,0):vector},_updatePreferredSize:function(){var size=this._computePreferredSize();this.preferredSize.width=size.width;this.preferredSize.height=size.height},_computePreferredSize:function(forPrint){var width=0;var height=0;if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)){if(this.positions.getSize()>=6){var context=this.canvas.getContext("2d");var textWidth=morpheus.CanvasUtil.getVectorStringWidth(context,this.getVector(),this.positions,forPrint?-1:this.isColumns?120:100);if(!forPrint){this.settings.maxTextWidth=textWidth}width+=textWidth}else if(!forPrint){this.settings.maxTextWidth=0}}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)){width+=this.settings.barSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){width+=this.settings.colorBarSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){width+=this.settings.colorBarSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){width+=300}if(this.isRenderAs(morpheus.VectorTrack.RENDER.ARC)){width+=this.settings.arcSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){width+=100}if(this.isRenderAs(morpheus.VectorTrack.RENDER.HEAT_MAP)){width+=100}var nkeys=this.settings.display.length;if(nkeys>0){width+=(nkeys-1)*2}width=Math.max(0,width);return this.isColumns?{width:height,height:width}:{width:width,height:height}},getPreferredSize:function(){return this.preferredSize},getPrintSize:function(){return this._computePreferredSize(true)},_createDiscreteValueMap:function(){var values=morpheus.VectorUtil.getValues(this.getFullVector());values.sort(morpheus.SortKey.ASCENDING_COMPARATOR);this.discreteValueMap=new morpheus.Map;for(var i=0,length=values.length;i<length;i++){this.discreteValueMap.set(values[i],i+1)}this.settings.min=0;this.settings.mid=0;this.settings.max=values.length},_setChartMinMax:function(){if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){if(!this.settings.stackedBar&&this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)&&!this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){if(!this.discreteValueMap){this._createDiscreteValueMap()}}else{if(this.settings.autoscaleAlways||this.settings.min==null||this.settings.max==null||this.settings.mid==null){var vector=this.getFullVector();var minMax=morpheus.VectorUtil.getMinMax(vector);var min=minMax.min;var max=minMax.max;if(this.settings.minMaxReversed){var tmp=max;max=min;min=tmp}if(this.settings.autoscaleAlways||this.settings.min==null){this.settings.min=Math.min(0,min)}if(this.settings.autoscaleAlways||this.settings.max==null){this.settings.max=Math.max(0,max)}if(this.settings.autoscaleAlways||this.settings.mid==null){this.settings.mid=this.settings.min<0?0:this.settings.min}}}}},_update:function(){if(this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)==null&&(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR))){if((this.isColumns?this.project.getColumnColorModel():this.project.getRowColorModel()).getContinuousColorScheme(this.getFullVector())!=null){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,false);this.settings.highlightMatchingValues=false}else if((this.isColumns?this.project.getColumnColorModel():this.project.getRowColorModel()).getDiscreteColorScheme(this.getFullVector())!=null){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,true);this.settings.highlightMatchingValues=true}else if(this.getFullVector().getProperties().has(morpheus.VectorKeys.FIELDS)||morpheus.VectorUtil.getDataType(this.getFullVector())==="number"||morpheus.VectorUtil.getDataType(this.getFullVector())==="[number]"){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,false);this.settings.highlightMatchingValues=false}}if(this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)==null){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,true)}if(this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){this.project.off(this.events,this.updateSpanMapFunction)}this._setChartMinMax();if(this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){this.project.on(this.events,this.updateSpanMapFunction);if(!this.moleculeCache){this.moleculeCache={};var _this=this;var valueToModelIndices=this.getFullVector().getProperties().get(morpheus.VectorKeys.VALUE_TO_INDICES);if(!valueToModelIndices){var fullVector=this.getFullVector();valueToModelIndices=morpheus.VectorUtil.createValueToIndicesMap(fullVector);fullVector.getProperties().set(morpheus.VectorKeys.VALUE_TO_INDICES,valueToModelIndices)}if(_this.heatmap.options.structureUrlProvider!==undefined){valueToModelIndices.forEach(function(indices,value){var url=_this.heatmap.options.structureUrlProvider(value);var image=new Image;image.src=url;_this.moleculeCache[value]=image});setTimeout(function(){_this.setInvalid(true);_this.repaint()},2e3)}else{var values=valueToModelIndices.keys();var doRequest=function(smile){$.ajax({contentType:"text/plain",context:{smile:smile},data:{string:smile,representation:"sdf"},url:"http://cactus.nci.nih.gov/chemical/structure"}).done(function(text){_this.moleculeCache[this.smile]=text;if(values.length>0){doRequest(values.pop())}_this.invalid=true;_this.repaint()})};for(var i=0;i<6;i++){doRequest(values.pop())}}this.updateSpanMapFunction()}}this._updatePreferredSize()},postPaint:function(clip,context){context.lineWidth=1;context.strokeStyle="Grey";var project=this.project;var setup=this._setup(context,clip);var vector=setup.vector;var start=setup.start;var end=setup.end;if(this.isColumns){if(project.getHoverColumnIndex()!==-1){this.drawColumnBorder(context,this.positions,project.getHoverColumnIndex(),this.getUnscaledHeight())}}else{if(project.getHoverRowIndex()!==-1){this.drawRowBorder(context,this.positions,project.getHoverRowIndex(),this.getUnscaledWidth())}}this._highlightMatchingValues(context,vector,start,end)},_highlightMatchingValues:function(context,viewVector,start,end){var project=this.project;var positions=this.positions;context.strokeStyle="black";context.lineWidth=3;var hoverIndex=this.isColumns?project.getHoverColumnIndex():project.getHoverRowIndex();var value=viewVector.getValue(hoverIndex);if(this.settings.highlightMatchingValues&&hoverIndex!==-1&&this.heatmap.mousePositionOptions&&this.heatmap.mousePositionOptions.name===viewVector.getName()){var valueToModelIndices=this.getFullVector().getProperties().get(morpheus.VectorKeys.VALUE_TO_INDICES);if(!valueToModelIndices){var fullVector=this.getFullVector();valueToModelIndices=morpheus.VectorUtil.createValueToIndicesMap(fullVector);fullVector.getProperties().set(morpheus.VectorKeys.VALUE_TO_INDICES,valueToModelIndices)}var indices=valueToModelIndices.get(value);if(indices==null){console.log("valueToModelIndices error");return}if(indices.length<=1){return}if(this.isColumns){if(project.getHoverColumnIndex()!==-1){var height=this.getUnscaledHeight();context.beginPath();for(var i=0,nindices=indices.length;i<nindices;i++){var viewIndex=project.convertModelColumnIndexToView(indices[i]);if(viewIndex>=start&&viewIndex<end){var size=positions.getItemSize(viewIndex);var pix=positions.getPosition(viewIndex);context.rect(pix,0,size,height)}}context.stroke()}}else{context.beginPath();var width=this.getUnscaledWidth();var indices=valueToModelIndices.get(value);for(var i=0,nindices=indices.length;i<nindices;i++){var viewIndex=project.convertModelRowIndexToView(indices[i]);if(viewIndex>=start&&viewIndex<end){var size=positions.getItemSize(viewIndex);var pix=positions.getPosition(viewIndex);context.rect(0,pix,width,size)}}context.stroke()}}},drawSelection:function(options){var project=this.project;var positions=this.positions;var context=options.context;var start=options.start;var end=options.end;context.lineWidth=1;context.fillStyle=this.settings.selectionColor;if(this.isColumns){var height=this.getUnscaledHeight();var viewIndices=project.getColumnSelectionModel().getViewIndices();viewIndices.forEach(function(i){if(i>=start&&i<=end){var size=positions.getItemSize(i);var pix=positions.getPosition(i);context.fillRect(pix,0,size,height)}})}else{var width=this.getUnscaledWidth();if(!this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){var viewIndices=project.getRowSelectionModel().getViewIndices();viewIndices.forEach(function(i){if(i>=start&&i<=end){var size=positions.getItemSize(i);var pix=positions.getPosition(i);context.fillRect(0,pix,width,size)}})}}},prePaint:function(clip,context){var project=this.project;var positions=this.positions;var setup=this._setup(context,clip);var start=setup.start;var end=setup.end;this.drawSelection({context:context,start:start,end:end});if(this.invalid||start!==this.lastPosition.start||end!==this.lastPosition.end){this.lastPosition.start=start;this.lastPosition.end=end;this.invalid=true}},drawRowBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(0,pix+size);context.lineTo(gridSize,pix+size);context.stroke();context.beginPath();context.moveTo(0,pix);context.lineTo(gridSize,pix);context.stroke()},drawColumnBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(pix+size,0);context.lineTo(pix+size,gridSize);context.stroke();context.beginPath();context.moveTo(pix,0);context.lineTo(pix,gridSize);context.stroke()},isSquished:function(){return this.settings.squished},_setup:function(context,clip){var start=0;var vector=this.getVector();var end=vector.size();var settings=this.settings;var positions=this.positions;var width=clip.width;var height=clip.height;if(!settings.squished){if(this.isColumns){start=morpheus.Positions.getLeft(clip,positions);end=morpheus.Positions.getRight(clip,positions)}else{start=morpheus.Positions.getTop(clip,positions);end=morpheus.Positions.getBottom(clip,positions)}}if(settings.squished){var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);if(!this.isColumns){var squishFactor=height/total;context.scale(1,squishFactor)}else{var squishFactor=width/total;context.scale(squishFactor,1)}}else{context.translate(-clip.x,-clip.y)}return{start:start,end:end,vector:vector}},draw:function(clip,context){var setup=this._setup(context,clip);this._draw({start:setup.start,end:setup.end,vector:setup.vector,context:context,availableSpace:this.isColumns?this.getUnscaledHeight():this.getUnscaledWidth(),clip:clip})},print:function(clip,context){var vector=this.getVector();this._draw({start:0,end:vector.size(),vector:vector,context:context,availableSpace:this.isColumns?clip.height:clip.width,clip:clip})},_draw:function(options){var _this=this;var context=options.context;var vector=options.vector;var availableSpace=options.availableSpace;var fullAvailableSpace=options.availableSpace;var start=options.start;var end=options.end;var clip=options.clip;var positions=this.positions;if(this.settings.autoscaleAlways){this._setChartMinMax()}context.textAlign="left";context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;var fontSize=Math.min(morpheus.VectorTrack.MAX_FONT_SIZE,positions.getSize()-2);var size=0;context.font=fontSize+"px "+morpheus.CanvasUtil.getFontFamily(context);context.strokeStyle=morpheus.HeatMapElementCanvas.GRID_COLOR;context.lineWidth=.1;if(this.heatmap.heatmap.isDrawGrid()&&!this.settings.squished){if(this.isColumns){var gridSize=availableSpace;context.beginPath();for(var i=start;i<end;i++){var size=positions.getItemSize(i);var pix=positions.getPosition(i);if(size>7){context.moveTo(pix+size,0);context.lineTo(pix+size,gridSize)}}context.stroke()}else{if(!this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){var gridSize=availableSpace;context.beginPath();for(var i=start;i<end;i++){var size=positions.getItemSize(i);var pix=positions.getPosition(i);if(size>7){context.moveTo(0,pix+size);context.lineTo(gridSize,pix+size)}}context.stroke()}}}context.lineWidth=1;var offset=1;if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){this.renderColor(context,vector,start,end,clip,this.isColumns?availableSpace:0,!this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE));offset+=this.settings.colorBarSize+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){this.renderShape(context,vector,start,end,clip,this.isColumns?availableSpace-offset:offset);offset+=this.settings.colorBarSize+2;availableSpace-=offset}if(this.isRenderAs(morpheus.VectorTrack.RENDER.ARC)){this.renderArc(context,vector,start,end,clip,this.settings.arcSize);offset+=this.settings.arcSize+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){this.renderMolecule(context,vector,start,end,clip,offset,availableSpace)}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){var barSize=!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)?availableSpace-2:this.settings.barSize;offset++;this.renderBoxPlot(context,vector,start,end,clip,offset,barSize);offset+=barSize+2;availableSpace-=offset}if(this.isRenderAs(morpheus.VectorTrack.RENDER.HEAT_MAP)){var barSize=!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)?availableSpace-2:this.settings.barSize;offset++;this.renderHeatMap(context,vector,start,end,clip,barSize);offset+=barSize+2;availableSpace-=offset}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)){var barSize=!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)?availableSpace-1:this.settings.barSize;if(this.settings.stackedBar){this.renderStackedBar(context,vector,start,end,clip,offset,barSize)}else{var fields=vector.getProperties().get(morpheus.VectorKeys.FIELDS);var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);if(fields!=null&&visibleFieldIndices==null){visibleFieldIndices=morpheus.Util.seq(fields.length)}if(fields!=null){this.renderUnstackedBar(context,vector,start,end,clip,offset,barSize,visibleFieldIndices)}else{this.renderBar(context,vector,start,end,clip,this.isColumns?fullAvailableSpace-offset-barSize:offset,barSize)}}offset+=barSize+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT))){context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;this.renderText(context,vector,this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR),this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT),start,end,clip,this.isColumns?fullAvailableSpace-offset:offset);offset+=this.settings.maxTextWidth+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)&&!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;var dataType=morpheus.VectorUtil.getDataType(vector);if(dataType==="url"){context.fillStyle="blue";this.canvas.style.cursor="pointer"}this.renderText(context,vector,false,false,start,end,clip,this.isColumns?fullAvailableSpace-offset:offset)}},showPopup:function(e,isHeader){var _this=this;var project=this.project;var isColumns=this.isColumns;var hasSelection=isColumns?project.getColumnSelectionModel().count()>0:project.getRowSelectionModel().count()>0;var ANNOTATE_SELECTION="Annotate Selection";var INVERT_SELECTION="Invert Selection";var SELECT_ALL="Select All";var SHOW_SELECTION_ONLY="Show Selection Only";var CLEAR_SELECTION="Clear Selection";var HIGHLIGHT_MATCHING_VALUES="Highlight Matching Values";var FIELDS="Choose Fields...";var DELETE="Delete...";var TOOLTIP="Show In Tooltip";var HIDE="Hide";var HIDE_OTHERS="Hide Others";var REMOVE_SHOW_SELECTION_ONLY="Show All";var SORT_ASC="Sort Ascending";var SORT_DESC="Sort Descending";var MOVE_TO_TOP="Move To Top";var SORT_SEL_ASC="Sort Heat Map Ascending ↑";var SORT_SEL_DESC="Sort Heat Map Descending ↓";var SORT_SEL_TOP_N="Sort Heat Map Descending/Ascending";var DISPLAY_BAR="Show Bar Chart";var NUMBER_FORMAT="Format";var DISPLAY_STACKED_BAR="Show Stacked Bar Chart";var DISPLAY_BOX_PLOT="Show Box Plot";var DISPLAY_COLOR="Show Color";var COLOR_BAR_SIZE="Color Bar Size...";var DISPLAY_TEXT="Show Text";var DISPLAY_SHAPE="Show Shape";var DISPLAY_ARC="Show Arc";var DISPLAY_TEXT_AND_COLOR="Encode Text Using Color";var DISPLAY_TEXT_AND_FONT="Encode Text Using Font";var DISPLAY_STRUCTURE="Show Chemical Structure";var DISPLAY_CONTINUOUS="Continuous";var positions=this.positions;var heatmap=this.heatmap;var sectionToItems={Sort:[],Selection:[],Display:[]};var customItems=this.heatmap.getPopupItems();if(customItems&&customItems.length>0){customItems.forEach(function(item){if(item.columns===isColumns){sectionToItems[item.section].push(item)}})}if(sectionToItems.Selection.length>0){sectionToItems.Selection.push({separator:true})}sectionToItems.Selection.push({name:MOVE_TO_TOP});if(this.heatmap.options.menu.Edit&&this.heatmap.options.menu.Edit.indexOf("Annotate"+" Selected Rows")!==-1){sectionToItems.Selection.push({name:ANNOTATE_SELECTION})}sectionToItems.Selection.push({name:"Copy",class:"copy"});sectionToItems.Selection.push({name:INVERT_SELECTION});sectionToItems.Selection.push({name:SELECT_ALL});sectionToItems.Selection.push({name:CLEAR_SELECTION});var combinedFilter=isColumns?project.getColumnFilter():project.getRowFilter();var showSelectionOnlyIndex=combinedFilter.indexOf(SHOW_SELECTION_ONLY);if(showSelectionOnlyIndex!==-1){sectionToItems.Selection.push({name:REMOVE_SHOW_SELECTION_ONLY})}if(!isHeader){sectionToItems["Sort"].push({name:SORT_SEL_ASC,disabled:!hasSelection});sectionToItems["Sort"].push({name:SORT_SEL_DESC,disabled:!hasSelection});sectionToItems["Sort"].push({name:SORT_SEL_TOP_N,disabled:!hasSelection})}var dataType=morpheus.VectorUtil.getDataType(this.getFullVector());var arrayFields=this.getFullVector().getProperties().get(morpheus.VectorKeys.FIELDS);var isArray=arrayFields!==undefined;var isNumber=dataType==="number"||dataType==="[number]";if(isNumber||isArray){sectionToItems.Display.push({name:NUMBER_FORMAT});sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:DISPLAY_BAR,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)})}if(isArray){sectionToItems.Display.push({name:DISPLAY_STACKED_BAR,checked:this.settings.stackedBar});sectionToItems.Display.push({name:DISPLAY_BOX_PLOT,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)});sectionToItems.Display.push({name:FIELDS})}if(dataType!=="url"){sectionToItems.Display.push({name:DISPLAY_TEXT,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)});if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)){sectionToItems.Display.push({name:DISPLAY_TEXT_AND_COLOR,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)});sectionToItems.Display.push({name:DISPLAY_TEXT_AND_FONT,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)})}sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:DISPLAY_COLOR,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)});if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){sectionToItems.Display.push({name:COLOR_BAR_SIZE})}}if(!isArray&&dataType!=="url"){sectionToItems.Display.push({name:DISPLAY_SHAPE,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)})}if(!isArray&&!isNumber&&!this.isColumns&&name.toLowerCase().indexOf("smile")!==-1){sectionToItems.Display.push({name:DISPLAY_STRUCTURE,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)})}sectionToItems.Display.push({name:TOOLTIP,checked:this.settings.inlineTooltip});if(!isArray&&dataType!=="url"){sectionToItems.Display.push({name:HIGHLIGHT_MATCHING_VALUES,checked:this.settings.highlightMatchingValues})}if(dataType!=="url"){}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){sectionToItems.Display.push({separator:true});if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)){sectionToItems.Display.push({name:"Edit Bar Color..."})}sectionToItems.Display.push({name:"Auto Range"});sectionToItems.Display.push({name:"Custom Range..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)||this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){sectionToItems.Display.push({separator:true});if(isNumber){sectionToItems.Display.push({name:DISPLAY_CONTINUOUS,checked:!this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)&&isArray){sectionToItems.Display.push({name:"Edit Colors..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){sectionToItems.Display.push({name:"Edit Shapes..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){sectionToItems.Display.push({name:"Edit Fonts..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)&&isArray){sectionToItems.Display.push({name:"Color Key",icon:"fa fa-key"})}}if(this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){sectionToItems.Display.push({name:"Shape Key",icon:"fa fa-key"})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){sectionToItems.Display.push({name:"Font Key",icon:"fa fa-key"})}sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:HIDE});sectionToItems.Display.push({name:HIDE_OTHERS,disabled:heatmap.getVisibleTrackNames(this.isColumns).length<=1});sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:DELETE});var items=[];function addSection(name){if(items.length>0){items.push({separator:true})}items=items.concat(sectionToItems[name])}addSection("Sort");_.each(sectionToItems.Selection,function(item){if(item.name!==REMOVE_SHOW_SELECTION_ONLY&&item.name!==SELECT_ALL){item.disabled=!hasSelection}});if(!isHeader){addSection("Selection")}else if(this.heatmap.options.toolbar.options){addSection("Display")}if(e.preventDefault){e.preventDefault()}if(items.length===0){return}morpheus.Popup.showPopup(items,{x:e.pageX,y:e.pageY},e.target,function(event,item){var customItem;if(item===NUMBER_FORMAT){var vector=_this.getFullVector();var formatter=vector.getProperties().get(morpheus.VectorKeys.FORMATTER);if(formatter!=null){if(typeof formatter==="object"){formatter=morpheus.Util.createNumberFormat(formatter.pattern);vector.getProperties().set(morpheus.VectorKeys.FORMATTER,formatter)}}var pattern=formatter!=null?formatter.toJSON().pattern:".2f";var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"number_of_fraction_digits",type:"number",value:morpheus.Util.getNumberFormatPatternFractionDigits(pattern),required:true,style:"max-width:60px;"});formBuilder.find("number_of_fraction_digits").on("keyup input",_.debounce(function(){var n=parseInt($(this).val());if(n>=0){vector.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"."+n+"f"});_this.setInvalid(true);_this.repaint()}},100));morpheus.FormBuilder.showInModal({title:"Format",close:"Close",html:formBuilder.$form,focus:heatmap.getFocusEl()})}else if(item==="Copy"){heatmap.getActionManager().execute(isColumns?"Copy Selected Columns":"Copy"+" Selected Rows")}else if(item===FIELDS){var visibleFieldIndices=_this.getFullVector().getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);var visibleFields;if(visibleFieldIndices==null){visibleFields=arrayFields.slice(0)}else{visibleFields=[];for(var i=0;i<visibleFieldIndices.length;i++){visibleFields.push(arrayFields[visibleFieldIndices[i]])}}var availableFields=[];for(var i=0;i<arrayFields.length;i++){if(visibleFields.indexOf(arrayFields[i])===-1){availableFields.push(arrayFields[i])}}var leftOptions=[];var rightOptions=[];for(var i=0;i<availableFields.length;i++){leftOptions.push(new Option(availableFields[i],availableFields[i]))}for(var i=0;i<visibleFields.length;i++){rightOptions.push(new Option(visibleFields[i],visibleFields[i]))}var list=new morpheus.DualList(leftOptions,rightOptions);morpheus.FormBuilder.showOkCancel({title:"Fields",okCallback:function(){var visibleFields=list.getOptions(false);var visibleFieldIndices=[];for(var i=0;i<visibleFields.length;i++){visibleFieldIndices.push(arrayFields.indexOf(visibleFields[i]))}var fullVector=_this.getFullVector();fullVector.getProperties().set(morpheus.VectorKeys.VISIBLE_FIELDS,visibleFieldIndices);var summaryFunction=fullVector.getProperties().get(morpheus.VectorKeys.ARRAY_SUMMARY_FUNCTION);if(summaryFunction){summaryFunction.indices=visibleFieldIndices}var updatedVector=_this.isColumns?_this.project.getFullDataset().getColumnMetadata().add(_this.name):_this.project.getFullDataset().getRowMetadata().add(_this.name);for(var i=0;i<updatedVector.size();i++){var array=fullVector.getValue(i);if(array!=null){array.summary=undefined}}_this.setInvalid(true);_this.repaint()},content:list.$el})}else if(item==="Edit Bar Color..."){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"bar_color",type:"color",value:_this.settings.barColor,required:true,style:"max-width:50px;"});formBuilder.find("bar_color").on("change",function(){_this.settings.barColor=$(this).val();_this.setInvalid(true);_this.repaint()});morpheus.FormBuilder.showInModal({title:"Bar Color",close:"Close",html:formBuilder.$form,focus:heatmap.getFocusEl()})}else if(item===COLOR_BAR_SIZE){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"size",type:"text",value:_this.settings.colorBarSize,required:true,style:"max-width:50px;"});formBuilder.find("size").on("change",function(){var val=parseFloat($(this).val());if(val>0){_this.settings.colorBarSize=val;_this.setInvalid(true);_this.repaint()}});morpheus.FormBuilder.showInModal({title:"Color Bar Size",close:"Close",html:formBuilder.$form,focus:heatmap.getFocusEl()})}else if(item===ANNOTATE_SELECTION){heatmap.getActionManager().execute(isColumns?"Annotate Selected Columns":"Annotate"+" Selected Rows")}else if(item===DELETE){morpheus.FormBuilder.showOkCancel({title:"Delete",content:"Are you sure you want to delete "+_this.name+"?",okCallback:function(){var metadata=isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata();metadata.remove(morpheus.MetadataUtil.indexOf(metadata,_this.name));var sortKeys=isColumns?project.getColumnSortKeys():project.getRowSortKeys();var sortKeyIndex=_.indexOf(sortKeys.map(function(key){return key.field}),_this.name);if(sortKeyIndex!==-1){sortKeys.splice(sortKeyIndex,1);if(isColumns){project.setColumnSortKeys(sortKeys,true)}else{project.setRowSortKeys(sortKeys,true)}}var groupByKeys=isColumns?project.getGroupColumns():project.getGroupRows();var groupByKeyIndex=_.indexOf(groupByKeys.map(function(key){return key.field}),_this.name);if(groupByKeyIndex!==-1){groupByKeys.splice(groupByKeyIndex,1);if(isColumns){project.setGroupColumns(groupByKeys,true)}else{project.setGroupRows(groupByKeys,true)}}if(!isColumns){project.trigger("rowTrackRemoved",{vector:_this.getFullVector()})}else{project.trigger("columnTrackRemoved",{vector:_this.getFullVector()})}}})}else if(item===CLEAR_SELECTION){heatmap.getActionManager().execute(isColumns?"Clear Selected Columns":"Clear"+" Selected Rows")}else if(item===INVERT_SELECTION){heatmap.getActionManager().execute(isColumns?"Invert Selected Columns":"Invert"+" Selected Rows")}else if(item===MOVE_TO_TOP){heatmap.getActionManager().execute(isColumns?"Move Selected Columns To Top":"Move"+" Selected Rows To Top")}else if(item===SORT_ASC||item===SORT_DESC){var sortKey=new morpheus.SortKey(_this.name,item===SORT_ASC?morpheus.SortKey.SortOrder.ASCENDING:morpheus.SortKey.SortOrder.DESCENDING);if(_this.isColumns){_this.project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getColumnSortKeys()),true)}else{_this.project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getRowSortKeys()),true)}}else if(item==SORT_SEL_ASC||item==SORT_SEL_DESC||item===SORT_SEL_TOP_N){var sortOrder;if(item===SORT_SEL_ASC){sortOrder=morpheus.SortKey.SortOrder.ASCENDING}else if(item===SORT_SEL_DESC){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}else{sortOrder=morpheus.SortKey.SortOrder.TOP_N}heatmap.sortBasedOnSelection(sortOrder,isColumns,e&&e.shiftKey)}else if(item===SELECT_ALL){heatmap.getActionManager().execute(isColumns?"Select All Columns":"Select All Rows")}else if(item==="Auto Range"){delete _this.settings.min;delete _this.settings.max;delete _this.settings.mid;_this._update();heatmap.revalidate()}else if(item==="Custom Range..."){var formBuilder=new morpheus.FormBuilder;var items=[{name:"min",required:true,type:"number",value:_this.settings.min},{name:"mid",required:true,type:"number",value:_this.settings.mid},{name:"max",required:true,type:"number",value:_this.settings.max}];_.each(items,function(item){formBuilder.append(item)});morpheus.FormBuilder.showOkCancel({title:"Range",content:formBuilder.$form,okCallback:function(){_this.settings.min=parseFloat(formBuilder.getValue("min"));_this.settings.mid=parseFloat(formBuilder.getValue("mid"));_this.settings.max=parseFloat(formBuilder.getValue("max"));_this._update();heatmap.revalidate()}})}else if(item==="Squished"){_this.settings.squished=!_this.settings.squished;heatmap.revalidate()}else if(item==="Color Key"){var legend=new morpheus.HeatMapTrackColorLegend([_this],isColumns?_this.project.getColumnColorModel():_this.project.getRowColorModel());var size=legend.getPreferredSize();legend.setBounds(size);legend.repaint();morpheus.FormBuilder.showInModal({title:"Color Key",html:legend.canvas,focus:heatmap.getFocusEl()})}else if(item==="Shape Key"){var legend=new morpheus.HeatMapTrackShapeLegend([_this],isColumns?_this.project.getColumnShapeModel():_this.project.getRowShapeModel());var size=legend.getPreferredSize();legend.setBounds(size);legend.repaint();morpheus.FormBuilder.showInModal({title:"Shape Key",html:legend.canvas,focus:heatmap.getFocusEl()})}else if(item==="Font Key"){var legend=new morpheus.HeatMapTrackFontLegend([_this],isColumns?_this.project.getColumnFontModel():_this.project.getRowFontModel());var size=legend.getPreferredSize();legend.setBounds(size);legend.repaint();morpheus.FormBuilder.showInModal({title:"Font Key",html:legend.canvas,focus:heatmap.getFocusEl()})}else if(item==="Edit Fonts..."){heatmap.getActionManager().execute("Edit Fonts")}else if(item==="Edit Shapes..."){var shapeFormBuilder=new morpheus.FormBuilder;var shapeModel=isColumns?_this.project.getColumnShapeModel():_this.project.getRowShapeModel();var chooser=new morpheus.ShapeChooser({map:shapeModel.getMap(_this.name)});chooser.on("change",function(event){shapeModel.setMappedValue(_this.getFullVector(),event.value,event.shape);_this.setInvalid(true);_this.repaint()});morpheus.FormBuilder.showInModal({title:"Edit Shapes",html:chooser.$div,close:"Close",focus:heatmap.getFocusEl()})}else if(item==="Edit Colors..."){var colorModel=isColumns?_this.project.getColumnColorModel():_this.project.getRowColorModel();var colorSchemeChooser=new morpheus.ColorSchemeChooser({track:_this,heatMap:_this.heatmap,colorModel:colorModel});morpheus.FormBuilder.showInModal({title:"Edit Colors",html:colorSchemeChooser.$div,close:"Close",focus:heatmap.getFocusEl()})}else if(item===TOOLTIP){_this.settings.inlineTooltip=!_this.settings.inlineTooltip}else if(item===HIGHLIGHT_MATCHING_VALUES){_this.settings.highlightMatchingValues=!_this.settings.highlightMatchingValues}else if(customItem=_.find(customItems,function(customItem){return customItem.name===item&&customItem.columns===isColumns})){if(customItem.task){var task={tabId:_this.heatmap.getTabManager().getActiveTabId()};_this.heatmap.getTabManager().addTask(task);setTimeout(function(){customItem.callback(heatmap);_this.heatmap.getTabManager().removeTask(task)},1)}else{customItem.callback(heatmap)}}else if(item===DISPLAY_CONTINUOUS){var discrete=_this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)||false;_this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,!discrete);_this._setChartMinMax();_this.setInvalid(true);_this.repaint()}else if(item===HIDE){heatmap.setTrackVisible(_this.name,false,_this.isColumns);heatmap.revalidate()}else if(item===HIDE_OTHERS){var names=heatmap.getVisibleTrackNames(_this.isColumns);for(var i=0;i<names.length;i++){if(names[i]!==_this.name){heatmap.setTrackVisible(names[i],false,_this.isColumns)}}heatmap.revalidate()}else if(item===DISPLAY_STACKED_BAR){_this.settings.stackedBar=!_this.settings.stackedBar;_this._update();heatmap.revalidate()}else{if(item===DISPLAY_BAR){item=morpheus.VectorTrack.RENDER.BAR}else if(item===DISPLAY_COLOR){item=morpheus.VectorTrack.RENDER.COLOR}else if(item===DISPLAY_TEXT){item=morpheus.VectorTrack.RENDER.TEXT}else if(item===DISPLAY_TEXT_AND_COLOR){item=morpheus.VectorTrack.RENDER.TEXT_AND_COLOR}else if(item===DISPLAY_TEXT_AND_FONT){item=morpheus.VectorTrack.RENDER.TEXT_AND_FONT}else if(item===DISPLAY_STRUCTURE){item=morpheus.VectorTrack.RENDER.MOLECULE}else if(item===DISPLAY_SHAPE){item=morpheus.VectorTrack.RENDER.SHAPE}else if(item===DISPLAY_ARC){item=morpheus.VectorTrack.RENDER.ARC}else if(item===DISPLAY_BOX_PLOT){item=morpheus.VectorTrack.RENDER.BOX_PLOT}else{console.log("Unknown item "+item)}var show=!_this.isRenderAs(item);var remove;if(!show){_this.settings.display.splice(_this.settings.display.indexOf(item),1);if(item===morpheus.VectorTrack.RENDER.TEXT){remove=[morpheus.VectorTrack.RENDER.TEXT_AND_FONT,morpheus.VectorTrack.RENDER.TEXT_AND_COLOR]}}else{if(item===morpheus.VectorTrack.RENDER.COLOR){remove=[morpheus.VectorTrack.RENDER.TEXT_AND_COLOR]}else if(item===morpheus.VectorTrack.RENDER.TEXT_AND_COLOR){remove=[morpheus.VectorTrack.RENDER.COLOR]}_this.settings.display.push(item)}if(remove){remove.forEach(function(key){var index=_this.settings.display.indexOf(key);if(index!==-1){_this.settings.display.splice(index,1)}})}_this._update();heatmap.revalidate();if(show&&item===morpheus.VectorTrack.RENDER.TEXT_AND_FONT){heatmap.getActionManager().execute("Edit Fonts")}}})},renderColor:function(context,vector,start,end,clip,offset,continuous){var isColumns=this.isColumns;var positions=this.positions;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();var settings=this.settings;var canvasSize=isColumns?this.getUnscaledHeight():this.getUnscaledWidth();var colorBarSize=settings.colorBarSize;if(colorBarSize>canvasSize){colorBarSize=canvasSize>=5?canvasSize-1:canvasSize}var getColor;if(!continuous){getColor=_.bind(colorModel.getMappedValue,colorModel)}else{getColor=_.bind(colorModel.getContinuousMappedValue,colorModel)}if(vector.getProperties().get(morpheus.VectorKeys.FIELDS)!=null){var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);if(visibleFieldIndices==null){visibleFieldIndices=morpheus.Util.seq(vector.getProperties().get(morpheus.VectorKeys.FIELDS).length)}colorBarSize/=visibleFieldIndices.length;var nvisibleFieldIndices=visibleFieldIndices.length;for(var i=start;i<end;i++){var array=vector.getValue(i);var position=positions.getPosition(i);var size=positions.getItemSize(i);var _offset=offset;if(array!=null){for(var j=0;j<nvisibleFieldIndices;j++){var value=array[visibleFieldIndices[j]];var color=getColor(vector,value);context.fillStyle=color;if(isColumns){context.beginPath();context.rect(position,_offset-colorBarSize,size,colorBarSize);context.fill()}else{context.beginPath();context.rect(_offset,position,colorBarSize,size);context.fill()}_offset+=colorBarSize}}}}else{for(var i=start;i<end;i++){var value=vector.getValue(i);var position=positions.getPosition(i);var size=positions.getItemSize(i);var color=getColor(vector,value);context.fillStyle=color;if(isColumns){context.beginPath();context.rect(position,offset-colorBarSize,size,settings.colorBarSize);context.fill()}else{context.beginPath();context.rect(offset,position,colorBarSize,size);context.fill()}}}},renderShape:function(context,vector,start,end,clip,offset){var isColumns=this.isColumns;var positions=this.positions;var shapeModel=isColumns?this.project.getColumnShapeModel():this.project.getRowShapeModel();var settings=this.settings;var canvasSize=isColumns?this.getUnscaledHeight():this.getUnscaledWidth();var colorBarSize=settings.colorBarSize;if(colorBarSize>canvasSize){colorBarSize=canvasSize>=5?canvasSize-1:canvasSize}context.fillStyle="black";context.strokeStyle="black";var lineWidth=context.lineWidth;context.lineWidth=1;for(var i=start;i<end;i++){var value=vector.getValue(i);var position=positions.getPosition(i);var itemSize=positions.getItemSize(i);var minSize=Math.min(colorBarSize,itemSize);var size2=minSize/2;var shape=shapeModel.getMappedValue(vector,value);var x=isColumns?position+itemSize/2:offset+size2;var y=isColumns?offset-size2:position+itemSize/2;size2-=.5;morpheus.CanvasUtil.drawShape(context,shape,x,y,size2)}context.lineWidth=lineWidth},renderHeatMap:function(context,vector,start,end,clip,size){var isColumns=this.isColumns;var positions=this.positions;var project=this.project;context.save();context.lineWidth=1;var width=clip.width;var height=clip.height;var colorScheme=this.heatmap.getHeatMapElementComponent().getColorScheme();var drawGrid=this.heatmap.getHeatMapElementComponent().isDrawGrid();var gridColor=this.heatmap.getHeatMapElementComponent().getGridColor();var gridThickness=this.heatmap.getHeatMapElementComponent().getGridThickness();for(var i=start;i<end;i++){var value=vector.getValue(i);if(value!=null){var pix=positions.getPosition(i);var itemSize=positions.getItemSize(i);var currentPix=0;var nvalues=value.length;var pixPer=size/nvalues;for(var j=0;j<nvalues;j++){var val=value[j];context.fillStyle=colorScheme.getColor(i,-1,val);context.fillRect(j*pixPer,pix,pixPer,itemSize)}if(drawGrid&&itemSize>10){context.strokeStyle=gridColor;context.lineWidth=gridThickness;context.beginPath();for(var j=0;j<nvalues;j++){var val=value[j];context.rect(j*pixPer,pix,pixPer,itemSize)}context.stroke()}}}context.restore()},renderArc:function(context,vector,start,end,clip,size){var isColumns=this.isColumns;var positions=this.positions;var project=this.project;context.save();context.lineWidth=1;var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);context.translate(clip.x,clip.y);var width=clip.width;var height=clip.height;for(var i=start;i<end;i++){var value=vector.getValue(i);if(value!=null){var startPix=positions.getPosition(i)+positions.getItemSize(i)/2;for(var j=0,nindices=value.length;j<nindices;j++){var viewIndex=value[j];var endPix=positions.getPosition(viewIndex)+positions.getItemSize(viewIndex)/2;var midPix=(endPix+startPix)/2;var distance=Math.abs(i-viewIndex);var arcRadius=size;if(isColumns){context.beginPath();context.moveTo(startPix,arcRadius);context.quadraticCurveTo(midPix,1,endPix,arcRadius)}else{console.log(i,viewIndex,startPix,endPix);context.beginPath();context.moveTo(1,startPix);context.quadraticCurveTo(arcRadius,midPix,1,endPix)}context.stroke()}}}context.restore()},sdfToSvg:function(sdf,width,height){if(!this.jsme&&typeof JSApplet!=="undefined"){this.jsmeId=_.uniqueId("m");this.$jsmeDiv=$('<div id="'+this.jsmeId+'" style="position:absolute;left:-10000px;top:-10000px;"></div>').appendTo($(document.body));this.jsme=new JSApplet.JSME(this.jsmeId,"380px","340px",{})}this.jsme.readMolFile(sdf);var svg=$("#"+this.jsmeId+" > div > div > div:nth-child(2) > svg");var svgWidth=svg.width.baseVal.value;var svgHeight=svg.height.baseVal.value;var scale=Math.min(width/svgWidth,height/svgHeight);var text='<svg><g transform="scale('+scale+')">'+svg.innerHTML+"</g></svg>";return text},renderMolecule:function(context,vector,start,end,clip,offset){var isColumns=this.isColumns;var positions=this.positions;context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.strokeStyle="black";var width=this.getUnscaledWidth();var customUrlProvider=this.heatmap.options.structureUrlProvider!==undefined;var dummyTarget={childNodes:[],getContext:function(){return context}};for(var i=start;i<end;i++){var spanEnd=this.spanMap.get(i);if(spanEnd!==undefined){var startPix=positions.getPosition(i);var endPix=positions.getPosition(spanEnd-1)+positions.getSize();var size=endPix-startPix;var value=vector.getValue(i);var cache=this.moleculeCache[value];if(cache){if(customUrlProvider){if(cache.complete){var scaleFactor=Math.min(size/cache.height,width/cache.width);var scaledWidth=cache.width*scaleFactor;var scaledHeight=cache.height*scaleFactor;var diff=cache.height-scaledHeight;startPix+=diff/2;try{context.drawImage(cache,offset,startPix,scaledWidth,scaledHeight)}catch(x){}}}else{var text=this.sdfToSvg(cache,width,size);canvg(dummyTarget,text,{ignoreMouse:true,ignoreAnimation:true,offsetY:startPix,ignoreClear:true,ignoreDimensions:true})}}}}},createChartScale:function(availableSpace){var domain;var range;if(this.settings.mid!==this.settings.min&&this.settings.mid!==this.settings.max){domain=[this.settings.min,this.settings.mid,this.settings.max];range=this.isColumns?[availableSpace,availableSpace/2,0]:[0,availableSpace/2,availableSpace]}else{domain=[this.settings.min,this.settings.max];range=this.isColumns?[availableSpace,0]:[0,availableSpace]}var scale=d3.scale.linear().domain(domain).range(range).clamp(true);return scale},renderBar:function(context,vector,start,end,clip,offset,availableSpace){var isColumns=this.isColumns;var positions=this.positions;context.fillStyle=this.settings.barColor;var scale=this.createChartScale(availableSpace);var midPix=scale(this.settings.mid);var settings=this.settings;var discrete=vector.getProperties().get(morpheus.VectorKeys.DISCRETE)&&this.discreteValueMap!=null;var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):null;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();for(var i=start;i<end;i++){var value=vector.getValue(i);if(discrete){value=this.discreteValueMap.get(value)}var position=positions.getPosition(i);var size=positions.getItemSize(i);var scaledValue=scale(value);if(colorByVector!==null){context.fillStyle=colorModel.getMappedValue(colorByVector,colorByVector.getValue(i))}if(isColumns){context.beginPath();context.rect(position,Math.min(midPix,scaledValue)+offset,size,Math.abs(midPix-scaledValue));context.fill()}else{context.beginPath();context.rect(offset+Math.min(midPix,scaledValue),position,Math.abs(midPix-scaledValue),size);context.fill()}}},renderBoxPlot:function(context,vector,start,end,clip,offset,availableSpace){var isColumns=this.isColumns;var positions=this.positions;context.strokeStyle="black";context.save();context.translate(offset,0);var scale=this.createChartScale(availableSpace);var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):null;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();for(var i=start;i<end;i++){var array=vector.getValue(i);if(array!=null){var itemSize=positions.getItemSize(i);if(itemSize<=3){continue}var radius=2;var pix=positions.getPosition(i);var start=pix+1;var end=pix+itemSize-1;var center=(start+end)/2;var _itemSize=itemSize-2;var lineHeight=Math.max(2,_itemSize-8);var box=array.summary;if(box==null){var v=morpheus.VectorUtil.arrayAsVector(array);box=morpheus.BoxPlotItem(visibleFieldIndices!=null?new morpheus.SlicedVector(v,visibleFieldIndices):v);array.summary=box}context.fillStyle="#bdbdbd";if(!isColumns){context.fillRect(Math.min(scale(box.q1),scale(box.q3)),start,Math.abs(scale(box.q1)-scale(box.q3)),_itemSize);context.fillRect(Math.min(scale(box.q1),scale(box.lowerAdjacentValue)),center-lineHeight/2,Math.abs(scale(box.q1)-scale(box.lowerAdjacentValue)),lineHeight);context.fillRect(Math.min(scale(box.q3),scale(box.upperAdjacentValue)),center-lineHeight/2,Math.abs(scale(box.q3)-scale(box.upperAdjacentValue)),lineHeight);context.fillStyle="#31a354";context.fillRect(scale(box.median)-3,start,3,end-start);context.fillStyle="#636363"}else{}}}context.restore()},renderStackedBar:function(context,vector,start,end,clip,offset,availableSpace){var isColumns=this.isColumns;var positions=this.positions;var scale=this.createChartScale(availableSpace);var midPix=scale(this.settings.mid);var settings=this.settings;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();context.strokeStyle="black";context.lineWidth=2;for(var i=start;i<end;i++){var array=vector.getValue(i);if(array!=null){var position=positions.getPosition(i);var size=positions.getItemSize(i);var positivePairs=[];var negativePairs=[];for(var j=0,length=array.length;j<length;j++){var value=array[j];if(value>=this.settings.mid){positivePairs.push({value:value,index:j})}else if(value<0){negativePairs.push({value:value,index:j})}}var positiveIndices=morpheus.Util.indexSortPairs(positivePairs,false);for(var j=0,length=positiveIndices.length;j<length;j++){var index=positiveIndices[j];var value=array[index];var color=colorModel.getMappedValue(vector,index);context.fillStyle=color;var scaledValue=scale(value);var nextScaledValue=j===length-1?midPix:scale(array[positiveIndices[j+1]]);if(isColumns){context.beginPath();context.rect(position,Math.min(nextScaledValue,scaledValue),size,Math.abs(nextScaledValue-scaledValue));context.fill()}else{context.beginPath();context.rect(offset+Math.min(nextScaledValue,scaledValue),position,Math.abs(nextScaledValue-scaledValue),size);context.fill()}}var negativeIndices=morpheus.Util.indexSortPairs(negativePairs,true);for(var j=0,length=negativeIndices.length;j<length;j++){var index=negativeIndices[j];var value=array[index];var color=colorModel.getMappedValue(vector,index);context.fillStyle=color;var scaledValue=scale(value);var nextScaledValue=j===length-1?midPix:scale(array[negativeIndices[j+1]]);if(isColumns){context.beginPath();context.rect(position,Math.min(nextScaledValue,scaledValue),size,Math.abs(nextScaledValue-scaledValue));context.fill()}else{context.beginPath();context.rect(offset+Math.min(nextScaledValue,scaledValue),position,Math.abs(nextScaledValue-scaledValue),size);context.fill()}}}}context.lineWidth=1},renderUnstackedBar:function(context,vector,start,end,clip,offset,availableSpace,fieldIndices){var isColumns=this.isColumns;var positions=this.positions;var nvalues=fieldIndices.length;var settings=this.settings;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();context.fillStyle=this.settings.barColor;var barSpacer=0;var barWidth=(availableSpace-(nvalues-1)*barSpacer)/nvalues;var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):null;context.strokeStyle="white";for(var i=start;i<end;i++){var array=vector.getValue(i);if(array!=null){var position=positions.getPosition(i);var itemSize=positions.getItemSize(i);var scale=this.createChartScale(itemSize-1);var midPix=scale(this.settings.mid);var xpix=0;for(var j=0;j<nvalues;j++){var value=array[fieldIndices[j]];if(colorByVector!=null){var colorByArray=colorByVector.getValue(i);var color=colorModel.getMappedValue(colorByVector,colorByArray!=null?colorByArray[fieldIndices[j]]:null);context.fillStyle=color}var scaledValue=scale(value);if(isColumns){context.beginPath();context.rect(Math.min(midPix,scaledValue),offset+xpix,Math.abs(midPix-scaledValue),barWidth);context.fill()}else{context.beginPath();var barHeight=Math.abs(midPix-scaledValue);var ypix=position+itemSize-Math.max(midPix,scaledValue);context.rect(offset+xpix,ypix,barWidth,barHeight);context.fill()}xpix+=barWidth+barSpacer}}}},renderText:function(context,vector,isColor,isFont,start,end,clip,offset,canvasSize){context.textBaseline="middle";if(typeof C2S!=="undefined"&&context instanceof C2S){context.translate(this.isColumns?2:0,this.isColumns?0:2)}var positions=this.positions;var isColumns=this.isColumns;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();var fontModel=isColumns?this.project.getColumnFontModel():this.project.getRowFontModel();if(isColumns){context.translate(clip.x,clip.y)}var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):vector;var getColor;if(colorByVector.getProperties().get(morpheus.VectorKeys.DISCRETE)){getColor=_.bind(colorModel.getMappedValue,colorModel)}else{getColor=_.bind(colorModel.getContinuousMappedValue,colorModel)}var fontVector=this.settings.fontField!=null?this.getVector(this.settings.fontField):vector;var toStringFunction=morpheus.VectorTrack.vectorToString(vector);var font=context.font;for(var i=start;i<end;i++){var size=this.positions.getItemSize(i);if(size<6){continue}var value=vector.getValue(i);if(value!=null){var stringValue=toStringFunction(value);var position=positions.getPosition(i);if(isColor){context.fillStyle=getColor(colorByVector,colorByVector.getValue(i))}if(isFont){context.font=fontModel.getMappedValue(fontVector,fontVector.getValue(i)).weight+" "+font}if(isColumns){context.save();context.translate(position+size/2-clip.x,offset-clip.y);context.rotate(-Math.PI/2);context.fillText(stringValue,0,0);context.restore()}else{context.fillText(stringValue,offset,position+size/2)}}}context.font=font}};morpheus.Util.extend(morpheus.VectorTrack,morpheus.AbstractCanvas);morpheus.VectorTrack.MAX_FONT_SIZE=18;morpheus.AverageLinkage=function(nelements,distmatrix){var j;var n;var clusterid;var number;var result;clusterid=[];number=[];result=[];for(var i=0;i<nelements-1;i++){result[i]={left:0,right:0,distance:0}}for(j=0;j<nelements;j++){number[j]=1;clusterid[j]=j}var r={};for(n=nelements;n>1;n--){morpheus.HCluster.findClosestPair(n,distmatrix,r);result[nelements-n]={};result[nelements-n].distance=r.distance;var is=r.ip;var js=r.jp;result[nelements-n].left=clusterid[is];result[nelements-n].right=clusterid[js];var sum=number[is]+number[js];for(j=0;j<js;j++){distmatrix[js][j]=distmatrix[is][j]*number[is]+distmatrix[js][j]*number[js];distmatrix[js][j]/=sum}for(j=js+1;j<is;j++){distmatrix[j][js]=distmatrix[is][j]*number[is]+distmatrix[j][js]*number[js];distmatrix[j][js]/=sum}for(j=is+1;j<n;j++){distmatrix[j][js]=distmatrix[j][is]*number[is]+distmatrix[j][js]*number[js];distmatrix[j][js]/=sum}for(j=0;j<is;j++){distmatrix[is][j]=distmatrix[n-1][j]}for(j=is+1;j<n-1;j++){distmatrix[j][is]=distmatrix[n-1][j]}number[js]=sum;number[is]=number[n-1];clusterid[js]=n-nelements-1;clusterid[is]=clusterid[n-1]}return result};morpheus.CollapseDataset=function(dataset,collapseToFields,summarizeFunction,shallowCopy){var vectors=[];for(var i=0;i<collapseToFields.length;i++){var v=dataset.getRowMetadata().getByName(collapseToFields[i]);if(!v){throw collapseToFields[i]+" not found. Available fields are "+morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata())}vectors.push(v)}var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);var collapsedDataset=new morpheus.Dataset({name:dataset.getName(),rows:idToIndices.size(),columns:dataset.getColumnCount(),dataType:"Float32"});var nseries=dataset.getSeriesCount();for(var series=1;series<nseries;series++){collapsedDataset.addSeries({name:dataset.getName(i),dataType:"Float32"})}if(shallowCopy){collapsedDataset.setColumnMetadata(dataset.getColumnMetadata())}else{morpheus.MetadataUtil.copy(dataset.getColumnMetadata(),collapsedDataset.getColumnMetadata())}var nfields=collapseToFields.length;var collapseToVectors=[];for(var i=0;i<nfields;i++){collapseToVectors.push(collapsedDataset.getRowMetadata().add(collapseToFields[i]))}var counter=0;idToIndices.forEach(function(rowIndices,key){var slice=morpheus.DatasetUtil.slicedView(dataset,rowIndices,null);var view=new morpheus.DatasetColumnView(slice);for(var series=0;series<nseries;series++){view.setSeriesIndex(series);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){view.setIndex(j);collapsedDataset.setValue(counter,j,summarizeFunction(view),series)}}for(var i=0;i<nfields;i++){var collapsedToVector=collapseToVectors[i];var vector=vectors[i];collapsedToVector.setValue(counter,vector.getValue(rowIndices[0]))}counter++});if(nfields===1){var newVector=collapseToVectors[0];vectors[0].getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){newVector.properties.set(key,val)}})}return collapsedDataset};morpheus.CompleteLinkage=function(nelements,distmatrix){var j;var n;var clusterid=[];var result=[];for(var i=0;i<nelements-1;i++){result[i]={left:0,right:0,distance:0}}for(j=0;j<nelements;j++){clusterid[j]=j}var r={};for(n=nelements;n>1;n--){morpheus.HCluster.findClosestPair(n,distmatrix,r);result[nelements-n].distance=r.distance;var is=r.ip;var js=r.jp;for(j=0;j<js;j++){distmatrix[js][j]=Math.max(distmatrix[is][j],distmatrix[js][j])}for(j=js+1;j<is;j++){distmatrix[j][js]=Math.max(distmatrix[is][j],distmatrix[j][js])}for(j=is+1;j<n;j++){distmatrix[j][js]=Math.max(distmatrix[j][is],distmatrix[j][js])}for(j=0;j<is;j++){distmatrix[is][j]=distmatrix[n-1][j]}for(j=is+1;j<n-1;j++){distmatrix[j][is]=distmatrix[n-1][j]}result[nelements-n].left=clusterid[is];result[nelements-n].right=clusterid[js];clusterid[js]=n-nelements-1;clusterid[is]=clusterid[n-1]}return result};morpheus.HClusterGroupBy=function(dataset,groupByFieldNames,distanceFunction,linkageMethod){var model=dataset.getRowMetadata();var vectors=morpheus.MetadataUtil.getVectors(dataset.getRowMetadata(),groupByFieldNames);var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);var reorderedIndices=[];var offset=0;var root={id:-1,children:[],height:0};var tree={maxHeight:0,rootNode:root,leafNodes:[],nLeafNodes:0};idToIndices.forEach(function(rowIndices,id){var originalIndicesForGroup=idToIndices.get(id);var subset=morpheus.DatasetUtil.slicedView(dataset,originalIndicesForGroup,null);var hcl;var distanceMatrix=morpheus.HCluster.computeDistanceMatrix(subset,distanceFunction);hcl=new morpheus.HCluster(distanceMatrix,linkageMethod);var reorderedGroupIndices=hcl.reorderedIndices;for(var i=0,rows=subset.getRowCount();i<rows;i++){var originalIndex=originalIndicesForGroup[reorderedGroupIndices[i]];reorderedIndices.push(originalIndex)}morpheus.DendrogramUtil.dfs(hcl.tree.rootNode,function(node){node.index+=offset;node.minIndex+=offset;node.maxIndex+=offset;node.id+=offset;return true});if(hcl.tree.leafNodes.length===0){tree.leafNodes=tree.leafNodes.concat([hcl.tree.rootNode])}else{tree.leafNodes=tree.leafNodes.concat(hcl.tree.leafNodes)}root.children.push(hcl.tree.rootNode);if(!isNaN(hcl.tree.maxHeight)){tree.maxHeight=Math.max(tree.maxHeight,hcl.tree.maxHeight)}offset+=subset.getRowCount()});tree.nLeafNodes=tree.leafNodes.length;tree.rootNode.height=tree.maxHeight;this.tree=tree;this.reorderedIndices=reorderedIndices};morpheus.HCluster=function(distmatrix,linkageAlgorithm){var nelements=distmatrix.length;var nNodes=nelements-1;if(nNodes===-1){var root={id:0,height:0,index:0,minIndex:0,maxIndex:0,depth:0};this.tree={maxHeight:0,rootNode:root,leafNodes:[],nLeafNodes:0};this.reorderedIndices=[0];return}var tree=linkageAlgorithm(nelements,distmatrix);var nodeorder=[];var nodecounts=[];var order=[];var nodeID=[];for(var i=0;i<nelements;i++){order[i]=i}var leftIds=[];var rightIds=[];for(var i=0;i<nNodes;i++){var min1=tree[i].left;var min2=tree[i].right;var order1;var order2;var counts1;var counts2;var ID1;var ID2;nodeID[i]=nNodes+(i+2);if(min1<0){var index1=-min1-1;order1=nodeorder[index1];counts1=nodecounts[index1];ID1=nodeID[index1];tree[i].distance=Math.max(tree[i].distance,tree[index1].distance)}else{order1=order[min1];counts1=1;ID1=min1}if(min2<0){var index2=-min2-1;order2=nodeorder[index2];counts2=nodecounts[index2];ID2=nodeID[index2];tree[i].distance=Math.max(tree[i].distance,tree[index2].distance)}else{order2=order[min2];counts2=1;ID2=min2}leftIds[i]=ID1;rightIds[i]=ID2;nodecounts[i]=counts1+counts2;nodeorder[i]=(counts1*order1+counts2*order2)/(counts1+counts2)}var reorderedIndices=morpheus.HCluster.treeSort(nNodes,order,nodeorder,nodecounts,tree);var idToIndex={};for(var i=0,length=reorderedIndices.length;i<length;i++){var index=reorderedIndices[i];idToIndex[index]=i}var nodeIdToNode={};var node;for(var i=0,length=nodeID.length;i<length;i++){var id=nodeID[i];var leftId=leftIds[i];var lnode=nodeIdToNode[leftId];if(lnode===undefined){lnode={id:leftId};var index=idToIndex[leftId];lnode.index=index;lnode.minIndex=index;lnode.maxIndex=index;nodeIdToNode[lnode.id]=lnode}var rightId=rightIds[i];var rnode=nodeIdToNode[rightId];if(rnode===undefined){rnode={id:rightId};var index=idToIndex[rightId];rnode.index=index;rnode.minIndex=index;rnode.maxIndex=index;nodeIdToNode[rnode.id]=rnode}node={id:id,children:lnode.index<rnode.index?[lnode,rnode]:[rnode,lnode],height:tree[i].distance,index:(rnode.index+lnode.index)/2};node.minIndex=Math.min(rnode.minIndex,lnode.minIndex);node.maxIndex=Math.max(rnode.maxIndex,lnode.maxIndex);lnode.parent=node;rnode.parent=node;nodeIdToNode[node.id]=node}this.reorderedIndices=reorderedIndices;var leafNodes=[];for(var i=0,length=reorderedIndices.length;i<length;i++){var leaf=nodeIdToNode[reorderedIndices[i]];leaf.height=0;leafNodes.push(leaf)}morpheus.DendrogramUtil.setNodeDepths(node);this.tree={maxHeight:node.height,rootNode:node,leafNodes:leafNodes,nLeafNodes:leafNodes.length}};morpheus.HCluster.findClosestPair=function(n,distmatrix,r){var i,j;var temp;var distance=distmatrix[1][0];var ip=1;var jp=0;for(i=1;i<n;i++){for(j=0;j<i;j++){temp=distmatrix[i][j];if(temp<distance){distance=temp;ip=i;jp=j}}}r.distance=distance;r.ip=ip;r.jp=jp};morpheus.HCluster.computeDistanceMatrix=function(dataset,distanceFunction){var matrix=[];var n=dataset.getRowCount();for(var i=1;i<n;i++){matrix[i]=new Float32Array(i)}if(distanceFunction===0){for(var i=1;i<n;i++){for(var j=0;j<i;j++){matrix[i][j]=dataset.getValue(i,j)}}}else if(distanceFunction===1){var max=-Number.MAX_VALUE;for(var i=1;i<n;i++){for(var j=0;j<i;j++){var value=dataset.getValue(i,j);if(!isNaN(value)){max=Math.max(value,max)}}}for(var i=1;i<n;i++){for(var j=0;j<i;j++){matrix[i][j]=max-dataset.getValue(i,j)}}}else{var list1=new morpheus.DatasetRowView(dataset);var list2=new morpheus.DatasetRowView(dataset);for(var i=1;i<n;i++){list1.setIndex(i);for(var j=0;j<i;j++){matrix[i][j]=distanceFunction(list1,list2.setIndex(j))}}}return matrix};morpheus.HCluster.treeSort=function(nNodes,order,nodeorder,nodecounts,tree){var nElements=nNodes+1;var i;var neworder=[];var clusterids=[];for(i=0;i<nElements;i++){clusterids[i]=i;neworder[i]=0}for(i=0;i<nNodes;i++){var i1=tree[i].left;var i2=tree[i].right;var order1=i1<0?nodeorder[-i1-1]:order[i1];var order2=i2<0?nodeorder[-i2-1]:order[i2];var count1=i1<0?nodecounts[-i1-1]:1;var count2=i2<0?nodecounts[-i2-1]:1;if(i1<i2){var increase=order1<order2?count1:count2;var j;for(j=0;j<nElements;j++){var clusterid=clusterids[j];if(clusterid==i1&&order1>=order2){neworder[j]+=increase}if(clusterid==i2&&order1<order2){neworder[j]+=increase}if(clusterid==i1||clusterid==i2){clusterids[j]=-i-1}}}else{var increase=order1<=order2?count1:count2;var j;for(j=0;j<nElements;j++){var clusterid=clusterids[j];if(clusterid==i1&&order1>order2){neworder[j]+=increase}if(clusterid==i2&&order1<=order2){neworder[j]+=increase}if(clusterid==i1||clusterid==i2){clusterids[j]=-i-1}}}}return morpheus.Util.indexSort(neworder,true)};morpheus.KMeansPlusPlusClusterer=function(k,maxIterations,distanceFunction){var distance=function(points1,points2){return distanceFunction(points1.getPoint(),points2.getPoint())};function nextInt(upperBound){return Math.floor(Math.random()*upperBound)|0}function nextDouble(){return Math.random()}function PointWrapper(point){this.getPoint=function(){return point}}function CentroidCluster(center){var centroidPoints=[];this.addPoint=function(p){centroidPoints.push(p)};this.getPoints=function(){return centroidPoints};this.getCenter=function(){return center}}function cluster(points){if(points.length<k){throw"Too many clusters"}var clusters=chooseInitialCenters(points);var assignments=new Int32Array(points.length);assignPointsToClusters(clusters,points,assignments);var max=maxIterations<0?Number.MAX_VALUE:maxIterations;for(var count=0;count<max;count++){var emptyCluster=false;var newClusters=[];for(var clusterIndex=0;clusterIndex<clusters.length;clusterIndex++){var cluster=clusters[clusterIndex];var newCenter;if(cluster.getPoints().length===0){newCenter=getPointFromLargestVarianceCluster(clusters);emptyCluster=true}else{newCenter=centroidOf(cluster.getPoints(),cluster.getCenter().getPoint().size())}newClusters.push(new CentroidCluster(newCenter))}var changes=assignPointsToClusters(newClusters,points,assignments);clusters=newClusters;if(changes===0&&!emptyCluster){return clusters}}return clusters}function assignPointsToClusters(clusters,points,assignments){var assignedDifferently=0;var pointIndex=0;for(var i=0;i<points.length;i++){var p=points[i];var clusterIndex=getNearestCluster(clusters,p);if(clusterIndex!=assignments[pointIndex]){assignedDifferently++}var cluster=clusters[clusterIndex];cluster.addPoint(p);assignments[pointIndex++]=clusterIndex}return assignedDifferently}function chooseInitialCenters(points){var pointList=points;var numPoints=pointList.length;var taken=new Array(numPoints);for(var i=0;i<taken.length;i++){taken[i]=false}var resultSet=[];var firstPointIndex=nextInt(numPoints);var firstPoint=pointList[firstPointIndex];resultSet.push(new CentroidCluster(firstPoint));taken[firstPointIndex]=true;var minDistSquared=new Float32Array(numPoints);for(var i=0;i<numPoints;i++){if(i!==firstPointIndex){var d=distance(firstPoint,pointList[i]);minDistSquared[i]=d*d}}while(resultSet.length<k){var distSqSum=0;for(var i=0;i<numPoints;i++){if(!taken[i]){distSqSum+=minDistSquared[i]}}var r=nextDouble()*distSqSum;var nextPointIndex=-1;var sum=0;for(var i=0;i<numPoints;i++){if(!taken[i]){sum+=minDistSquared[i];if(sum>=r){nextPointIndex=i;break}}}if(nextPointIndex===-1){for(var i=numPoints-1;i>=0;i--){if(!taken[i]){nextPointIndex=i;break}}}if(nextPointIndex>=0){var p=pointList[nextPointIndex];resultSet.push(new CentroidCluster(p));taken[nextPointIndex]=true;if(resultSet.length<k){for(var j=0;j<numPoints;j++){if(!taken[j]){var d=distance(p,pointList[j]);var d2=d*d;if(d2<minDistSquared[j]){minDistSquared[j]=d2}}}}}else{break}}return resultSet}function getPointFromLargestVarianceCluster(clusters){var maxVariance=-Number.MAX_VALUE;var selected=null;for(var clusterIndex=0;clusterIndex<clusters.length;clusterIndex++){var cluster=clusters[clusterIndex];if(cluster.getPoints().length>0){var center=cluster.getCenter();var points=cluster.getPoints();var distances=new Float32Array(points.length);for(var i=0;i<points.length;i++){distances[i]=distance(points[i],center)}var variance=morpheus.Variance(morpheus.VectorUtil.arrayAsVector(distances));if(variance>maxVariance){maxVariance=variance;selected=cluster}}}if(selected==null){throw"All clusters are empty"}var selectedPoints=selected.getPoints();return selectedPoints.splice(nextInt(selectedPoints.length),1)}function getNearestCluster(clusters,point){var minDistance=Number.MAX_VALUE;var clusterIndex=0;var minCluster=0;for(var i=0;i<clusters.length;i++){var c=clusters[i];var d=distance(point,c.getCenter());if(d<minDistance){minDistance=d;minCluster=clusterIndex}clusterIndex++}return minCluster}function centroidOf(points,dimension){var centroid=new Float32Array(dimension);for(var i=0;i<centroid.length;i++){var sum=0;var count=0;for(var pointIndex=0;pointIndex<points.length;pointIndex++){var p=points[pointIndex];var point=p.getPoint();var val=point.getValue(i);if(!isNaN(val)){sum+=val;count++}}centroid[i]=sum/count}return new PointWrapper(morpheus.VectorUtil.arrayAsVector(centroid))}this.execute=function(vectors){var points=[];var npoints=vectors.length;for(var i=0;i<npoints;i++){var p=new PointWrapper(vectors[i]);p.i=i;points.push(p)}return cluster(points)};this.cluster=cluster};morpheus.PermutationPValues=function(dataset,aIndices,bIndices,numPermutations,f,continuousList){var numRows=dataset.getRowCount();var scores=new Float32Array(numRows);var smoothPValues=true;var permuter;var permutationScore;if(aIndices!=null){var list1=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,aIndices));var list2=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,bIndices));dataset=new morpheus.SlicedDatasetView(dataset,null,aIndices.concat(bIndices));permuter=new morpheus.UnbalancedPermuter(aIndices.length,bIndices.length);permutationScore=new morpheus.TwoClassPermutationScore;permutationScore.init(dataset,f);for(var i=0;i<numRows;i++){scores[i]=f(list1.setIndex(i),list2.setIndex(i))}}else{permuter=new morpheus.UnbalancedContinuousPermuter(continuousList.size());permutationScore=new morpheus.ContinuousPermutationScore(continuousList);permutationScore.init(dataset,f);var list=new morpheus.DatasetRowView(dataset);for(var i=0;i<numRows;i++){scores[i]=f(continuousList,list.setIndex(i))}}var rowSpecificPValues=new Float32Array(numRows);for(var permutationIndex=0;permutationIndex<numPermutations;permutationIndex++){permutationScore.setPermutation(permuter.next());for(var i=0;i<numRows;i++){var permutedScore=permutationScore.getScore(i);var score=scores[i];if(permutedScore>=score){rowSpecificPValues[i]++}}}var N=numPermutations;var kArray=new Uint32Array(numRows);for(var i=0;i<numRows;i++){var k=rowSpecificPValues[i];kArray[i]=k;var p;if(smoothPValues){p=(k+1)/(N+2)}else{p=k/N}var oneMinusP=1-p;if(oneMinusP<p){p=oneMinusP}p*=2;if(p===0){var val=dataset.getValue(i,0);var flat=true;for(var j=1,cols=dataset.getColumnCount();j<cols&&flat;j++){if(dataset.getValue(i,j)!=val){flat=false}}if(flat){p=1}}rowSpecificPValues[i]=p}this.rowSpecificPValues=rowSpecificPValues;this.k=kArray;this.fdr=morpheus.FDR_BH(rowSpecificPValues);this.scores=scores};morpheus.PermutationPValues.prototype={getBonferroni:function(index){return Math.min(this.rowSpecificPValues[index]*this.numRows,1)}};morpheus.UnbalancedContinuousPermuter=function(size){var indices=new Uint32Array(size);for(var i=0;i<indices.length;i++){indices[i]=i}var n=indices.length;function getRandomIntInclusive(min,max){return Math.floor(Math.random()*(max-min+1))+min}this.next=function(){for(var i=n-1;i>=1;i--){var j=getRandomIntInclusive(0,i);var tmp=indices[j];indices[j]=indices[i];indices[i]=tmp}return indices}};morpheus.UnbalancedPermuter=function(numClassZero,numClassOne){var assignments=new Uint32Array(numClassZero+numClassOne);var indices=new Uint32Array(numClassZero+numClassOne);for(var i=0;i<indices.length;i++){indices[i]=i}var n=indices.length;function getRandomIntInclusive(min,max){return Math.floor(Math.random()*(max-min+1))+min}this.next=function(){for(var i=n-1;i>=1;i--){var j=getRandomIntInclusive(0,i);var tmp=indices[j];indices[j]=indices[i];indices[i]=tmp}for(var i=0;i<n;i++){assignments[i]=0}for(var i=0;i<numClassOne;i++){assignments[indices[i]]=1}return assignments}};morpheus.TwoClassPermutationScore=function(){this.classZeroView=null;this.classOneView=null};morpheus.TwoClassPermutationScore.prototype={getScore:function(index){this.classZeroView.setIndex(index);this.classOneView.setIndex(index);return this.f(this.classZeroView,this.classOneView)},init:function(dataset,f){this.dataset=dataset;this.classZeroView=new morpheus.DatasetRowView(dataset);this.classOneView=new morpheus.DatasetRowView(dataset);this.f=f},setPermutation:function(permutedAssignments){var zeroIndices=[];var oneIndices=[];for(var i=0,length=permutedAssignments.length;i<length;i++){if(permutedAssignments[i]===0){zeroIndices.push(i)}else{oneIndices.push(i)}}this.classZeroView.setDataset(new morpheus.SlicedDatasetView(this.dataset,null,zeroIndices));this.classOneView.setDataset(new morpheus.SlicedDatasetView(this.dataset,null,oneIndices))}};morpheus.ContinuousPermutationScore=function(referenceList){this.referenceList=referenceList};morpheus.ContinuousPermutationScore.prototype={getScore:function(index){this.datasetRowView.setIndex(index);return this.f(this.referenceListView,this.datasetRowView)},init:function(dataset,f){this.dataset=dataset;this.referenceListView=null;this.datasetRowView=new morpheus.DatasetRowView(dataset);this.f=f},setPermutation:function(indices){this.referenceListView=new morpheus.SlicedVector(this.referenceList,indices)}};morpheus.Ranking=function(values){var ranks=[];for(var i=0,length=values.length;i<length;i++){ranks.push({value:values[i],position:i})}if(ranks.length===0){return[]}ranks.sort(function(a,b){return a.value<b.value?-1:a.value===b.value?0:1});var out=[];var pos=1;out[ranks[0].position]=pos;var tiesTrace=[];tiesTrace.push(ranks[0].position);for(var i=1;i<ranks.length;i++){if(ranks[i].value>ranks[i-1].value){pos=i+1;if(tiesTrace.length>1){morpheus.Ranking.fillAverage(out,tiesTrace)}tiesTrace=[];tiesTrace.push(ranks[i].position)}else{tiesTrace.push(ranks[i].position)}out[ranks[i].position]=pos}if(tiesTrace.length>1){morpheus.Ranking.fillAverage(out,tiesTrace)}return out};morpheus.Ranking.fill=function(data,tiesTrace,value){for(var i=0,length=tiesTrace.length;i<length;i++){data[tiesTrace[i]]=value}};morpheus.Ranking.fillAverage=function(ranks,tiesTrace){var c=ranks[tiesTrace[0]];var length=tiesTrace.length;morpheus.Ranking.fill(ranks,tiesTrace,(2*c+length-1)/2)};morpheus.SingleLinkage=function(nelements,distmatrix){var i,j,k;var nnodes=nelements-1;var temp=[];var index=[];var vector=[];var result=[];for(i=0;i<nelements;i++){result[i]={left:0,right:0,distance:0}}for(i=0;i<nnodes;i++){vector[i]=i}for(i=0;i<nelements;i++){result[i].distance=Number.MAX_VALUE;for(j=0;j<i;j++){temp[j]=distmatrix[i][j]}for(j=0;j<i;j++){k=vector[j];if(result[j].distance>=temp[j]){if(result[j].distance<temp[k]){temp[k]=result[j].distance}result[j].distance=temp[j];vector[j]=i}else if(temp[j]<temp[k]){temp[k]=temp[j]}}for(j=0;j<i;j++){if(result[j].distance>=result[vector[j]].distance){vector[j]=i}}}for(i=0;i<nnodes;i++){result[i].left=i}result.sort(function(node1,node2){var term1=node1.distance;var term2=node2.distance;if(term1<term2)return-1;if(term1>term2)return+1;return 0});for(i=0;i<nelements;i++){index[i]=i}for(i=0;i<nnodes;i++){j=result[i].left;k=vector[j];result[i].left=index[j];result[i].right=index[k];index[k]=-i-1}var result2=[];for(i=0;i<nelements-1;i++){result2[i]=result[i]}return result2}})(typeof window!=="undefined"?window:this);
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navigator!=="undefined"&&navigator.onLine){if(morpheus.Util.TRACKING_CODE_LOADED){return}else if(typeof ga==="undefined"){morpheus.Util.TRACKING_CODE_LOADED=true;(function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date;a=s.createElement(o),m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)})(window,document,"script","https://www.google-analytics.com/analytics.js","ga")}if(typeof ga!=="undefined"){ga("create","UA-53973555-1","auto","morpheus");ga("morpheus.send","pageview")}morpheus.Util.TRACKING_CODE_LOADED=true}};morpheus.Util.measureScrollbar=function(){var $c=$("<div style='position:absolute; top:-10000px; left:-10000px; width:100px; height:100px; overflow:scroll;'></div>").appendTo("body");var dim={width:Math.max(0,$c.width()-$c[0].clientWidth),height:$c.height()-$c[0].clientHeight};$c.remove();return dim};morpheus.Util.trackEvent=function(options){if(typeof 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false};morpheus.Util.getWindowSearchObject=function(){var searchObject={};var hashObject={};if(window.location.search.length>0){searchObject=morpheus.Util.getQueryParams(window.location.search.substring(1))}if(window.location.hash.length>0){hashObject=morpheus.Util.getQueryParams(window.location.hash.substring(1))}return _.extend(hashObject,searchObject)};morpheus.Util.copyString=function(s){return(" "+s).substr(1)};morpheus.Util.getQueryParams=function(s){var params={};if(!s){return params}var search=decodeURIComponent(s);var keyValuePairs=search.split("&");for(var i=0;i<keyValuePairs.length;i++){var pair=keyValuePairs[i].split("=");if(pair[1]!=null&&pair[1]!==""){var array=params[pair[0]];if(array===undefined){array=[];params[pair[0]]=array}array.push(pair[1])}}return params};morpheus.Util.getScriptPath=function(name){if(!name){name="morpheus-latest.min.js"}var scripts=document.getElementsByTagName("script");for(var i=scripts.length-1;i>=0;i--){var src=scripts[i].src;var index=src.lastIndexOf("/");if(index!==-1){src=src.substring(index+1)}if(src===name){return scripts[i].src}}if(name==="morpheus-latest.min.js"){return morpheus.Util.getScriptPath("morpheus.js")}return scripts.length>0?scripts[0].src:""};morpheus.Util.forceDelete=function(obj){try{var _garbageCollector=function(){var ef=URL.createObjectURL(new Blob([""],{type:"text/javascript"})),w=new Worker(ef);URL.revokeObjectURL(ef);return w}();_garbageCollector.postMessage(obj,[obj])}catch(x){console.log("Unable to delete")}};morpheus.Util.getFileName=function(fileOrUrl){if(morpheus.Util.isFile(fileOrUrl)){return fileOrUrl.name}if(fileOrUrl.name!==undefined){return fileOrUrl.name}var name=""+fileOrUrl;var question=name.indexOf("?");if(question!==-1){var params=name.substring(question+1);var keyValuePairs=decodeURIComponent(params).split("&");for(var i=0;i<keyValuePairs.length;i++){var pair=keyValuePairs[i].split("=");if(pair[0]==="file"||pair[0]==="name"){name=pair[1];break}}}else{var slash=name.lastIndexOf("/");if(slash===name.length-1){name=name.substring(0,name.length-1);slash=name.lastIndexOf("/")}if(slash!==-1){name=name.substring(slash+1)}}return name};morpheus.Util.prefixWithZero=function(value){return value<10?"0"+value:value};morpheus.Util.getExtension=function(name){name=""+name;var dotIndex=name.lastIndexOf(".");if(dotIndex>0){var suffix=name.substring(dotIndex+1).toLowerCase();if(suffix==="txt"||suffix==="gz"||suffix==="tsv"){var newPath=name.substring(0,dotIndex);var secondDotIndex=newPath.lastIndexOf(".");if(secondDotIndex>0){var secondSuffix=newPath.substring(secondDotIndex+1,newPath.length).toLowerCase();if(secondSuffix==="segtab"||secondSuffix==="seg"||secondSuffix==="maf"||secondSuffix==="gct"||secondSuffix==="txt"||secondSuffix==="gmt"){return secondSuffix}}}return suffix}return""};morpheus.Util.getBaseFileName=function(name){var dotIndex=name.lastIndexOf(".");if(dotIndex>0){var suffix=name.substring(dotIndex+1,name.length);if(suffix==="gz"||suffix==="zip"||suffix==="bz2"){return morpheus.Util.getBaseFileName(name.substring(0,dotIndex))}return name.substring(0,dotIndex)}return name};morpheus.Util.seq=function(length){var array=[];for(var i=0;i<length;i++){array.push(i)}return array};morpheus.Util.sequ32=function(length){var array=new Uint32Array(length);for(var i=0;i<length;i++){array[i]=i}return array};morpheus.Util.paramsToObject=function(hash){var search=hash?window.location.hash:window.location.search;if(search.length<=1){return{}}search=decodeURIComponent(search);var keyValuePairs=search.substring(1).split("&");var result={};for(var i=0,length=keyValuePairs.length;i<length;i++){var pair=keyValuePairs[i].split("=");var values=result[pair[0]];if(values===undefined){values=[];result[pair[0]]=values}values.push(pair[1])}return result};morpheus.Util.isHeadless=function(){return typeof $.ui==="undefined"};morpheus.Util.isFile=function(f){return typeof File!=="undefined"&&f instanceof File};morpheus.Util.endsWith=function(string,suffix){return string.length>=suffix.length&&string.substr(string.length-suffix.length)===suffix};morpheus.Util.measureSvgText=function(text,classname){if(!text||text.length===0){return{height:0,width:0}}var container=d3.select("body").append("svg");if(classname){container.attr("class",classname)}container.append("text").attr({x:-1e3,y:-1e3}).text(text);var bbox=container.node().getBBox();container.remove();return{height:bbox.height,width:bbox.width}};morpheus.Util.IS_MAC=false;if(typeof navigator!=="undefined"){morpheus.Util.IS_MAC=navigator.platform.match(/(Mac|iPhone|iPod|iPad)/i)?true:false}morpheus.Util.COMMAND_KEY=morpheus.Util.IS_MAC?"&#8984;":"Ctrl+";morpheus.Util.hammer=function(el,recognizers){if(typeof Hammer!=="undefined"){var hammer=new Hammer(el,{recognizers:[]});if(_.indexOf(recognizers,"pan")!==-1){hammer.add(new Hammer.Pan({threshold:1,direction:Hammer.DIRECTION_ALL}))}else if(_.indexOf(recognizers,"panh")!==-1){hammer.add(new Hammer.Pan({threshold:1,direction:Hammer.DIRECTION_HORIZONTAL}))}else if(_.indexOf(recognizers,"panv")!==-1){hammer.add(new Hammer.Pan({threshold:1,direction:Hammer.DIRECTION_VERTICAL}))}if(_.indexOf(recognizers,"tap")!==-1){hammer.add(new Hammer.Tap)}if(_.indexOf(recognizers,"pinch")!==-1){hammer.add(new Hammer.Pinch)}if(_.indexOf(recognizers,"longpress")!==-1){hammer.add(new Hammer.Press({event:"longpress",time:1e3}))}if(_.indexOf(recognizers,"press")!==-1){hammer.add(new Hammer.Press)}if(_.indexOf(recognizers,"swipe")!==-1){hammer.add(new Hammer.Swipe)}return hammer}else{return $()}};morpheus.Util.createTextDecoder=function(){if(typeof TextDecoder!=="undefined"){var textDecoder=new TextDecoder;return function(buf,start,end){return textDecoder.decode(buf.subarray(start,end))}}else{return function(buf,start,end){var s=[];for(var i=start;i<end;i++){s.push(String.fromCharCode(buf[i]))}return s.join("")}}};morpheus.Util.autocompleteArrayMatcher=function(token,cb,array,fields,max){var filteredSet=new morpheus.Set;var regex=new RegExp(morpheus.Util.escapeRegex(token),"i");var regexMatch=new RegExp("("+morpheus.Util.escapeRegex(token)+")","i");if(fields){var nfields=fields.length;for(var i=0,n=array.length;i<n;i++){var item=array[i];for(var j=0;j<nfields;j++){var field=fields[j];var value=item[field];if(regex.test(value)){filteredSet.add(value);break}}if(filteredSet.size()===max){break}}}else{for(var i=0,n=array.length;i<n;i++){var value=array[i];if(regex.test(value)){filteredSet.add(value);if(filteredSet.size()===max){break}}}}var matches=[];filteredSet.forEach(function(value){var quotedValue=value;if(quotedValue.indexOf(" ")!==-1){quotedValue='"'+quotedValue+'"'}matches.push({value:quotedValue,label:"<span>"+value.replace(regexMatch,"<b>$1</b>")+"</span>"})});cb(matches)};morpheus.Util.setClipboardData=function(clipboardData,delay){var isRTL=document.documentElement.getAttribute("dir")=="rtl";var fakeElem=document.createElement("div");fakeElem.contentEditable=true;fakeElem.style.fontSize="12pt";fakeElem.style.border="0";fakeElem.style.padding="0";fakeElem.style.margin="0";fakeElem.style.position="absolute";fakeElem.style[isRTL?"right":"left"]="-999999px";fakeElem.style.top=(window.pageYOffset||document.documentElement.scrollTop)+"px";fakeElem.setAttribute("readonly","");var f=function(e){clipboardData.forEach(function(elem){e.clipboardData.setData(elem.format,elem.data)});e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();fakeElem.removeEventListener("copy",f)};fakeElem.addEventListener("copy",f);document.body.appendChild(fakeElem);fakeElem.focus();var selection=window.getSelection();var range=document.createRange();range.selectNodeContents(fakeElem);selection.removeAllRanges();selection.addRange(range);if(delay){setTimeout(function(){if(!document.execCommand("copy")){console.log("copy failed")}document.body.removeChild(fakeElem)},20)}else{if(!document.execCommand("copy")){console.log("copy failed")}document.body.removeChild(fakeElem)}};morpheus.Util.autosuggest=function(options){options=$.extend({},{multi:true,delay:500,minLength:0,suggestWhenEmpty:true},options);var searching=false;function _select(event,ui,isKey){if(ui.item.skip){return false}if(options.multi){var terms=morpheus.Util.getAutocompleteTokens(options.$el[0].value,{trim:false,selectionStart:options.$el[0].selectionStart});var field=event.toElement&&event.toElement.dataset?event.toElement.dataset.autocomplete:null;var value=field?ui.item[field]:ui.item.value;var show=ui.item.show;if(terms.length===0){terms.push(value)}else if(ui.item.clear){terms=[value]}else{terms[terms.selectionStartIndex===-1||terms.selectionStartIndex===undefined?terms.length-1:terms.selectionStartIndex]=value}options.$el[0].value=terms.join(" ");if(show&&!isKey||isKey&&event.which===13){searching=true;setTimeout(function(){options.$el.autocomplete("search",options.$el.val())},20);setTimeout(function(){searching=false},100)}if(!isKey&&options.select){options.select()}return false}if(!isKey&&options.select){options.select()}if(!isKey&&event.which===13){event.stopImmediatePropagation()}}options.$el.on("keydown",function(event){if(event.keyCode===$.ui.keyCode.TAB&&$(this).data("ui-autocomplete").menu.active){event.preventDefault()}}).autocomplete({minLength:options.minLength,delay:options.delay,source:function(request,response){if(request.term.history&&options.history){return options.history(response)}var terms=morpheus.Util.getAutocompleteTokens(request.term,{trim:false,selectionStart:options.$el[0].selectionStart});if(terms.selectionStartIndex===undefined||terms.selectionStartIndex===-1){terms.selectionStartIndex=terms.length-1}if(options.suggestWhenEmpty||terms.length>0){options.filter(terms,response)}},focus:function(event,ui){var original=event.originalEvent;while(original.originalEvent!=null){original=original.originalEvent}if(original&&/^key/.test(original.type)){return _select(original,ui,true)}return false},select:function(event,ui){return _select(event,ui,false)}});var instance=options.$el.autocomplete("instance");if(instance!=null){instance._renderItem=function(ul,item){if(item.value==null){return $('<li class="'+(item.class?" "+item.class:"")+' search-category">').append($("<div>").html(item.label)).appendTo(ul)}return $('<li class="'+(item.class?" "+item.class:"")+' search-item">').append($("<div>").html(item.label)).appendTo(ul)};instance._normalize=function(items){return items};instance._resizeMenu=function(){var ul=this.menu.element;ul.outerWidth(instance.element.outerWidth())}}var menu=options.$el.autocomplete("widget");menu.menu("option","items","> :not(.search-category)");if(menu){menu.addClass("search-menu")}if(options.suggestWhenEmpty){options.$el.on("focus",function(){options.$el.autocomplete("search",options.$el.val())})}options.$el.on("keyup",function(e){if(e.which===13&&!searching){options.$el.autocomplete("close")}else if(e.which===38&&options.history){options.$el.autocomplete("search",{history:true})}else if(options.suggestWhenEmpty&&options.$el.val()===""){options.$el.autocomplete("search","")}})};morpheus.Util.getAutocompleteTokens=function(text,options){options=$.extend({},{trim:true},options);if(options.trim){text=$.trim(text)}if(text===""){return[]}var inQuote=false;var inParen=false;var tokens=[];var currentToken=[];for(var i=0,n=text.length;i<n;i++){var c=text[i];if(c==='"'){inQuote=!inQuote;currentToken.push(c)}else if(c==="("||c===")"){inParen=c==="(";currentToken.push(c)}else{if((c===" "||c==="\t")&&!inQuote&&!inParen){tokens.push({s:currentToken.join(""),inSelectionStart:currentToken.inSelectionStart});currentToken=[]}else{currentToken.push(c)}}if(i===options.selectionStart-1){currentToken.inSelectionStart=true}}tokens.push({s:currentToken.join(""),inSelectionStart:currentToken.inSelectionStart});if(!options.trim&&!inQuote&&text[text.length-1]===" "){tokens.push({s:" ",inSelectionStart:false})}var filteredTokens=[];var selectionStartIndex=-1;for(var i=0,ntokens=tokens.length;i<ntokens;i++){var token=tokens[i];var s=token.s;if(options.trim||i<ntokens-1){s=$.trim(s)}if(s!==""){if(token.inSelectionStart){selectionStartIndex=filteredTokens.length}filteredTokens.push(s)}}filteredTokens.selectionStartIndex=selectionStartIndex;return filteredTokens};morpheus.Util.showDialog=function($el,title,options){var $dialog=$("<div></div>");$el.appendTo($dialog);$dialog.appendTo($(document.body));if(!options){options={}}$dialog.dialog({width:670,height:590,title:title,close:function(event,ui){$dialog.remove();if(options.close){options.close()}}})};morpheus.Util.sheetToArray=function(sheet,delim){var r=XLSX.utils.decode_range(sheet["!ref"]);var rows=[];var colors=[];var header=[];for(var C=r.s.c;C<=r.e.c;++C){var val=sheet[XLSX.utils.encode_cell({c:C,r:r.s.r})];var txt=String(XLSX.utils.format_cell(val));header.push(txt)}for(var R=r.s.r;R<=r.e.r;++R){var row=[];var isRowEmpty=true;for(var C=r.s.c;C<=r.e.c;++C){var val=sheet[XLSX.utils.encode_cell({c:C,r:R})];if(!val){row.push("");continue}isRowEmpty=false;var txt=String(XLSX.utils.format_cell(val));if(val.s!=null&&val.s.fgColor!=null){var color="#"+val.s.fgColor.rgb;colors.push({header:header[row.length],color:color,value:txt})}row.push(txt)}if(!isRowEmpty){rows.push(delim?row.join(delim):row)}}rows.colors=colors;return rows};morpheus.Util.linesToObjects=function(lines){var header=lines[0];var array=[];var nfields=header.length;for(var i=1,length=lines.length;i<length;i++){var line=lines[i];var obj={};for(var f=0;f<nfields;f++){var value=line[f];var field=header[f];obj[field]=value}array.push(obj)}return array};morpheus.Util.xlsxTo2dArray=function(options,callback){var workbook=XLSX.read(options.data,{type:"binary",cellFormula:false,cellHTML:false,cellStyles:true});var sheetNames=workbook.SheetNames;if(options.prompt&&sheetNames.length>1){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"sheet",type:"bootstrap-select",options:sheetNames,required:true,style:"max-width:100px;"});morpheus.FormBuilder.showInModal({title:"Choose Sheet",html:formBuilder.$form,focus:document.activeElement,onClose:function(){var worksheet=workbook.Sheets[formBuilder.getValue("sheet")];var lines=morpheus.Util.sheetToArray(worksheet);callback(null,lines)}})}else{var worksheet=workbook.Sheets[sheetNames[0]];var lines=morpheus.Util.sheetToArray(worksheet);callback(null,lines)}};morpheus.Util.xlsxTo1dArray=function(options,callback){var workbook=XLSX.read(options.data,{type:"binary",cellFormula:false,cellHTML:false,cellStyles:true});var sheetNames=workbook.SheetNames;if(options.prompt&&sheetNames.length>1){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"sheet",type:"bootstrap-select",options:sheetNames,required:true,style:"max-width:100px;"});morpheus.FormBuilder.showOkCancel({title:"Choose Sheet",cancel:false,focus:document.activeElement,content:formBuilder.$form,okCallback:function(){var worksheet=workbook.Sheets[formBuilder.getValue("sheet")];callback(null,morpheus.Util.sheetToArray(worksheet,"\t"))}})}else{var worksheet=workbook.Sheets[sheetNames[0]];callback(null,morpheus.Util.sheetToArray(worksheet,"\t"))}};morpheus.Util.getText=function(fileOrUrl){var deferred=$.Deferred();if(morpheus.Util.isString(fileOrUrl)){fetch(fileOrUrl).then(function(response){if(response.ok){return response.text()}else{deferred.reject(response.status+" "+response.statusText)}}).then(function(text){deferred.resolve(text)}).catch(function(err){deferred.reject(err)})}else if(morpheus.Util.isFile(fileOrUrl)){var reader=new FileReader;reader.onload=function(event){deferred.resolve(event.target.result)};reader.readAsText(fileOrUrl)}else{deferred.resolve(fileOrUrl)}return deferred.promise()};morpheus.Util.createOptions=function(values,none){var html=[];if(none){html.push('<option value="">(None)</option>')}_.each(values,function(val){html.push('<option value="');html.push(val);html.push('">');html.push(val);html.push("</option>")});return html.join("")};morpheus.Util.rankIndexArray=function(index){var rank=[];var n=index.length;for(var j=0;j<n;j++){rank[index[j]]=j+1}return rank};morpheus.Util.indexSort=function(array,ascending){var pairs=[];for(var i=0,length=array.length;i<length;i++){pairs.push({value:array[i],index:i})}return morpheus.Util.indexSortPairs(pairs,ascending)};morpheus.Util.indexSortPairs=function(array,ascending){if(ascending){array.sort(function(a,b){return a.value<b.value?-1:a.value===b.value?a.index<b.index?-1:1:1})}else{array.sort(function(a,b){return a.value<b.value?1:a.value===b.value?a.index<b.index?1:-1:-1})}var indices=[];array.forEach(function(item){indices.push(item.index)});return indices};morpheus.Util.arrayEquals=function(array1,array2,comparator){if(array1==array2){return true}if(array1==null||array2==null){return false}if(!comparator){comparator=function(a,b){return a===b}}var length=array1.length;if(array2.length!==length){return false}for(var i=0;i<length;i++){if(!comparator(array1[i],array2[i])){return false}}return true};morpheus.Util._intFormat=typeof d3!=="undefined"?d3.format(",i"):function(d){return""+Math.round(d)};morpheus.Util.intFormat=function(n){return morpheus.Util._intFormat(n)};morpheus.Util._nf=typeof d3!=="undefined"?d3.format(".2f"):function(d){return""+d};morpheus.Util.getNumberFormatPatternFractionDigits=function(pattern){return parseInt(pattern.substring(1,pattern.length-1))||0};morpheus.Util.nf=function(n){return morpheus.Util._nf(n)};morpheus.Util.createNumberFormat=function(pattern){var f=d3.format(pattern);f.toJSON=function(){return{pattern:pattern}};return f};morpheus.Util.wrapNumber=function(value,object){var n=new Number(value);n.toObject=function(){return object};return n};morpheus.Util.toString=function(value){if(value==null){return""}else if(_.isNumber(value)){return morpheus.Util.nf(value)}else if(morpheus.Util.isArray(value)){return morpheus.Util.arrayToString(value,", ")}return""+value};morpheus.Util.arrayToString=function(value,sep){var s=[];for(var i=0,length=value.length;i<length;i++){var val_i=value[i];if(_.isNumber(val_i)){s.push(morpheus.Util.nf(val_i))}else{s.push(""+val_i)}}return s.join(sep)};morpheus.Util.removeTrailingZerosInFraction=function(str){var index=str.lastIndexOf(".");if(index!==-1){var len=str.length;var zeros=len;for(var i=len-1;i>index;i--,zeros--){if(str[i]!="0"){break}}if(zeros===index+1){return str.substring(0,index)}if(zeros<len){return str.substring(0,index)+str.substring(index,zeros)}}return str};morpheus.Util.s=function(n){return n===1?"":"s"};morpheus.Util.create2dArray=function(rows,columns){var array2d=[];for(var i=0;i<rows;i++){var array=[];for(var j=0;j<columns;j++){array[j]=NaN}array2d.push(array)}return array2d};morpheus.Util.escapeRegex=function(value){return value.replace(/[*]/g,".*").replace(/[-[\]{}()+?,\\^$|#\s]/g,"\\$&")};morpheus.Util.createSearchPredicates=function(options){options=$.extend({},{validateFieldNames:true,caseSensitive:true},options);var tokens=options.tokens;if(tokens==null){return[]}var availableFields=options.fields;if(!options.caseSensitive&&availableFields!=null){for(var i=0;i<availableFields.length;i++){availableFields[i]=availableFields[i].toLowerCase()}}var validateFieldNames=options.validateFieldNames;var fieldSearchEnabled=!validateFieldNames||availableFields!=null&&availableFields.length>0;var fieldRegExp=/\\:/g;var predicates=[];var defaultIsExactMatch=options.defaultMatchMode==="exact";tokens.forEach(function(token){var isNot=false;if(token[0]==="-"){token=token.substring(1);isNot=true}var field=null;var semi=token.indexOf(":");if(semi>0){if(!fieldSearchEnabled||token.charCodeAt(semi-1)===92){token=token.replace(fieldRegExp,":")}else{var possibleToken=$.trim(token.substring(semi+1));var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[possibleField.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}else if(possibleField.length>0&&possibleField[0]==='"'&&possibleToken[possibleToken.length-1]==='"'&&possibleToken[0]!=='"'){possibleField=possibleField.substring(1,possibleField.length);possibleToken='"'+possibleToken}if(!validateFieldNames||availableFields.indexOf(options.caseSensitive?possibleField:possibleField.toLowerCase())!==-1){token=possibleToken;field=possibleField}}}var predicate;var rangeIndex=-1;var rangeToken=null;var rangeIndicators=["..",">=",">","<=","<","="];for(var i=0;i<rangeIndicators.length;i++){rangeIndex=token.indexOf(rangeIndicators[i]);if(rangeIndex!==-1){rangeToken=rangeIndicators[i];break}}if(rangeIndex!==-1){if(rangeToken===".."){var start=parseFloat(token.substring(0,rangeIndex));var end=parseFloat(token.substring(rangeIndex+2));if(!isNaN(start)&&!isNaN(end)){predicate=new morpheus.Util.NumberRangePredicate(field,start,end)}}else if(rangeToken===">"){var val=parseFloat(token.substring(rangeIndex+1));if(!isNaN(val)){predicate=new morpheus.Util.GreaterThanPredicate(field,val)}}else if(rangeToken===">="){var val=parseFloat(token.substring(rangeIndex+2));if(!isNaN(val)){predicate=new morpheus.Util.GreaterThanOrEqualPredicate(field,val)}}else if(rangeToken==="<"){var val=parseFloat(token.substring(rangeIndex+1));if(!isNaN(val)){predicate=new morpheus.Util.LessThanPredicate(field,val)}}else if(rangeToken==="<="){var val=parseFloat(token.substring(rangeIndex+2));if(!isNaN(val)){predicate=new morpheus.Util.LessThanOrEqualPredicate(field,val)}}else if(rangeToken==="="){var val=parseFloat(token.substring(rangeIndex+1));predicate=new morpheus.Util.EqualsPredicate(field,val)}else{console.log("Unknown range token:"+rangeToken)}}else if(token[0]==='"'&&token[token.length-1]==='"'){token=token.substring(1,token.length-1);predicate=new morpheus.Util.ExactTermPredicate(field,token)}else if(token[0]==="("&&token[token.length-1]===")"){token=token.substring(1,token.length-1);var values=morpheus.Util.getAutocompleteTokens(token);if(values.length>0){predicate=new morpheus.Util.ExactTermsPredicate(field,values.map(function(val){if(val[0]==='"'&&val[val.length-1]==='"'){val=val.substring(1,val.length-1)}return val.toLowerCase()}))}}else if(token.indexOf("*")!==-1){predicate=new morpheus.Util.RegexPredicate(field,token)}else{predicate=defaultIsExactMatch?new morpheus.Util.ExactTermPredicate(field,token):new morpheus.Util.RegexPredicate(field,token)}if(predicate!=null){predicates.push(isNot?new morpheus.Util.NotPredicate(predicate):predicate)}});return predicates};morpheus.Util.createRegExpStringToMatchText=function(text){var tokens=morpheus.Util.getAutocompleteTokens(text);if(tokens.length===0){return null}var regex=[];_.each(tokens,function(token){if(token[0]==='"'&&token[token.length-1]==='"'){token=token.substring(1,token.length-1);regex.push("^"+morpheus.Util.escapeRegex(token)+"$")}else{regex.push(morpheus.Util.escapeRegex(token))}});return"("+regex.join("|")+")"};morpheus.Util.createRegExpToMatchText=function(text){var s=morpheus.Util.createRegExpStringToMatchText(text);return s==null?null:new RegExp(s,"i")};morpheus.Util.reorderArray=function(array,index){var newArray=[];for(var i=0;i<index.length;i++){newArray.push(array[index[i]])}return newArray};morpheus.Util.getSearchString=function(){var s=window.location.search;return s.length>1?s.substring(1):""};morpheus.Util.splitLines=function(lines){var tab=/\t/;var tokens=[];for(var i=0,nlines=lines.length;i<nlines;i++){var line=lines[i];if(line===""){continue}tokens.push(line.split(tab))}return tokens};morpheus.Util.readLines=function(fileOrUrl,interactive){var isFile=morpheus.Util.isFile(fileOrUrl);var isString=morpheus.Util.isString(fileOrUrl);var name=morpheus.Util.getFileName(fileOrUrl);var ext=morpheus.Util.getExtension(name);var deferred=$.Deferred();if(isString){if(ext==="xlsx"){var fetchOptions={};if(fileOrUrl.headers){fetchOptions.headers=new Headers;for(var header in fileOrUrl.headers){fetchOptions.headers.append(header,fileOrUrl.headers[header])}}fetch(fileOrUrl,fetchOptions).then(function(response){if(response.ok){return response.arrayBuffer()}else{deferred.reject(response)}}).then(function(arrayBuffer){if(arrayBuffer){var data=new Uint8Array(arrayBuffer);var arr=[];for(var i=0;i!=data.length;++i){arr[i]=String.fromCharCode(data[i])}var bstr=arr.join("");morpheus.Util.xlsxTo1dArray({data:bstr,prompt:interactive},function(err,lines){deferred.resolve(lines)})}else{deferred.reject()}})}else{fetch(fileOrUrl,fetchOptions).then(function(response){if(response.ok){return response.text()}else{deferred.reject()}}).then(function(text){deferred.resolve(morpheus.Util.splitOnNewLine(text))}).catch(function(err){deferred.reject(err)})}}else if(isFile){var reader=new FileReader;reader.onerror=function(){console.log("Unable to read file");deferred.reject("Unable to read file")};reader.onload=function(event){if(ext==="xlsx"||ext==="xls"){var data=new Uint8Array(event.target.result);var arr=[];for(var i=0;i!=data.length;++i){arr[i]=String.fromCharCode(data[i])}var bstr=arr.join("");morpheus.Util.xlsxTo1dArray({data:bstr,prompt:interactive},function(err,lines){deferred.resolve(lines)})}else{deferred.resolve(morpheus.Util.splitOnNewLine(event.target.result))}};if(ext==="xlsx"||ext==="xls"){reader.readAsArrayBuffer(fileOrUrl)}else{reader.readAsText(fileOrUrl)}}else{deferred.resolve(fileOrUrl)}return deferred};morpheus.Util.createValueToIndices=function(array,field){var map=new morpheus.Map;_.each(array,function(item){var key=item[field];var values=map.get(key);if(values===undefined){values=[];map.set(key,values)}values.push(item)});return map};morpheus.Util.createMorpheusHeader=function(){var html=[];html.push('<div style="display:inline-block;'+' vertical-align:top;font-size:24px;font-family:sans-serif;">');html.push("<span>M</span>");html.push("<span>O</span>");html.push("<span>R</span>");html.push("<span>P</span>");html.push("<span>H</span>");html.push("<span>E</span>");html.push("<span>U</span>");html.push("<span>S</span>");html.push("</span>");html.push("</div>");var $div=$(html.join(""));var colorScale=d3.scale.linear().domain([0,4,7]).range(["#ca0020","#999999","#0571b0"]).clamp(true);var brands=$div.find("span");var index=0;var step=function(){brands[index].style.color=colorScale(index);index++;if(index<brands.length){setTimeout(step,200)}};setTimeout(step,500);return $div};morpheus.Util.createLoadingEl=function(){return $('<div style="overflow:hidden;text-align:center;"><i class="fa fa-spinner fa-spin fa-3x"></i><span style="padding-left:4px;vertical-align:middle;font-weight:bold;">Loading...</span></div>')};morpheus.Util.splitOnNewLine=function(text,commentChar){var commentCharCode=commentChar!==undefined?commentChar.charCodeAt(0):undefined;var lines=text.split(/\n/);if(lines.length===1){var tmp=text.split(/\r/);if(tmp.length>1){lines=tmp}}var rows=[];var rtrim=/\s+$/;for(var i=0,nlines=lines.length;i<nlines;i++){var line=lines[i].replace(rtrim,"");if(line!==""){if(commentCharCode!==undefined){if(line.charCodeAt(0)!==commentCharCode){rows.push(line)}}else{rows.push(line)}}}return rows};morpheus.Util.ContainsPredicate=function(field,text){this.field=field;text=text.toLowerCase();this.text=text};morpheus.Util.ContainsPredicate.prototype={accept:function(value){if(value==null){return false}value=(""+value).toLowerCase();return value.indexOf(this.text)!==-1},getField:function(){return this.field},getText:function(){return this.text},isNumber:function(){return false},toString:function(){return"ContainsPredicate "+this.field+":"+this.text}};morpheus.Util.ExactTermsPredicate=function(field,values){this.field=field;this.values=new morpheus.Set;for(var i=0,nvalues=values.length;i<nvalues;i++){this.values.add(values[i])}};morpheus.Util.ExactTermsPredicate.prototype={accept:function(value){if(value==null){return false}value=(""+value).toLowerCase();return this.values.has(value)},getField:function(){return this.field},getValues:function(){return this.values},isNumber:function(){return false},toString:function(){return"ExactTermsPredicate "+this.field+":"+this.text}};morpheus.Util.ExactTermPredicate=function(field,term){this.field=field;term=term.toLowerCase();this.text=term};morpheus.Util.ExactTermPredicate.prototype={accept:function(value){if(value==null){return false}value=(""+value).toLowerCase();return value===this.text},getField:function(){return this.field},getText:function(){return this.text},isNumber:function(){return false},toString:function(){return"ExactTermPredicate "+this.field+":"+this.text}};morpheus.Util.RegexPredicate=function(field,text){this.field=field;this.text=text;this.regex=new RegExp(morpheus.Util.escapeRegex(text),"i")};morpheus.Util.RegexPredicate.prototype={accept:function(value){return this.regex.test(""+value)},getField:function(){return this.field},getText:function(){return this.text},isNumber:function(){return false},toString:function(){return"RegexPredicate "+this.field+":"+this.regex}};morpheus.Util.NumberRangePredicate=function(field,min,max){this.field=field;this.min=min;this.max=max};morpheus.Util.NumberRangePredicate.prototype={accept:function(value){return value>=this.min&&value<=this.max},getField:function(){return this.field},isNumber:function(){return true},toString:function(){return"NumberRangePredicate "+this.field+":"+this.min+"..."+this.max}};morpheus.Util.GreaterThanPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.GreaterThanPredicate.prototype={accept:function(value){return value>this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.GreaterThanOrEqualPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.GreaterThanOrEqualPredicate.prototype={accept:function(value){return value>=this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.LessThanPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.LessThanPredicate.prototype={accept:function(value){return value<this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.LessThanOrEqualPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.LessThanOrEqualPredicate.prototype={accept:function(value){return value<=this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.EqualsPredicate=function(field,val){this.field=field;this.val=val};morpheus.Util.EqualsPredicate.prototype={accept:function(value){return value===this.val},getField:function(){return this.field},isNumber:function(){return true}};morpheus.Util.NotPredicate=function(p){this.p=p};morpheus.Util.NotPredicate.prototype={accept:function(value){return!this.p.accept(value)},getField:function(){return this.p.getField()},isNumber:function(){return this.p.isNumber()},toString:function(){return"NotPredicate "+this.p}};morpheus.Events=function(){};morpheus.Events.prototype={on:function(evtStr,handler){if(!handler){throw Error("Handler not specified")}if(!this.eventListeners){this.eventListeners={}}var events=evtStr.split(" "),len=events.length,n,event,parts,baseEvent,name;for(n=0;n<len;n++){event=events[n];parts=event.split(".");baseEvent=parts[0];name=parts[1]||"";if(!this.eventListeners[baseEvent]){this.eventListeners[baseEvent]=[]}this.eventListeners[baseEvent].push({name:name,handler:handler})}return this},getListeners:function(){if(!this.eventListeners){this.eventListeners={}}return this.eventListeners},setListeners:function(eventListeners){this.eventListeners=eventListeners},trigger:function(eventType,evt){if(!this.eventListeners){this.eventListeners={}}if(!evt){evt={}}evt.type=eventType;if(!evt.source){evt.source=this}var events=this.eventListeners[eventType];if(events){var len=events.length;for(var i=0;i<len;i++){events[i].handler.apply(this,[evt])}}return this},off:function(evtStr,handler){if(!this.eventListeners){this.eventListeners={}}var events=(evtStr||"").split(" "),len=events.length,n,t,event,parts,baseEvent,name;if(!evtStr){for(t in this.eventListeners){this._off(t,null,handler)}}for(n=0;n<len;n++){event=events[n];parts=event.split(".");baseEvent=parts[0];name=parts[1];if(baseEvent){if(this.eventListeners[baseEvent]){this._off(baseEvent,name,handler)}}else{for(t in this.eventListeners){this._off(t,name,handler)}}}return this},_off:function(type,name,handler){var evtListeners=this.eventListeners[type],i,evtName;for(i=0;i<evtListeners.length;i++){evtName=evtListeners[i].name;if((!name||evtName===name)&&(handler==null||handler==evtListeners[i].handler)){evtListeners.splice(i,1);if(evtListeners.length===0){delete this.eventListeners[type];break}i--}}}};morpheus.Identifier=function(array){this.array=array};morpheus.Identifier.prototype={toString:function(){return this.array.join(",")},equals:function(otherId){var other=otherId.getArray();var length=this.array.length;if(other.length!==length){return false}for(var i=0;i<length;i++){if(this.array[i]!==other[i]){return false}}return true},getArray:function(){return this.array}};morpheus.Map=function(){this.map={};this.n=0};morpheus.Map.prototype={toJSON:function(){var json={};this.forEach(function(value,key){json[key]=value});return json},toString:function(){var s=[];this.forEach(function(value,key){if(s.length>0){s.push(", ")}s.push(key);s.push("=");s.push(value)});return s.join("")},keys:function(){var keys=[];for(var key in this.map){var pair=this.map[key];keys.push(pair.key)}return keys},size:function(){return this.n},equals:function(m){if(m.size()!==this.size()){return false}var ret=true;try{this.forEach(function(value,key){if(value!==m.get(key)){ret=false;throw"break"}})}catch(e){}return ret},setAll:function(map){var _this=this;map.forEach(function(value,key){_this.set(key,value)})},set:function(key,value){var skey="\0"+key;var previous=this.map[skey];if(previous===undefined){this.n++}this.map[skey]={key:key,value:value}},forEach:function(callback){for(var key in this.map){var pair=this.map[key];callback(pair.value,pair.key)}},entries:function(){var array=[];this.forEach(function(value,key){array.push({value:value,key:key})});return array},values:function(){var values=[];for(var key in this.map){var pair=this.map[key];values.push(pair.value)}return values},get:function(key){var skey="\0"+key;var pair=this.map[skey];return pair!==undefined?pair.value:undefined},clear:function(){this.map={};this.n=0},remove:function(key){var skey="\0"+key;var pair=this.map[skey];if(pair!==undefined){delete this.map[skey];this.n--;return pair.value}},has:function(key){var skey="\0"+key;return this.map[skey]!==undefined}};morpheus.Map.fromJSON=function(json){var map=new morpheus.Map;for(var key in json){map.set(key,json[key])}return map};morpheus.Set=function(){this._map=new morpheus.Map};morpheus.Set.prototype={toJSON:function(){var json=[];this.forEach(function(value){json.push(value)});return json},toString:function(){var s=[];this.forEach(function(key){if(s.length>0){s.push(", ")}s.push(key)});return s.join("")},size:function(){return this._map.size()},equals:function(m){return this._map.equals(m)},forEach:function(callback){this._map.forEach(function(value,key){callback(key)})},add:function(value){this._map.set(value,true)},values:function(){var values=[];this._map.forEach(function(value,key){values.push(key)});return values},clear:function(){this._map.clear()},remove:function(key){this._map.remove(key)},has:function(key){return this._map.has(key)}};morpheus.Set.fromJSON=function(json){var set=new morpheus.Set;for(var i=0,length=json.length;i<length;i++){set.add(json[i])}return set};morpheus.ArrayBufferReader=function(buffer){this.buffer=buffer;this.bufferLength=buffer.length;this.index=0;this.decoder=morpheus.Util.createTextDecoder()};morpheus.ArrayBufferReader.prototype={readLine:function(){var index=this.index;var bufferLength=this.bufferLength;if(index>=bufferLength){return null}var buffer=this.buffer;var start=index;var end=start;for(;index<bufferLength;index++){var c=buffer[index];if(c===10||c===13){end=index;if(index!==bufferLength-1&&buffer[index+1]===10){index++}index++;break}}this.index=index;if(start===end&&index===bufferLength){return this.decoder(this.buffer,start,bufferLength)}return this.decoder(this.buffer,start,end)}};morpheus.ArrayBufferReader.getArrayBuffer=function(fileOrUrl,callback){var isString=typeof fileOrUrl==="string"||fileOrUrl instanceof String;if(isString){var fetchOptions={};if(fileOrUrl.headers){fetchOptions.headers=new Headers;for(var header in fileOrUrl.headers){fetchOptions.headers.append(header,fileOrUrl.headers[header])}}fetch(fileOrUrl,fetchOptions).then(function(response){if(response.ok){return response.arrayBuffer()}else{callback(new Error(fileOrUrl+" status: "+response.status))}}).then(function(buf){callback(null,buf)}).catch(function(error){console.log("Fetch error",error);callback(error)})}else{var reader=new FileReader;reader.onload=function(event){callback(null,event.target.result)};reader.onerror=function(event){callback(event)};reader.readAsArrayBuffer(fileOrUrl)}};morpheus.Array2dReaderInteractive=function(){};morpheus.Array2dReaderInteractive.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));var html=[];html.push("<div>");html.push("<label>Click the table cell containing the first data row and column.</label>");html.push('<div class="checkbox"> <label> <input name="transpose" type="checkbox">'+" Tranpose </label>"+" </div>");html.push("<div"+' style="display:inline-block;width:10px;height:10px;background-color:#b3cde3;"></div><span> Data Matrix</span>');html.push("<br /><div"+' style="display:inline-block;width:10px;height:10px;background-color:#fbb4ae;"></div><span> Column'+" Annotations</span>");html.push("<br /><div"+' style="display:inline-block;'+' width:10px;height:10px;background-color:#ccebc5;"></div><span> Row'+" Annotations</span>");html.push('<div class="slick-bordered-table" style="width:550px;height:300px;"></div>');html.push("</div>");var $el=$(html.join(""));morpheus.Util.readLines(fileOrUrl,true).done(function(lines){var tab=/\t/;for(var i=0,nrows=lines.length;i<nrows;i++){lines[i]=lines[i].split(tab)}var grid;var columns=[];for(var j=0,ncols=lines[0].length;j<ncols;j++){columns.push({id:j,field:j})}var dataRowStart=1;var dataColumnStart=1;var _lines=lines;var grid=new Slick.Grid($el.find(".slick-bordered-table")[0],lines,columns,{enableCellNavigation:true,headerRowHeight:0,showHeaderRow:false,multiColumnSort:false,multiSelect:false,topPanelHeight:0,enableColumnReorder:false,enableTextSelectionOnCells:true,forceFitColumns:false,defaultFormatter:function(row,cell,value,columnDef,dataContext){var color="white";if(cell>=dataColumnStart&&row>=dataRowStart){color="#b3cde3"}else if(row<=dataRowStart-1&&cell>=dataColumnStart){color="#fbb4ae"}else if(cell<dataColumnStart&&row>=dataRowStart){color="#ccebc5"}var html=['<div style="width:100%;height:100%;background-color:'+color+'">'];if(_.isNumber(value)){html.push(morpheus.Util.nf(value))}else if(morpheus.Util.isArray(value)){var s=[];for(var i=0,length=value.length;i<length;i++){if(i>0){s.push(", ")}var val=value[i];s.push(value[i])}html.push(s.join(""))}else{html.push(value)}html.push("</div>");return html.join("")}});var transposedLines;var transposedColumns;$el.find("[name=transpose]").on("click",function(e){if($(this).prop("checked")){if(transposedLines==null){transposedLines=[];for(var j=0,ncols=lines[0].length;j<ncols;j++){var row=[];transposedLines.push(row);for(var i=0,nrows=lines.length;i<nrows;i++){row.push(lines[i][j])}}transposedColumns=[];for(var j=0,ncols=transposedLines[0].length;j<ncols;j++){transposedColumns.push({id:j,field:j})}}lines=transposedLines;grid.setData(transposedLines);grid.setColumns(transposedColumns);grid.resizeCanvas();grid.invalidate()}else{grid.setData(_lines);grid.setColumns(columns);grid.resizeCanvas();grid.invalidate();lines=_lines}});grid.onClick.subscribe(function(e,args){dataRowStart=args.row;dataColumnStart=args.cell;grid.invalidate()});$el.find(".slick-header").remove();var footer=[];footer.push('<button name="ok" type="button" class="btn btn-default">OK</button>');footer.push('<button name="cancel" type="button" data-dismiss="modal" class="btn btn-default">Cancel</button>');var $footer=$(footer.join(""));morpheus.FormBuilder.showOkCancel({title:"Open",content:$el,close:false,focus:document.activeElement,cancelCallback:function(){callback(null)},okCallback:function(){_this._read(name,lines,dataColumnStart,dataRowStart,callback)}});grid.resizeCanvas()}).fail(function(err){callback(err)})},_read:function(datasetName,lines,dataColumnStart,dataRowStart,cb){var columnCount=lines[0].length;var columns=columnCount-dataColumnStart;var rows=lines.length-dataRowStart;var dataset=new morpheus.Dataset({name:datasetName,rows:rows,columns:columns,dataType:"Float32"});if(dataColumnStart>0){for(var i=0;i<dataRowStart;i++){var name=lines[i][0];if(name==null||name===""||name==="na"){name="id"}var unique=1;while(dataset.getColumnMetadata().getByName(name)!=null){name=name+"-"+unique;unique++}var v=dataset.getColumnMetadata().add(name);var nonEmpty=false;for(var j=0;j<columns;j++){var s=lines[i][j+dataColumnStart];if(s!=null&&s!==""){nonEmpty=true;v.setValue(j,s)}}if(!nonEmpty){dataset.getColumnMetadata().remove(morpheus.MetadataUtil.indexOf(dataset.getColumnMetadata(),v.getName()))}}}if(dataRowStart>0){for(var j=0;j<dataColumnStart;j++){var name=lines[0][j];if(name==null||name===""){name="id"}var unique=1;while(dataset.getRowMetadata().get(name)!=null){name=name+"-"+unique;unique++}dataset.getRowMetadata().add(name)}}for(var i=0;i<rows;i++){for(var j=0,k=0;k<dataset.getRowMetadata().getMetadataCount();j++,k++){var metaDataValue=lines[i+dataRowStart][j];dataset.getRowMetadata().get(j).setValue(i,metaDataValue)}}for(var i=0;i<rows;i++){for(var j=0;j<columns;j++){var s=lines[i+dataRowStart][j+dataColumnStart];dataset.setValue(i,j,parseFloat(s))}}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);cb(null,dataset)}};morpheus.BufferedReader=function(reader,callback,doneCallback){var textDecoder=morpheus.Util.createTextDecoder();var skipLF=false;var text="";reader.read().then(function processResult(result){text+=result.done?"":textDecoder(result.value,0,result.value.length);var start=0;for(var i=0,length=text.length;i<length;i++){var c=text[i];if(skipLF&&c==="\n"){start++;skipLF=false}else if(c==="\n"||c==="\r"){skipLF=c==="\r";var s=morpheus.Util.copyString(text.substring(start,i));callback(s);start=i+1}else{skipLF=false}}text=start<text.length?text.substring(start):"";if(!result.done){return reader.read().then(processResult)}else{if(text!==""&&text!=="\r"){callback(text)}doneCallback()}})};morpheus.BufferedReader.parse=function(url,options){var delim=options.delimiter;var regex=new RegExp(delim);var handleTokens=options.handleTokens;var complete=options.complete;var fetchOptions={};if(url.headers){fetchOptions.headers=new Headers;for(var header in url.headers){fetchOptions.headers.append(header,url.headers[header])}}fetch(url,fetchOptions).then(function(response){if(response.ok){var reader=response.body.getReader();new morpheus.BufferedReader(reader,function(line){handleTokens(line.split(regex))},function(){complete()})}else{options.error("Network error")}}).catch(function(error){options.error(error)})};morpheus.ClsReader=function(){};morpheus.ClsReader.prototype={read:function(lines){var regex=/[ ,]+/;var header=lines[0].split(regex);if(header.length<3){throw new Error("Header line needs three numbers")}var headerNumbers=[];try{for(var i=0;i<3;i++){headerNumbers[i]=parseInt($.trim(header[i]))}}catch(e){throw new Error("Header line element "+i+" is not a number")}if(headerNumbers[0]<=0){throw new Error("Header line missing first number, number of data points")}if(headerNumbers[1]<=0){throw new Error("Header line missing second number, number of classes")}var numClasses=headerNumbers[1];var numItems=headerNumbers[0];var classDefinitionLine=lines[1];classDefinitionLine=classDefinitionLine.substring(classDefinitionLine.indexOf("#")+1);var classNames=$.trim(classDefinitionLine).split(regex);if(classNames.length<numClasses){throw new Error("First line specifies "+numClasses+" classes, but found "+classNames.length+".")}var dataLine=lines[2];var assignments=dataLine.split(regex);for(var i=0;i<assignments.length;i++){var assignment=$.trim(assignments[i]);var index=parseInt(assignment);var tmp=classNames[index];if(tmp!==undefined){assignments[i]=tmp}}return assignments}};morpheus.ClsWriter=function(){};morpheus.ClsWriter.prototype={write:function(vector){var pw=[];var size=vector.size();pw.push(size);pw.push(" ");var set=morpheus.VectorUtil.getSet(vector);pw.push(set.size());pw.push(" ");pw.push("1\n");pw.push("#");var valueToIndex=new morpheus.Map;var index=0;set.forEach(function(name){pw.push(" ");pw.push(name);valueToIndex.set(name,index++)});pw.push("\n");for(var i=0;i<size;i++){if(i>0){pw.push(" ")}pw.push(valueToIndex.get(vector.getValue(i)))}pw.push("\n");return pw.join("")}};morpheus.GctReader=function(){};morpheus.GctReader.prototype={getFormatName:function(){return"gct"},read:function(fileOrUrl,callback){var _this=this;if(morpheus.Util.isFile(fileOrUrl)){this._readChunking(fileOrUrl,callback,false)}else{if(morpheus.Util.isFetchStreamingSupported()){this._readChunking(fileOrUrl,callback,true)}else{this._readNoChunking(fileOrUrl,callback)}}},_readChunking:function(fileOrUrl,callback,useFetch){var _this=this;var lineNumber=0;var version;var numRowAnnotations=1;var numColumnAnnotations=0;var nrows=-1;var ncols=-1;var version=2;var rowMetadataNames=[];var columnMetadataNames=[];var rowMetadata=[[]];var columnMetadata=[[]];var dataColumnStart;var matrix=[];var dataMatrixLineNumberStart;var columnIdFieldName="id";var rowIdFieldName="id";var columnNamesArray;var handleTokens=function(tokens){if(lineNumber===0){var text=tokens[0].trim();if("#1.2"===text){version=2}else if("#1.3"===text){version=3}else{console.log("Unknown version: assuming version 2")}}else if(lineNumber===1){var dimensions=tokens;if(version===3){if(dimensions.length>=4){nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);numRowAnnotations=parseInt(dimensions[2]);numColumnAnnotations=parseInt(dimensions[3])}else{numRowAnnotations=parseInt(dimensions[0]);numColumnAnnotations=parseInt(dimensions[1])}}else{nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);if(nrows<=0||ncols<=0){callback("Number of rows and columns must be greater than 0.")}}dataColumnStart=numRowAnnotations+1}else if(lineNumber===2){columnNamesArray=tokens;for(var i=0;i<columnNamesArray.length;i++){columnNamesArray[i]=morpheus.Util.copyString(columnNamesArray[i])}if(ncols===-1){ncols=columnNamesArray.length-numRowAnnotations-1}if(version==2){var expectedColumns=ncols+2;if(columnNamesArray.length!==expectedColumns){if(columnNamesArray.length>expectedColumns){var skip=columnNamesArray.length-1;for(var i=columnNamesArray.length-1;i>=0;i--,skip--){if(columnNamesArray[i]!==""){break}}if(skip!==columnNamesArray.length-1){columnNamesArray=columnNamesArray.slice(0,skip+1)}}if(columnNamesArray.length!==expectedColumns){return callback("Expected "+(expectedColumns-2)+" column names, but read "+(columnNamesArray.length-2)+" column names.")}}}var name=columnNamesArray[0];var slashIndex=name.lastIndexOf("/");if(slashIndex!=-1&&slashIndex<name.length-1){rowIdFieldName=name.substring(0,slashIndex);columnIdFieldName=name.substring(slashIndex+1)}rowMetadataNames.push(rowIdFieldName);columnMetadataNames.push(columnIdFieldName);for(var j=0;j<ncols;j++){var index=j+numRowAnnotations+1;var columnName=index<columnNamesArray.length?columnNamesArray[index]:null;columnMetadata[0].push(morpheus.Util.copyString(columnName))}for(var j=0;j<numRowAnnotations;j++){var rowMetadataName=""===columnNamesArray[1]?"description":columnNamesArray[j+1];rowMetadataNames.push(rowMetadataName);rowMetadata.push([])}dataMatrixLineNumberStart=3+numColumnAnnotations}else{if(lineNumber<dataMatrixLineNumberStart){var metadataName=morpheus.Util.copyString(tokens[0]);var v=[];columnMetadata.push(v);columnMetadataNames.push(metadataName);for(var j=0;j<ncols;j++){v.push(morpheus.Util.copyString(tokens[j+dataColumnStart]))}}else{if(tokens[0]!==""){var array=new Float32Array(ncols);matrix.push(array);for(var rowAnnotationIndex=0;rowAnnotationIndex<=numRowAnnotations;rowAnnotationIndex++){var rowMetadataValue=tokens[rowAnnotationIndex];rowMetadata[rowAnnotationIndex].push(morpheus.Util.copyString(rowMetadataValue))}for(var columnIndex=0;columnIndex<ncols;columnIndex++){var token=tokens[columnIndex+dataColumnStart];array[columnIndex]=parseFloat(token)}}}}lineNumber++};(useFetch?morpheus.BufferedReader:Papa).parse(fileOrUrl,{delimiter:"\t",newline:"",header:false,dynamicTyping:false,preview:0,encoding:"",worker:false,comments:false,handleTokens:handleTokens,step:function(result){handleTokens(result.data[0])},complete:function(){var dataset=new morpheus.Dataset({name:morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl)),rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});for(var i=0;i<rowMetadataNames.length;i++){dataset.getRowMetadata().add(rowMetadataNames[i]).array=rowMetadata[i]}for(var i=0;i<columnMetadataNames.length;i++){dataset.getColumnMetadata().add(columnMetadataNames[i]).array=columnMetadata[i]}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);callback(null,dataset)},error:function(err){callback(err)},download:!morpheus.Util.isFile(fileOrUrl),skipEmptyLines:false,chunk:undefined,fastMode:true,beforeFirstChunk:undefined,withCredentials:undefined})},_read:function(datasetName,reader){var tab=/\t/;var versionLine=morpheus.Util.copyString(reader.readLine().trim());if(versionLine===""){throw new Error("Missing version line")}var version=2;if("#1.2"===versionLine){version=2}else if("#1.3"===versionLine){version=3}else{console.log("Unknown version: assuming version 2")}var dimensionsLine=morpheus.Util.copyString(reader.readLine());if(dimensionsLine==null){throw new Error("No dimensions specified")}var dimensions=dimensionsLine.split(/[ \t]/);var numRowAnnotations=1;var numColumnAnnotations=0;var nrows=-1;var ncols=-1;if(version===3){if(dimensions.length>=4){nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);numRowAnnotations=parseInt(dimensions[2]);numColumnAnnotations=parseInt(dimensions[3])}else{numRowAnnotations=parseInt(dimensions[0]);numColumnAnnotations=parseInt(dimensions[1])}}else{nrows=parseInt(dimensions[0]);ncols=parseInt(dimensions[1]);if(nrows<=0||ncols<=0){throw new Error("Number of rows and columns must be greater than 0.")}}var columnNamesLine=morpheus.Util.copyString(reader.readLine());if(columnNamesLine==null){throw new Error("No column annotations")}var columnNamesArray=columnNamesLine.split(tab);if(ncols===-1){ncols=columnNamesArray.length-numRowAnnotations-1}if(version==2){var expectedColumns=ncols+2;if(columnNamesArray.length!==expectedColumns){throw new Error("Expected "+(expectedColumns-2)+" column names, but read "+(columnNamesArray.length-2)+" column names.")}}var name=columnNamesArray[0];var slashIndex=name.lastIndexOf("/");var columnIdFieldName="id";var rowIdFieldName="id";if(slashIndex!=-1&&slashIndex<name.length-1){rowIdFieldName=name.substring(0,slashIndex);columnIdFieldName=name.substring(slashIndex+1)}if(nrows===-1){var matrix=[];var rowMetadataNames=[rowIdFieldName];var columnMetadataNames=[columnIdFieldName];var rowMetadata=[[]];var columnMetadata=[[]];for(var j=0;j<ncols;j++){var index=j+numRowAnnotations+1;var columnName=index<columnNamesArray.length?columnNamesArray[index]:null;columnMetadata[0].push(morpheus.Util.copyString(columnName))}for(var j=0;j<numRowAnnotations;j++){var rowMetadataName=""===columnNamesArray[1]?"description":columnNamesArray[j+1];rowMetadataNames.push(rowMetadataName);rowMetadata.push([])}var dataColumnStart=numRowAnnotations+1;var ntokens=ncols+numRowAnnotations+1;var linen=3;if(numColumnAnnotations>0){for(var columnAnnotationIndex=0;columnAnnotationIndex<numColumnAnnotations;columnAnnotationIndex++){var tokens=reader.readLine().split(tab);var metadataName=tokens[0];var v=[];columnMetadata.push(v);columnMetadataNames.push(metadataName);for(var j=0;j<ncols;j++){v.push(morpheus.Util.copyString(tokens[j+dataColumnStart]))}}}var nonEmptyDescriptionFound=false;var numRowAnnotationsPlusOne=numRowAnnotations+1;var s;while((s=reader.readLine())!==null){if(s!==""){var array=new Float32Array(ncols);matrix.push(array);var tokens=s.split(tab);for(var rowAnnotationIndex=0;rowAnnotationIndex<numRowAnnotationsPlusOne;rowAnnotationIndex++){var rowMetadataValue=tokens[rowAnnotationIndex];rowMetadata[rowAnnotationIndex].push(morpheus.Util.copyString(rowMetadataValue))}for(var columnIndex=0;columnIndex<ncols;columnIndex++){var token=tokens[columnIndex+dataColumnStart];array[columnIndex]=parseFloat(token)}}}var dataset=new morpheus.Dataset({name:datasetName,rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});for(var i=0;i<rowMetadataNames.length;i++){dataset.getRowMetadata().add(rowMetadataNames[i]).array=rowMetadata[i]}for(var i=0;i<columnMetadataNames.length;i++){dataset.getColumnMetadata().add(columnMetadataNames[i]).array=columnMetadata[i]}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);return dataset}else{var dataset=new morpheus.Dataset({dataType:"Float32",name:datasetName,rows:nrows,columns:ncols});var columnIds=dataset.getColumnMetadata().add(columnIdFieldName);if(version==3){for(var j=0;j<ncols;j++){var index=j+numRowAnnotations+1;var columnName=index<columnNamesArray.length?columnNamesArray[index]:null;columnIds.setValue(j,morpheus.Util.copyString(columnName))}}else{for(var j=0;j<ncols;j++){var columnName=columnNamesArray[j+numRowAnnotations+1];columnIds.setValue(j,morpheus.Util.copyString(columnName))}}var rowAnnotationVectors=[dataset.getRowMetadata().add(rowIdFieldName)];if(version===3){for(var j=0;j<numRowAnnotations;j++){var rowMetadataName=""===columnNamesArray[1]?"description":columnNamesArray[j+1];rowAnnotationVectors.push(dataset.getRowMetadata().add(rowMetadataName))}}else{rowAnnotationVectors.push(dataset.getRowMetadata().add(columnNamesArray[1]))}var dataColumnStart=numRowAnnotations+1;var ntokens=ncols+numRowAnnotations+1;var linen=3;if(numColumnAnnotations>0){for(var columnAnnotationIndex=0;columnAnnotationIndex<numColumnAnnotations;columnAnnotationIndex++){var tokens=reader.readLine().split(tab);var metadataName=tokens[0];var v=dataset.getColumnMetadata().add(metadataName);for(var j=0;j<ncols;j++){v.setValue(j,morpheus.Util.copyString(tokens[j+dataColumnStart]))}}}var nonEmptyDescriptionFound=false;var numRowAnnotationsPlusOne=numRowAnnotations+1;for(var rowIndex=0,nrows=dataset.getRowCount();rowIndex<nrows;rowIndex++){var s=reader.readLine();if(s===null){throw new Error("Missing data rows.")}var tokens=s.split(tab);if(version===2){rowAnnotationVectors[0].setValue(rowIndex,morpheus.Util.copyString(tokens[0]));var desc=tokens[1];if(!nonEmptyDescriptionFound){nonEmptyDescriptionFound=desc!==""}rowAnnotationVectors[1].setValue(rowIndex,morpheus.Util.copyString(desc))}else{for(var rowAnnotationIndex=0;rowAnnotationIndex<numRowAnnotationsPlusOne;rowAnnotationIndex++){var rowMetadataValue=tokens[rowAnnotationIndex];rowAnnotationVectors[rowAnnotationIndex].setValue(rowIndex,morpheus.Util.copyString(rowMetadataValue))}}for(var columnIndex=0;columnIndex<ncols;columnIndex++){var token=tokens[columnIndex+dataColumnStart];dataset.setValue(rowIndex,columnIndex,parseFloat(token))}}if(version===2&&!nonEmptyDescriptionFound){dataset.getRowMetadata().remove(1)}if(rowIndex!==nrows){throw new Error("Missing data rows")}morpheus.MetadataUtil.maybeConvertStrings(dataset.getRowMetadata(),1);morpheus.MetadataUtil.maybeConvertStrings(dataset.getColumnMetadata(),1);return dataset}},_readNoChunking:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}})}};morpheus.GctWriter=function(){this.nf=morpheus.Util.createNumberFormat(".2f")};morpheus.GctWriter.idFirst=function(model){var fields=["id","Id","pr_id"];var idIndex=-1;for(var i=0;i<fields.length;i++){idIndex=morpheus.MetadataUtil.indexOf(model,fields[i]);if(idIndex!==-1){break}}if(idIndex!==-1){var order=[];order[0]=idIndex;for(var i=0,j=1,count=model.getMetadataCount();i<count;i++){if(i!==idIndex){order[j++]=i}}return new morpheus.MetadataModelColumnView(model,order)}return model};morpheus.GctWriter.prototype={setNumberFormat:function(nf){this.nf=nf},getExtension:function(){return"gct"},write:function(dataset,pw){if(pw==null){pw=[]}var rowMetadata=morpheus.GctWriter.idFirst(dataset.getRowMetadata());var columnMetadata=morpheus.GctWriter.idFirst(dataset.getColumnMetadata());this.writeHeader(rowMetadata,columnMetadata,pw);this.writeData(dataset,rowMetadata,pw);return pw.join("")},writeData:function(dataset,rowMetadata,pw){var ncols=dataset.getColumnCount();var rowMetadataCount=rowMetadata.getMetadataCount();var nf=this.nf;for(var i=0,rows=dataset.getRowCount();i<rows;i++){for(var rowMetadataIndex=0;rowMetadataIndex<rowMetadataCount;rowMetadataIndex++){if(rowMetadataIndex>0){pw.push("\t")}var vector=rowMetadata.get(rowMetadataIndex);var value=vector.getValue(i);if(value!==null){var toString=morpheus.VectorTrack.vectorToString(vector);pw.push(toString(value))}}for(var j=0;j<ncols;j++){pw.push("\t");var value=dataset.getValue(i,j);pw.push(nf(value))}pw.push("\n")}},writeHeader:function(rowMetadata,columnMetadata,pw){var rows=rowMetadata.getItemCount();var ncols=columnMetadata.getItemCount();pw.push("#1.3\n");var rowMetadataCount=rowMetadata.getMetadataCount();pw.push(rows+"\t"+ncols+"\t"+(rowMetadataCount-1)+"\t"+(columnMetadata.getMetadataCount()-1));pw.push("\n");for(var i=0;i<rowMetadataCount;i++){if(i>0){pw.push("\t")}var name=rowMetadata.get(i).getName();if(i===0&&name!==columnMetadata.get(0).getName()){name=name+"/"+columnMetadata.get(0).getName()}pw.push(name)}var toString=morpheus.VectorTrack.vectorToString(columnMetadata.get(0));for(var j=0;j<ncols;j++){pw.push("\t");pw.push(toString(columnMetadata.get(0).getValue(j)))}pw.push("\n");for(var columnMetadataIndex=1,metadataSize=columnMetadata.getMetadataCount();columnMetadataIndex<metadataSize;columnMetadataIndex++){pw.push(columnMetadata.get(columnMetadataIndex).getName());for(var i=1;i<rowMetadataCount;i++){pw.push("\t");pw.push("na")}for(var j=0;j<ncols;j++){pw.push("\t");var vector=columnMetadata.get(columnMetadataIndex);var value=vector.getValue(j);if(value!=null){toString=morpheus.VectorTrack.vectorToString(columnMetadata.get(0));pw.push(toString(value))}}pw.push("\n")}}};morpheus.GctWriter12=function(){this.options={rowDescription:"Description",rowId:"id",columnId:"id"};this.nf=morpheus.Util.createNumberFormat(".2f")};morpheus.GctWriter12.prototype={setNumberFormat:function(nf){this.nf=nf},getExtension:function(){return"gct"},write:function(dataset,pw){if(pw==null){pw=[]}var rows=dataset.getRowCount();var columns=dataset.getColumnCount();var version="#1.2";pw.push(version);pw.push("\n");pw.push(rows+"\t"+columns);pw.push("\n");var rowMetadata=morpheus.GctWriter.idFirst(dataset.getRowMetadata());var columnMetadata=morpheus.GctWriter.idFirst(dataset.getColumnMetadata());pw.push("Name");pw.push("\t");pw.push("Description");var columnIds=columnMetadata.getByName(this.options.columnId);if(!columnIds){columnIds=columnMetadata.get(0)}var columnIdToString=morpheus.VectorTrack.vectorToString(columnIds);for(var j=0;j<columns;j++){pw.push("\t");pw.push(columnIdToString(columnIds.getValue(j)))}var rowIds=rowMetadata.get(this.options.rowId);if(!rowIds){rowIds=rowMetadata.get(0)}var rowDescriptions=rowMetadata.getByName(this.options.rowDescription);if(rowDescriptions==null&&rowMetadata.getMetadataCount()>1){rowDescriptions=rowMetadata.get(1)}var rowIdToString=morpheus.VectorTrack.vectorToString(rowIds);var rowDescriptionToString=rowDescriptions!=null?morpheus.VectorTrack.vectorToString(rowDescriptions):null;var nf=this.nf;for(var i=0;i<rows;i++){pw.push("\n");pw.push(rowIdToString(rowIds.getValue(i)));pw.push("\t");var rowDescription=rowDescriptions!=null?rowDescriptions.getValue(i):null;if(rowDescription!=null){pw.push(rowDescriptionToString(rowDescription))}for(var j=0;j<columns;j++){pw.push("\t");pw.push(nf(dataset.getValue(i,j)))}}pw.push("\n");return pw.join("")}};morpheus.GisticReader=function(){};morpheus.GisticReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}catch(x){if(x.stack){console.log(x.stack)}callback(x)}}})},_read:function(datasetName,reader){var tab=/\t/;var header=reader.readLine().trim().split(tab);var ncols=header.length-9;var matrix=[];var s;var rowIds=[];var qValues=[];while((s=reader.readLine())!==null){s=s.trim();if(s!==""){var tokens=s.split(tab);if(tokens[8]==="Actual Copy Change Given"){var array=new Float32Array(ncols);matrix.push(array);rowIds.push(String($.trim(tokens[1])));qValues.push(parseFloat(tokens[5]));for(var j=9;j<=ncols;j++){var token=tokens[j];array[j-9]=parseFloat(token)}}}}var dataset=new morpheus.Dataset({name:datasetName,rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});var columnIds=dataset.getColumnMetadata().add("id");for(var j=0;j<ncols;j++){columnIds.setValue(j,String(header[j+9]))}dataset.getRowMetadata().add("id").array=rowIds;dataset.getRowMetadata().add("q_value").array=qValues;return dataset}};morpheus.GmtDatasetReader=function(){};morpheus.GmtDatasetReader.prototype={getFormatName:function(){return"gmt"},read:function(fileOrUrl,callback){var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,morpheus.DatasetUtil.geneSetsToDataset(name,(new morpheus.GmtReader).read(new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer)))))}catch(x){callback(x)}}})}};morpheus.GmtReader=function(){};morpheus.GmtReader.prototype={read:function(reader){var sets=[];var tab=/\t/;var s;while((s=reader.readLine())!=null){if(s===""||s[0]==="#"){continue}var tokens=s.split(tab);var name=tokens[0].trim();var description=tokens.length>1?tokens[1].trim():"";if("BLANK"===description){description=""}var ids=[];for(var i=2;i<tokens.length;i++){var geneName=tokens[i].trim();if(geneName!==""){ids.push(geneName)}}var set={name:name,description:description,ids:ids};set.toString=function(){return this.name};sets.push(set)}return sets}};morpheus.JsonDatasetReader=function(){};morpheus.JsonDatasetReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));var isString=typeof fileOrUrl==="string"||fileOrUrl instanceof String;if(isString){fetch(fileOrUrl).then(function(response){if(response.ok){return response.text()}else{callback(response.status+" "+response.statusText)}}).then(function(text){callback(null,morpheus.Dataset.fromJSON(JSON.parse(text.trim())))}).catch(function(err){callback(err)})}else{var reader=new FileReader;reader.onload=function(event){callback(null,morpheus.Dataset.fromJSON(JSON.parse(event.target.result)))};reader.onerror=function(event){callback(event)};reader.readAsText(fileOrUrl)}}};morpheus.MafFileReader=function(){this.geneFilter=null};morpheus.MafFileReader.summarizeMutations=function(options){var dataset=options.dataset;var fields=options.fields;var count=fields.length;var vector=dataset.getRowMetadata().add("mutation_summary");vector.getProperties().set(morpheus.VectorKeys.FIELDS,fields);vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"[number]");for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var bins=new Int32Array(count);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(value>0){bins[value-1]++}}vector.setValue(i,bins)}};morpheus.MafFileReader.getField=function(fieldNames,headerToIndex){var name;var index;for(var i=0;i<fieldNames.length;i++){name=fieldNames[i];var lc=name.toLowerCase();index=headerToIndex[lc];if(index!==undefined){break}}if(index!==undefined){return{name:name,index:index}}};morpheus.MafFileReader.VARIANT_MAP=new morpheus.Map;morpheus.MafFileReader.VARIANT_MAP.set("Silent",1);morpheus.MafFileReader.VARIANT_MAP.set("In_Frame_Del",2);morpheus.MafFileReader.VARIANT_MAP.set("In_Frame_Ins",2);morpheus.MafFileReader.VARIANT_MAP.set("Inframe_Del",2);morpheus.MafFileReader.VARIANT_MAP.set("Inframe_Ins",2);morpheus.MafFileReader.VARIANT_MAP.set("Translation_Start_Site",3);morpheus.MafFileReader.VARIANT_MAP.set("Nonstop_Mutation",3);morpheus.MafFileReader.VARIANT_MAP.set("3'UTR",3);morpheus.MafFileReader.VARIANT_MAP.set("3'Flank",3);morpheus.MafFileReader.VARIANT_MAP.set("5'UTR",3);morpheus.MafFileReader.VARIANT_MAP.set("5'Flank",3);morpheus.MafFileReader.VARIANT_MAP.set("IGR",3);morpheus.MafFileReader.VARIANT_MAP.set("Intron",3);morpheus.MafFileReader.VARIANT_MAP.set("RNA",3);morpheus.MafFileReader.VARIANT_MAP.set("Targeted_Region",3);morpheus.MafFileReader.VARIANT_MAP.set("Unknown",3);morpheus.MafFileReader.VARIANT_MAP.set("1DEL",3);morpheus.MafFileReader.VARIANT_MAP.set("HA",3);morpheus.MafFileReader.VARIANT_MAP.set("Missense_Mutation",4);morpheus.MafFileReader.VARIANT_MAP.set("Missense",4);morpheus.MafFileReader.VARIANT_MAP.set("Splice_Site",5);morpheus.MafFileReader.VARIANT_MAP.set("Splice_Acceptor",5);morpheus.MafFileReader.VARIANT_MAP.set("Splice_Region",5);morpheus.MafFileReader.VARIANT_MAP.set("Frame_Shift_Del",6);morpheus.MafFileReader.VARIANT_MAP.set("Frame_Shift_Ins",6);morpheus.MafFileReader.VARIANT_MAP.set("Frameshift",6);morpheus.MafFileReader.VARIANT_MAP.set("Nonsense_Mutation",7);morpheus.MafFileReader.VARIANT_MAP.set("Nonsense",7);morpheus.MafFileReader.VARIANT_MAP.set("2DEL",7);morpheus.MafFileReader.FIELD_NAMES=["Synonymous","In Frame Indel","Other Non-Synonymous","Missense","Splice Site","Frame Shift","Nonsense"];morpheus.MafFileReader.prototype={setGeneFilter:function(geneFilter){this.geneFilter=geneFilter},getFormatName:function(){return"maf"},_getGeneLevelDataset:function(datasetName,reader){var _this=this;var tab=/\t/;var header=reader.readLine().split(tab);var headerToIndex={};for(var i=0,length=header.length;i<length;i++){headerToIndex[header[i].toLowerCase()]=i}var sampleField=morpheus.MafFileReader.getField(["Tumor_Sample_Barcode","tumor_name","Tumor_Sample_UUID"],headerToIndex);var encodingField=morpheus.MafFileReader.getField(["encoding"],headerToIndex);if(sampleField==null){throw new Error("Sample id column not found.")}var encodingColumnIndex=encodingField==null?-1:encodingField.index;var sampleColumnName=sampleField.name;var sampleIdColumnIndex=sampleField.index;var tumorFractionField=morpheus.MafFileReader.getField(["ccf_hat","tumor_f","i_tumor_f"],headerToIndex);var ccfColumnName;var ccfColumnIndex;if(tumorFractionField!==undefined){ccfColumnName=tumorFractionField.name;ccfColumnIndex=tumorFractionField.index}var chromosomeColumn=headerToIndex["Chromosome".toLowerCase()];var startPositionColumn=headerToIndex["Start_position".toLowerCase()];var refAlleleColumn=headerToIndex["Reference_Allele".toLowerCase()];var tumorAllelColumn=headerToIndex["Tumor_Seq_Allele2".toLowerCase()];var proteinChangeColumn=headerToIndex["Protein_Change".toLowerCase()];if(proteinChangeColumn==null){proteinChangeColumn=headerToIndex["Protein".toLowerCase()]}var geneSymbolColumn=headerToIndex["Hugo_Symbol".toLowerCase()];if(geneSymbolColumn==null){geneSymbolColumn=headerToIndex["gene"]}if(geneSymbolColumn==null){throw new Error("Gene symbol column not found.")}var variantColumnIndex=headerToIndex["Variant_Classification".toLowerCase()];if(variantColumnIndex==null){variantColumnIndex=headerToIndex["variant".toLowerCase()]}if(variantColumnIndex==null){throw new Error("Variant_Classification not found")}var geneSymbolToIndex=new morpheus.Map;var sampleIdToIndex=new morpheus.Map;var variantMatrix=[];var ccfMatrix=[];var s;var customNumberToValueMap=new morpheus.Map;var hasMutationInfo=chromosomeColumn!==undefined&&startPositionColumn!==undefined&&refAlleleColumn!==undefined&&tumorAllelColumn!==undefined;while((s=reader.readLine())!==null){var tokens=s.split(tab);var sample=String(tokens[sampleIdColumnIndex]);var columnIndex=sampleIdToIndex.get(sample);if(columnIndex===undefined){columnIndex=sampleIdToIndex.size();sampleIdToIndex.set(sample,columnIndex)}var gene=String(tokens[geneSymbolColumn]);if(gene==="Unknown"){continue}if(this.geneFilter==null||this.geneFilter.has(tokens[geneSymbolColumn])){var rowIndex=geneSymbolToIndex.get(gene);if(rowIndex===undefined){rowIndex=geneSymbolToIndex.size();geneSymbolToIndex.set(gene,rowIndex)}var value=String(tokens[variantColumnIndex]);var variantCode;if(encodingColumnIndex===-1){variantCode=morpheus.MafFileReader.VARIANT_MAP.get(value);if(variantCode===undefined){variantCode=3}}else{variantCode=parseInt(tokens[encodingColumnIndex]);customNumberToValueMap.set(variantCode,value)}var variantObject={};var Protein_Change=tokens[proteinChangeColumn];if(Protein_Change){variantObject.Protein=String(Protein_Change)}variantObject.__v=variantCode;variantObject.Variant=value;if(hasMutationInfo){variantObject.Mutation=String(tokens[chromosomeColumn])+":"+String(tokens[startPositionColumn])+" "+String(tokens[refAlleleColumn])+" > "+String(tokens[tumorAllelColumn])}var wrappedVariant=morpheus.Util.wrapNumber(variantCode,variantObject);var variantRow=variantMatrix[rowIndex];if(variantRow===undefined){variantRow=[];variantMatrix[rowIndex]=variantRow}var ccf=-1;var priorCcf=-1;if(ccfColumnIndex!==undefined){var ccfRow=ccfMatrix[rowIndex];if(ccfRow===undefined){ccfRow=[];ccfMatrix[rowIndex]=ccfRow}ccf=parseFloat(tokens[ccfColumnIndex]);priorCcf=ccfRow[columnIndex]||-1}var priorValue=variantRow[columnIndex]||-1;if(variantCode>priorValue){variantRow[columnIndex]=wrappedVariant;if(ccfColumnIndex!==undefined){ccfRow[columnIndex]=ccf}}else if(variantCode===priorValue&&ccf>priorCcf){variantRow[columnIndex]=wrappedVariant;ccfRow[columnIndex]=ccf}}}var dataset=new morpheus.Dataset({name:datasetName,array:variantMatrix,dataType:"Number",rows:geneSymbolToIndex.size(),columns:sampleIdToIndex.size()});var columnIds=dataset.getColumnMetadata().add("id");sampleIdToIndex.forEach(function(index,id){columnIds.setValue(index,id)});var rowIds=dataset.getRowMetadata().add("id");geneSymbolToIndex.forEach(function(index,id){rowIds.setValue(index,id)});for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){if(variantMatrix[i][j]===undefined){variantMatrix[i][j]=0}}}if(ccfColumnIndex!==undefined){dataset.addSeries({dataType:"Float32",name:"allelic_fraction",array:ccfMatrix})}if(this.geneFilter){var orderVector=dataset.getRowMetadata().add("order");for(var i=0,size=orderVector.size();i<size;i++){var gene=rowIds.getValue(i);var order=this.geneFilter.get(gene);orderVector.setValue(i,order)}var project=new morpheus.Project(dataset);project.setRowSortKeys([new morpheus.SortKey("order",morpheus.SortKey.SortOrder.ASCENDING)],true);var tmp=project.getSortedFilteredDataset();project=new morpheus.Project(tmp);var columnIndices=morpheus.Util.seq(tmp.getColumnCount());columnIndices.sort(function(a,b){for(var i=0,nrows=tmp.getRowCount();i<nrows;i++){for(var seriesIndex=0,nseries=tmp.getSeriesCount();seriesIndex<nseries;seriesIndex++){var f1=tmp.getValue(i,a,seriesIndex);if(isNaN(f1)){f1=Number.NEGATIVE_INFINITY}f1=f1.valueOf();var f2=tmp.getValue(i,b,seriesIndex);if(isNaN(f2)){f2=Number.NEGATIVE_INFINITY}f2=f2.valueOf();var returnVal=f1===f2?0:f1<f2?1:-1;if(returnVal!==0){return returnVal}}}return 0});dataset=new morpheus.SlicedDatasetView(dataset,null,columnIndices)}var fieldNames=morpheus.MafFileReader.FIELD_NAMES;if(customNumberToValueMap.size()>0){var pairs=[];customNumberToValueMap.forEach(function(value,key){pairs.push({key:key,value:value})});pairs.sort(function(a,b){return a.key===b.key?0:a.key<b.key?-1:1});fieldNames=pairs.map(function(p){return p.value})}var numUniqueValues=fieldNames.length;morpheus.MafFileReader.summarizeMutations({dataset:dataset,fields:fieldNames});morpheus.MafFileReader.summarizeMutations({dataset:new morpheus.TransposedDatasetView(dataset),fields:fieldNames});var mutationSummarySelectionVector=dataset.getColumnMetadata().add("mutation_summary_selection");mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.FIELDS,fieldNames);mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"[number]");mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.RECOMPUTE_FUNCTION_SELECTION,true);var datasetName=dataset.getName();mutationSummarySelectionVector.getProperties().set(morpheus.VectorKeys.FUNCTION,{binSize:1,domain:[1,8],cumulative:false});return dataset},read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,_this._getGeneLevelDataset(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}catch(err){callback(err)}}})}};morpheus.SegTabReader=function(){this.regions=null};morpheus.SegTabReader.binByRegion=function(dataset,regions){var chromosomeVector=dataset.getRowMetadata().getByName("Chromosome");var startVector=dataset.getRowMetadata().getByName("Start_bp");var endVector=dataset.getRowMetadata().getByName("End_bp");var collapsedDataset=new morpheus.Dataset({name:dataset.getName(),rows:regions.length,columns:dataset.getColumnCount(),dataType:"Float32"});morpheus.DatasetUtil.fill(collapsedDataset,NaN);var regionIdVector=collapsedDataset.getRowMetadata().add("id");var newChromosomeVector=collapsedDataset.getRowMetadata().add("chromosome");var newStartVector=collapsedDataset.getRowMetadata().add("start");var newEndVector=collapsedDataset.getRowMetadata().add("end");var nsegmentsVector=collapsedDataset.getRowMetadata().add("nsegments");var nseries=dataset.getSeriesCount();for(var series=1;series<nseries;series++){collapsedDataset.addSeries({name:dataset.getName(series),dataType:"Float32"})}var summarizeFunction=morpheus.Mean;collapsedDataset.setColumnMetadata(dataset.getColumnMetadata());for(var regionIndex=0;regionIndex<regions.length;regionIndex++){var region=regions[regionIndex];var rowIndices=[];for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var chromosome=chromosomeVector.getValue(i);var start=startVector.getValue(i);var end=endVector.getValue(i);if(region.chromosome==chromosome&&start>=region.start&&end<=region.end){rowIndices.push(i)}}if(rowIndices.length>0){var slice=morpheus.DatasetUtil.slicedView(dataset,rowIndices,null);var columnView=new morpheus.DatasetColumnView(slice);for(var j=0;j<dataset.getColumnCount();j++){columnView.setIndex(j);for(var series=0;series<nseries;series++){columnView.setSeriesIndex(series);collapsedDataset.setValue(regionIndex,j,summarizeFunction(columnView),series)}}}nsegmentsVector.setValue(regionIndex,rowIndices.length);regionIdVector.setValue(regionIndex,region.id);newChromosomeVector.setValue(regionIndex,region.chromosome);newStartVector.setValue(regionIndex,region.start);newEndVector.setValue(regionIndex,region.end)}return collapsedDataset};morpheus.SegTabReader.prototype={getFormatName:function(){return"seg"},setRegions:function(regions){this.regions=regions},_read:function(datasetName,reader){var tab=/\t/;var header=reader.readLine().split(tab);var fieldNameToIndex={};for(var i=0,length=header.length;i<length;i++){var name=header[i].toLowerCase();fieldNameToIndex[name]=i}var sampleField=morpheus.MafFileReader.getField(["pair_id","Tumor_Sample_Barcode","tumor_name","Tumor_Sample_UUID","Sample"],fieldNameToIndex);var sampleColumnName=sampleField.name;var sampleIdColumnIndex=sampleField.index;var tumorFractionField=morpheus.MafFileReader.getField(["ccf_hat","tumor_f","i_tumor_f"],fieldNameToIndex);var ccfColumnName;var ccfColumnIndex;if(tumorFractionField!==undefined){ccfColumnName=tumorFractionField.name;ccfColumnIndex=tumorFractionField.index}var chromosomeColumn=fieldNameToIndex.Chromosome;var startPositionColumn=morpheus.MafFileReader.getField(["Start_bp","Start"],fieldNameToIndex).index;var endPositionColumn=morpheus.MafFileReader.getField(["End_bp","End"],fieldNameToIndex,{remove:false,lc:true}).index;var valueField=morpheus.MafFileReader.getField(["tau","Segment_Mean"]).index;var s;var matrix=[];var ccfMatrix=[];var sampleIdToIndex=new morpheus.Map;var chromosomeStartEndToIndex=new morpheus.Map;while((s=reader.readLine())!==null){if(s===""){continue}var tokens=s.split(tab);var sample=String(tokens[sampleIdColumnIndex]);var columnIndex=sampleIdToIndex.get(sample);if(columnIndex===undefined){columnIndex=sampleIdToIndex.size();sampleIdToIndex.set(sample,columnIndex)}var rowId=new morpheus.Identifier([String(tokens[chromosomeColumn]),String(tokens[startPositionColumn]),String(tokens[endPositionColumn])]);var rowIndex=chromosomeStartEndToIndex.get(rowId);if(rowIndex===undefined){rowIndex=chromosomeStartEndToIndex.size();chromosomeStartEndToIndex.set(rowId,rowIndex)}var value=parseFloat(String(tokens[valueField]));value=isNaN(value)?value:morpheus.Log2(value)-1;var matrixRow=matrix[rowIndex];if(matrixRow===undefined){matrixRow=[];matrix[rowIndex]=matrixRow;if(ccfColumnIndex!==undefined){ccfMatrix[rowIndex]=[]}}matrixRow[columnIndex]=value;if(ccfColumnIndex!==undefined){ccfMatrix[rowIndex][columnIndex]=parseFloat(tokens[ccfColumnIndex])}}var dataset=new morpheus.Dataset({name:datasetName,array:matrix,dataType:"number",rows:chromosomeStartEndToIndex.size(),columns:sampleIdToIndex.size()});var columnIds=dataset.getColumnMetadata().add("id");sampleIdToIndex.forEach(function(index,id){columnIds.setValue(index,id)});var chromosomeVector=dataset.getRowMetadata().add("Chromosome");var startVector=dataset.getRowMetadata().add("Start_bp");var endVector=dataset.getRowMetadata().add("End_bp");chromosomeStartEndToIndex.forEach(function(index,id){chromosomeVector.setValue(index,id.getArray()[0]);startVector.setValue(index,id.getArray()[1]);endVector.setValue(index,id.getArray()[2])});if(ccfColumnIndex!==undefined){dataset.addSeries({dataType:"number",name:"ccf",array:ccfMatrix})}if(this.regions!=null&&this.regions.length>0){dataset=morpheus.SegTabReader.binByRegion(dataset,this.regions)}return dataset},read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}})}};morpheus.TcgaUtil=function(){};morpheus.TcgaUtil.DISEASE_STUDIES={ACC:"Adrenocortical carcinoma",BLCA:"Bladder Urothelial Carcinoma",BRCA:"Breast invasive carcinoma",CESC:"Cervical squamous cell carcinoma and endocervical adenocarcinoma",CHOL:"Cholangiocarcinoma",COAD:"Colon adenocarcinoma",COADREAD:"Colonrectal adenocarcinoma",DLBC:"Lymphoid Neoplasm Diffuse Large B-cell Lymphoma",ESCA:"Esophageal carcinoma ",GBM:"Glioblastoma multiforme",GBMLGG:"Glioma",HNSC:"Head and Neck squamous cell carcinoma",KICH:"Kidney Chromophobe",KIPAN:"Pan-Kidney Cohort",KIRC:"Kidney renal clear cell carcinoma",KIRP:"Kidney renal papillary cell carcinoma",LAML:"Acute Myeloid Leukemia",LCML:"Chronic Myelogenous Leukemia",LGG:"Brain Lower Grade Glioma",LIHC:"Liver hepatocellular carcinoma",LUAD:"Lung adenocarcinoma",LUSC:"Lung squamous cell carcinoma",MESO:"Mesothelioma",OV:"Ovarian serous cystadenocarcinoma",PAAD:"Pancreatic adenocarcinoma",PCPG:"Pheochromocytoma and Paraganglioma",PRAD:"Prostate adenocarcinoma",READ:"Rectum adenocarcinoma",SARC:"Sarcoma",SKCM:"Skin Cutaneous Melanoma",STAD:"Stomach adenocarcinoma",STES:"Stomach and Esophageal Carcinoma",TGCT:"Testicular Germ Cell Tumors",THCA:"Thyroid carcinoma",THYM:"Thymoma",UCEC:"Uterine Corpus Endometrial Carcinoma",UCS:"Uterine Carcinosarcoma",UVM:"Uveal Melanoma"};morpheus.TcgaUtil.SAMPLE_TYPES={"01":"Primary solid Tumor","02":"Recurrent Solid Tumor","03":"Primary Blood Derived Cancer - Peripheral Blood","04":"Recurrent Blood Derived Cancer - Bone Marrow","05":"Additional - New Primary","06":"Metastatic","07":"Additional Metastatic","08":"Human Tumor Original Cells","09":"Primary Blood Derived Cancer - Bone Marrow",10:"Blood Derived Normal",11:"Solid Tissue Normal",12:"Buccal Cell Normal",13:"EBV Immortalized Normal",14:"Bone Marrow Normal",20:"Control Analyte",40:"Recurrent Blood Derived Cancer - Peripheral Blood",50:"Cell Lines",60:"Primary Xenograft Tissue",61:"Cell Line Derived Xenograft Tissue"};morpheus.TcgaUtil.barcode=function(s){var tokens=s.split("-");var id=tokens[2];var sampleType;if(tokens.length>3){sampleType=tokens[3];if(sampleType.length>2){sampleType=sampleType.substring(0,2)}sampleType=morpheus.TcgaUtil.SAMPLE_TYPES[sampleType]}else{sampleType=morpheus.TcgaUtil.SAMPLE_TYPES["01"]}return{id:id.toLowerCase(),sampleType:sampleType}};morpheus.TcgaUtil.setIdAndSampleType=function(dataset){var idVector=dataset.getColumnMetadata().get(0);var participantId=dataset.getColumnMetadata().add("participant_id");var sampleType=dataset.getColumnMetadata().add("sample_type");for(var i=0,size=idVector.size();i<size;i++){var barcode=morpheus.TcgaUtil.barcode(idVector.getValue(i));idVector.setValue(i,barcode.id+"-"+barcode.sampleType);sampleType.setValue(i,barcode.sampleType);participantId.setValue(i,barcode.id)}};morpheus.TcgaUtil.getDataset=function(options){var promises=[];var datasets=[];var returnDeferred=$.Deferred();if(options.mrna){var mrna=$.Deferred();promises.push(mrna);(new morpheus.TxtReader).read(options.mrna,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}mrna.resolve()})}var sigGenesLines;if(options.mutation){var mutation=$.Deferred();promises.push(mutation);(new morpheus.MafFileReader).read(options.mutation,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}mutation.resolve()});var sigGenesAnnotation=morpheus.Util.readLines(options.sigGenes);sigGenesAnnotation.done(function(lines){sigGenesLines=lines});promises.push(sigGenesAnnotation)}if(options.gistic){var gistic=$.Deferred();promises.push(gistic);(new morpheus.GisticReader).read(options.gistic,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}gistic.resolve()})}if(options.gisticGene){var gisticGene=$.Deferred();promises.push(gisticGene);new morpheus.TxtReader({dataColumnStart:3}).read(options.gisticGene,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}gisticGene.resolve()})}if(options.seg){var seg=$.Deferred();promises.push(seg);(new morpheus.SegTabReader).read(options.seg,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}seg.resolve()})}if(options.rppa){var rppa=$.Deferred();promises.push(rppa);new morpheus.TxtReader({dataColumnStart:2}).read(options.rppa,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}rppa.resolve()})}if(options.methylation){var methylation=$.Deferred();promises.push(methylation);new morpheus.TxtReader({}).read(options.methylation,function(err,dataset){if(err){console.log("Error reading file:"+err)}else{datasets.push(dataset);morpheus.TcgaUtil.setIdAndSampleType(dataset)}methylation.resolve()})}var mrnaClustPromise=morpheus.Util.readLines(options.mrnaClust);promises.push(mrnaClustPromise);var sampleIdToClusterId;mrnaClustPromise.done(function(lines){sampleIdToClusterId=new morpheus.Map;var lineNumber=0;while(lines[lineNumber].indexOf("SampleName")!==-1){lineNumber++}var tab=/\t/;for(;lineNumber<lines.length;lineNumber++){var tokens=lines[lineNumber].split(tab);var barcode=morpheus.TcgaUtil.barcode(tokens[0]);sampleIdToClusterId.set(barcode.id+"-"+barcode.sampleType,tokens[1])}});var annotationCallbacks=[];var annotationDef=null;if(options.columnAnnotations){annotationDef=morpheus.DatasetUtil.annotate({annotations:options.columnAnnotations,isColumns:true});promises.push(annotationDef);annotationDef.done(function(array){annotationCallbacks=array})}$.when.apply($,promises).then(function(){var datasetToReturn=null;if(datasets.length===1){var sourceName=datasets[0].getName();var sourceVector=datasets[0].getRowMetadata().add("Source");for(var i=0;i<sourceVector.size();i++){sourceVector.setValue(i,sourceName)}datasetToReturn=datasets[0]}else{var maxIndex=0;var maxColumns=datasets[0].getColumnCount();for(var i=1;i<datasets.length;i++){if(datasets[i].getColumnCount()>maxColumns){maxColumns=datasets[i].getColumnCount();maxIndex=i}if(datasets[i].getName()==="mutations_merged.maf"){maxColumns=Number.MAX_VALUE;maxIndex=i}}var datasetIndices=[];datasetIndices.push(maxIndex);for(var i=0;i<datasets.length;i++){if(i!==maxIndex){datasetIndices.push(i)}}var joined=new morpheus.JoinedDataset(datasets[datasetIndices[0]],datasets[datasetIndices[1]],"id","id");for(var i=2;i<datasetIndices.length;i++){joined=new morpheus.JoinedDataset(joined,datasets[datasetIndices[i]],"id","id")}datasetToReturn=joined}var clusterIdVector=datasetToReturn.getColumnMetadata().add("mRNAseq_cluster");var idVector=datasetToReturn.getColumnMetadata().getByName("id");for(var j=0,size=idVector.size();j<size;j++){clusterIdVector.setValue(j,sampleIdToClusterId.get(idVector.getValue(j)))}if(options.mutation){var sourceToIndices=morpheus.VectorUtil.createValueToIndicesMap(datasetToReturn.getRowMetadata().getByName("Source"));var mutationDataset=new morpheus.SlicedDatasetView(datasetToReturn,sourceToIndices.get("mutations_merged.maf"));(new morpheus.OpenFileTool).annotate(sigGenesLines,mutationDataset,false,null,"id","gene",["q"]);var qVector=mutationDataset.getRowMetadata().getByName("q");var qValueVector=mutationDataset.getRowMetadata().getByName("q_value");if(qValueVector==null){qValueVector=mutationDataset.getRowMetadata().add("q_value")}for(var i=0,size=qValueVector.size();i<size;i++){qValueVector.setValue(i,qVector.getValue(i))}mutationDataset.getRowMetadata().remove(morpheus.MetadataUtil.indexOf(mutationDataset.getRowMetadata(),"q"))}if(annotationDef){annotationCallbacks.forEach(function(f){f(datasetToReturn)})}returnDeferred.resolve(datasetToReturn)});return returnDeferred};morpheus.TxtReader=function(options){if(options==null){options={}}this.options=options};morpheus.TxtReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{callback(null,_this._read(name,new morpheus.ArrayBufferReader(new Uint8Array(arrayBuffer))))}catch(x){callback(x)}}})},_read:function(datasetName,reader){var dataColumnStart=this.options.dataColumnStart;var dataRowStart=this.options.dataRowStart;if(dataRowStart==null){dataRowStart=1}var tab=/\t/;var header=reader.readLine().trim().split(tab);if(dataRowStart>1){for(var i=1;i<dataRowStart;i++){reader.readLine()}}var testLine=null;if(dataColumnStart==null){testLine=reader.readLine().trim();var tokens=testLine.split(tab);for(var i=1;i<tokens.length;i++){var token=tokens[i];if(token===""||token==="NA"||token==="NaN"||$.isNumeric(token)){dataColumnStart=i;break}}if(dataColumnStart==null){dataColumnStart=1}}var ncols=header.length-dataColumnStart;var matrix=[];var s;var arrayOfRowArrays=[];for(var i=0;i<dataColumnStart;i++){arrayOfRowArrays.push([])}if(testLine!=null){var array=new Float32Array(ncols);matrix.push(array);var tokens=testLine.split(tab);for(var j=0;j<dataColumnStart;j++){arrayOfRowArrays[j].push(morpheus.Util.copyString(tokens[j]))}for(var j=dataColumnStart,k=0;k<ncols;j++,k++){var token=tokens[j];array[j-dataColumnStart]=parseFloat(token)}}while((s=reader.readLine())!==null){s=s.trim();if(s!==""){var array=new Float32Array(ncols);matrix.push(array);var tokens=s.split(tab);for(var j=0;j<dataColumnStart;j++){arrayOfRowArrays[j].push(morpheus.Util.copyString(tokens[j]))}for(var j=dataColumnStart,k=0;k<ncols;j++,k++){var token=tokens[j];array[j-dataColumnStart]=parseFloat(token)}}}var dataset=new morpheus.Dataset({name:datasetName,rows:matrix.length,columns:ncols,array:matrix,dataType:"Float32"});var columnIds=dataset.getColumnMetadata().add("id");for(var i=0,j=dataColumnStart;i<ncols;i++,j++){columnIds.setValue(i,morpheus.Util.copyString(header[j]))}var rowIdVector=dataset.getRowMetadata().add("id");rowIdVector.array=arrayOfRowArrays[0];for(var i=1;i<dataColumnStart;i++){var v=dataset.getRowMetadata().add(header[i]);v.array=arrayOfRowArrays[i]}return dataset}};morpheus.XlsxDatasetReader=function(){};morpheus.XlsxDatasetReader.prototype={read:function(fileOrUrl,callback){var _this=this;var name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl));morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,arrayBuffer){if(err){callback(err)}else{try{var data=new Uint8Array(arrayBuffer);var arr=[];for(var i=0;i!=data.length;++i){arr[i]=String.fromCharCode(data[i])}var bstr=arr.join("");_this._read(name,bstr,callback)}catch(x){callback(x)}}})},_read:function(datasetName,bstr,callback){morpheus.Util.xlsxTo2dArray({data:bstr},function(err,lines){var nrows=lines.length-1;var header=lines[0];var ncols=header.length-1;var dataset=new morpheus.Dataset({name:datasetName,rows:nrows,columns:ncols});var columnIds=dataset.getColumnMetadata().add("id");for(var j=1;j<=ncols;j++){columnIds.setValue(j-1,header[j])}var rowIds=dataset.getRowMetadata().add("id");for(var i=1;i<lines.length;i++){var tokens=lines[i];rowIds.setValue(i-1,tokens[0]);for(var j=1;j<=ncols;j++){var token=tokens[j];var value=parseFloat(token);dataset.setValue(i-1,j-1,value)}}callback(null,dataset)})}};morpheus.VectorAdapter=function(v){if(v==null){throw"vector is null"}this.v=v};morpheus.VectorAdapter.prototype={setValue:function(i,value){this.v.setValue(i,value)},getValue:function(i){return this.v.getValue(i)},getProperties:function(){return this.v.getProperties()},size:function(){return this.v.size()},getName:function(){return this.v.getName()},setName:function(name){this.v.setName(name)}};morpheus.AbstractDataset=function(rows,columns){this.seriesNames=[];this.seriesArrays=[];this.seriesDataTypes=[];this.rows=rows;this.columns=columns;this.rowMetadataModel=new morpheus.MetadataModel(rows);this.columnMetadataModel=new morpheus.MetadataModel(columns)};morpheus.AbstractDataset.prototype={setRowMetadata:function(metadata){this.rowMetadataModel=metadata},setColumnMetadata:function(metadata){this.columnMetadataModel=metadata},getName:function(seriesIndex){return this.seriesNames[seriesIndex||0]},setName:function(seriesIndex,name){this.seriesNames[seriesIndex||0]=name},getRowMetadata:function(){return this.rowMetadataModel},getColumnMetadata:function(){return this.columnMetadataModel},getRowCount:function(){return this.rows},getColumnCount:function(){return this.columns},getValue:function(rowIndex,columnIndex,seriesIndex){},setValue:function(rowIndex,columnIndex,value,seriesIndex){},addSeries:function(options){},removeSeries:function(seriesIndex){this.seriesArrays.splice(seriesIndex,1);this.seriesNames.splice(seriesIndex,1);this.seriesDataTypes.splice(seriesIndex,1)},getSeriesCount:function(){return this.seriesArrays.length},getDataType:function(seriesIndex){return this.seriesDataTypes[seriesIndex||0]},toString:function(){return this.getName()}};morpheus.AbstractVector=function(name,size){this.name=name;this.n=size;this.properties=new morpheus.Map};morpheus.AbstractVector.prototype={getValue:function(index){throw new Error("Not implemented")},getProperties:function(){return this.properties},size:function(){return this.n},getName:function(){return this.name}};morpheus.SignalToNoise=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var s1=Math.sqrt(morpheus.Variance(list1,m1));var s2=Math.sqrt(morpheus.Variance(list2,m2));return(m1-m2)/(s1+s2)};morpheus.SignalToNoise.toString=function(){return"Signal to noise"};morpheus.createSignalToNoiseAdjust=function(percent){percent=percent||.2;var f=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var s1=Math.sqrt(morpheus.Variance(list1,m1));var s2=Math.sqrt(morpheus.Variance(list2,m2));s1=morpheus.SignalToNoise.thresholdStandardDeviation(m1,s1,percent);s2=morpheus.SignalToNoise.thresholdStandardDeviation(m2,s2,percent);return(m1-m2)/(s1+s2)};f.toString=function(){return"Signal to noise (adjust standard deviation)"};return f};morpheus.SignalToNoise.thresholdStandardDeviation=function(mean,standardDeviation,percent){var returnValue=standardDeviation;var absMean=Math.abs(mean);var minStdev=percent*absMean;if(minStdev>standardDeviation){returnValue=minStdev}if(returnValue<percent){returnValue=percent}return returnValue};morpheus.createContingencyTable=function(listOne,listTwo,groupingValue){if(groupingValue==null||isNaN(groupingValue)){groupingValue=1}var aHit=0;var aMiss=0;for(var j=0,size=listOne.size();j<size;j++){var val=listOne.getValue(j);if(!isNaN(val)){if(val>=groupingValue){aHit++}else{aMiss++}}}var bHit=0;var bMiss=0;for(var j=0,size=listTwo.size();j<size;j++){var val=listTwo.getValue(j);if(!isNaN(val)){if(val>=groupingValue){bHit++}else{bMiss++}}}var N=aHit+aMiss+bHit+bMiss;var K=aHit+bHit;var n=aHit+aMiss;var k=aHit;var a=k;var b=K-k;var c=n-k;var d=N+k-n-K;return[a,b,c,d]};morpheus.FisherExact=function(listOne,listTwo){var abcd=morpheus.createContingencyTable(listOne,listTwo,1);return morpheus.FisherExact.fisherTest(abcd[0],abcd[1],abcd[2],abcd[3])};morpheus.createFisherExact=function(groupingValue){var f=function(listOne,listTwo){var abcd=morpheus.createContingencyTable(listOne,listTwo,groupingValue);return morpheus.FisherExact.fisherTest(abcd[0],abcd[1],abcd[2],abcd[3])};return f};morpheus.FisherExact.phyper=function(a,b,c,d){return Math.exp(morpheus.FisherExact.logFactorial(a+b)+morpheus.FisherExact.logFactorial(c+d)+morpheus.FisherExact.logFactorial(a+c)+morpheus.FisherExact.logFactorial(b+d)-(morpheus.FisherExact.logFactorial(a)+morpheus.FisherExact.logFactorial(b)+morpheus.FisherExact.logFactorial(c)+morpheus.FisherExact.logFactorial(d)+morpheus.FisherExact.logFactorial(a+b+c+d)))};morpheus.FisherExact.logFactorials=[0,0,.6931471805599453,1.791759469228055,3.1780538303479458,4.787491742782046,6.579251212010101,8.525161361065415,10.60460290274525,12.801827480081469,15.104412573075516,17.502307845873887,19.987214495661885,22.552163853123425,25.19122118273868,27.89927138384089,30.671860106080672,33.50507345013689,36.39544520803305,39.339884187199495,42.335616460753485,45.38013889847691,48.47118135183523,51.60667556776438,54.78472939811232,58.00360522298052,61.261701761002,64.55753862700634,67.88974313718154,71.25703896716801];morpheus.FisherExact.logFactorial=function(k){if(k>=30){var C0=.9189385332046728;var C1=.08333333333333333;var C3=-.002777777777777778;var C5=.0007936507936507937;var C7=-.0005952380952380953;var r=1/k;var rr=r*r;return(k+.5)*Math.log(k)-k+C0+r*(C1+rr*(C3+rr*(C5+rr*C7)))}return morpheus.FisherExact.logFactorials[k]};morpheus.FisherExact.fisherTest=function(a,b,c,d){var p=morpheus.FisherExact.phyper(a,b,c,d);var sum=p;for(var _a=0,n=a+b+c+d;_a<=n;_a++){var _b=a+b-_a;var _c=a+c-_a;var _d=b+d-_b;if(_a!==a&&_b>=0&&_c>=0&&_d>=0){var _p=morpheus.FisherExact.phyper(_a,_b,_c,_d);if(_p<=p){sum+=_p}}}return Math.min(1,sum)};morpheus.FisherExact.toString=function(){return"Fisher Exact Test"};morpheus.FoldChange=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);return m1/m2};morpheus.FoldChange.toString=function(){return"Fold Change"};morpheus.MeanDifference=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var diff=m1-m2;return diff};morpheus.MeanDifference.toString=function(){return"Mean Difference"};morpheus.TTest=function(list1,list2){var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var s1=Math.sqrt(morpheus.Variance(list1,m1));var s2=Math.sqrt(morpheus.Variance(list2,m2));var n1=morpheus.CountNonNaN(list1);var n2=morpheus.CountNonNaN(list2);return(m1-m2)/Math.sqrt(s1*s1/n1+s2*s2/n2)};morpheus.TTest.toString=function(){return"T-Test"};morpheus.DegreesOfFreedom=function(v1,v2,n1,n2){return(v1/n1+v2/n2)*(v1/n1+v2/n2)/(v1*v1/(n1*n1*(n1-1))+v2*v2/(n2*n2*(n2-1)))};morpheus.Spearman=function(list1,list2){var flist1=[];var flist2=[];for(var i=0,n=list1.size();i<n;i++){var v1=list1.getValue(i);var v2=list2.getValue(i);if(isNaN(v1)||isNaN(v2)){continue}flist1.push(v1);flist2.push(v2)}var rank1=morpheus.Ranking(flist1);var rank2=morpheus.Ranking(flist2);return morpheus.Pearson(new morpheus.Vector("",rank1.length).setArray(rank1),new morpheus.Vector("",rank2.length).setArray(rank2))};morpheus.Spearman.toString=function(){return"Spearman rank correlation"};morpheus.WeightedMean=function(weights,values){var numerator=0;var denom=0;for(var i=0,size=values.size();i<size;i++){var value=values.getValue(i);if(!isNaN(value)){var weight=Math.abs(weights.getValue(i));if(!isNaN(weight)){numerator+=weight*value;denom+=weight}}}return denom===0?NaN:numerator/denom};morpheus.WeightedMean.toString=function(){return"Weighted average"};morpheus.createOneMinusMatrixValues=function(dataset){var f=function(listOne,listTwo){return 1-dataset.getValue(listOne.getIndex(),listTwo.getIndex())};f.toString=function(){return"One minus matrix values (for a precomputed similarity matrix)"};return f};morpheus.Pearson=function(listOne,listTwo){var sumx=0;var sumxx=0;var sumy=0;var sumyy=0;var sumxy=0;var N=0;for(var i=0,size=listOne.size();i<size;i++){var x=listOne.getValue(i);var y=listTwo.getValue(i);if(isNaN(x)||isNaN(y)){continue}sumx+=x;sumxx+=x*x;sumy+=y;sumyy+=y*y;sumxy+=x*y;N++}var numr=sumxy-sumx*sumy/N;var denr=Math.sqrt((sumxx-sumx*sumx/N)*(sumyy-sumy*sumy/N));return denr==0?1:numr/denr};morpheus.Pearson.toString=function(){return"Pearson correlation"};morpheus.Jaccard=function(listOne,listTwo){var orCount=0;var andCount=0;for(var i=0,size=listOne.size();i<size;i++){var xval=listOne.getValue(i);var yval=listTwo.getValue(i);if(isNaN(xval)||isNaN(yval)){continue}var x=xval>0;var y=yval>0;if(x&&y){andCount++}else if(x||y){orCount++}}if(orCount===0){return 1}return 1-andCount/orCount};morpheus.Jaccard.toString=function(){return"Jaccard distance"};morpheus.Cosine=function(listOne,listTwo){var sumX2=0;var sumY2=0;var sumXY=0;for(var i=0,size=listOne.size();i<size;i++){var x=listOne.getValue(i);var y=listTwo.getValue(i);if(isNaN(x)||isNaN(y)){continue}sumX2+=x*x;sumY2+=y*y;sumXY+=x*y}return sumXY/Math.sqrt(sumX2*sumY2)};morpheus.Cosine.toString=function(){return"Cosine similarity"};morpheus.Euclidean=function(x,y){var dist=0;for(var i=0,size=x.size();i<size;++i){var x_i=x.getValue(i);var y_i=y.getValue(i);if(isNaN(x_i)||isNaN(y_i)){continue}dist+=(x_i-y_i)*(x_i-y_i)}return Math.sqrt(dist)};morpheus.Euclidean.toString=function(){return"Euclidean distance"};morpheus.OneMinusFunction=function(f){var dist=function(x,y){return 1-f(x,y)};dist.toString=function(){var s=f.toString();return"One minus "+s[0].toLowerCase()+s.substring(1)};return dist};morpheus.LinearRegression=function(xVector,yVector){var sumX=0;var sumY=0;var sumXX=0;var sumXY=0;var count=0;for(var i=0,size=xVector.size();i<size;i++){var x=xVector.getValue(i);var y=yVector.getValue(i);if(!isNaN(x)&&!isNaN(y)){sumX+=x;sumY+=y;sumXX+=x*x;sumXY+=x*y;count++}}var m=(count*sumXY-sumX*sumY)/(count*sumXX-sumX*sumX);var b=sumY/count-m*sumX/count;return{m:m,b:b}};morpheus.KendallsCorrelation=function(x,y){function sum(n){return n*(n+1)/2}var xArray=[];var yArray=[];for(var i=0,size=x.size();i<size;++i){var x_i=x.getValue(i);var y_i=y.getValue(i);if(isNaN(x_i)||isNaN(y_i)){continue}xArray.push(x_i);yArray.push(y_i)}var n=xArray.length;var numPairs=sum(n-1);var pairs=[];for(var i=0;i<n;i++){pairs[i]=[xArray[i],yArray[i]]}pairs.sort(function(pair1,pair2){var a=pair1[0];var b=pair2[0];var compareFirst=a===b?0:a<b?-1:1;if(compareFirst!==0){return compareFirst}a=pair1[1];b=pair2[1];return a===b?0:a<b?-1:1});var tiedXPairs=0;var tiedXYPairs=0;var consecutiveXTies=1;var consecutiveXYTies=1;var prev=pairs[0];for(var i=1;i<n;i++){var curr=pairs[i];if(curr[0]===prev[0]){consecutiveXTies++;if(curr[1]===prev[1]){consecutiveXYTies++}else{tiedXYPairs+=sum(consecutiveXYTies-1);consecutiveXYTies=1}}else{tiedXPairs+=sum(consecutiveXTies-1);consecutiveXTies=1;tiedXYPairs+=sum(consecutiveXYTies-1);consecutiveXYTies=1}prev=curr}tiedXPairs+=sum(consecutiveXTies-1);tiedXYPairs+=sum(consecutiveXYTies-1);var swaps=0;var pairsDestination=[];for(var segmentSize=1;segmentSize<n;segmentSize<<=1){for(var offset=0;offset<n;offset+=2*segmentSize){var i=offset;var iEnd=Math.min(i+segmentSize,n);var j=iEnd;var jEnd=Math.min(j+segmentSize,n);var copyLocation=offset;while(i<iEnd||j<jEnd){if(i<iEnd){if(j<jEnd){var c=pairs[i][1]===pairs[j][1]?0:pairs[i][1]<pairs[j][1]?-1:1;if(c<=0){pairsDestination[copyLocation]=pairs[i];i++}else{pairsDestination[copyLocation]=pairs[j];j++;swaps+=iEnd-i}}else{pairsDestination[copyLocation]=pairs[i];i++}}else{pairsDestination[copyLocation]=pairs[j];j++}copyLocation++}}var pairsTemp=pairs;pairs=pairsDestination;pairsDestination=pairsTemp}var tiedYPairs=0;var consecutiveYTies=1;prev=pairs[0];for(var i=1;i<n;i++){var curr=pairs[i];if(curr[1]===prev[1]){consecutiveYTies++}else{tiedYPairs+=sum(consecutiveYTies-1);consecutiveYTies=1}prev=curr}tiedYPairs+=sum(consecutiveYTies-1);var concordantMinusDiscordant=numPairs-tiedXPairs-tiedYPairs+tiedXYPairs-2*swaps;var nonTiedPairsMultiplied=(numPairs-tiedXPairs)*(numPairs-tiedYPairs);return concordantMinusDiscordant/Math.sqrt(nonTiedPairsMultiplied)};morpheus.KendallsCorrelation.toString=function(){return"Kendall's correlation"};morpheus.ComputedVector=function(name,size,callback){morpheus.AbstractVector.call(this,name,size);this.callback=callback};morpheus.ComputedVector.prototype={getValue:function(index){return this.callback(index)}};morpheus.Util.extend(morpheus.ComputedVector,morpheus.AbstractVector);morpheus.DatasetAdapter=function(dataset,rowMetadata,columnMetadata){if(dataset==null){throw"dataset is null"}this.dataset=dataset;this.rowMetadata=rowMetadata||dataset.getRowMetadata();this.columnMetadata=columnMetadata||dataset.getColumnMetadata()};morpheus.DatasetAdapter.prototype={getDataset:function(){return this.dataset},getName:function(seriesIndex){return this.dataset.getName(seriesIndex)},setName:function(seriesIndex,name){this.dataset.setName(seriesIndex,name)},getRowMetadata:function(){return this.rowMetadata},getColumnMetadata:function(){return this.columnMetadata},getRowCount:function(){return this.dataset.getRowCount()},getColumnCount:function(){return this.dataset.getColumnCount()},getValue:function(rowIndex,columnIndex,seriesIndex){return this.dataset.getValue(rowIndex,columnIndex,seriesIndex)},setValue:function(rowIndex,columnIndex,value,seriesIndex){this.dataset.setValue(rowIndex,columnIndex,value,seriesIndex)},addSeries:function(options){return this.dataset.addSeries(options)},removeSeries:function(seriesIndex){this.dataset.removeSeries(seriesIndex)},getSeriesCount:function(){return this.dataset.getSeriesCount()},getDataType:function(seriesIndex){return this.dataset.getDataType(seriesIndex)},toString:function(){return this.dataset.toString()}};morpheus.DatasetColumnView=function(dataset){this.dataset=dataset;this.columnIndex=0;this.seriesIndex=0};morpheus.DatasetColumnView.prototype={columnIndex:-1,size:function(){return this.dataset.getRowCount()},getValue:function(rowIndex){return this.dataset.getValue(rowIndex,this.columnIndex,this.seriesIndex)},setIndex:function(newColumnIndex){this.columnIndex=newColumnIndex;return this},setSeriesIndex:function(seriesIndex){this.seriesIndex=seriesIndex;return this}};morpheus.DatasetRowView=function(dataset){this.dataset=dataset;this.index=0;this.seriesIndex=0};morpheus.DatasetRowView.prototype={size:function(){return this.dataset.getColumnCount()},getIndex:function(){return this.index},getValue:function(columnIndex){return this.dataset.getValue(this.index,columnIndex,this.seriesIndex)},setIndex:function(newRowIndex){this.index=newRowIndex;return this},setSeriesIndex:function(seriesIndex){this.seriesIndex=seriesIndex;return this},setDataset:function(dataset){this.dataset=dataset;return this}};morpheus.DatasetSeriesView=function(dataset,seriesIndices){morpheus.DatasetAdapter.call(this,dataset);this.seriesIndices=seriesIndices};morpheus.DatasetSeriesView.prototype={getValue:function(i,j,seriesIndex){seriesIndex=seriesIndex||0;return this.dataset.getValue(i,j,this.seriesIndices[seriesIndex])},setValue:function(i,j,value,seriesIndex){seriesIndex=seriesIndex||0;this.dataset.setValue(i,j,value,this.seriesIndices[seriesIndex])},getName:function(seriesIndex){seriesIndex=seriesIndex||0;return this.dataset.getName(this.seriesIndices[seriesIndex])},setName:function(seriesIndex,name){seriesIndex=seriesIndex||0;this.dataset.setName(this.seriesIndices[seriesIndex],name)},addSeries:function(options){var index=this.dataset.addSeries(options);this.seriesIndices.push(index);return index},getSeriesCount:function(){return this.seriesIndices.length},toString:function(){return this.getName()}};morpheus.Util.extend(morpheus.DatasetSeriesView,morpheus.DatasetAdapter);morpheus.DatasetUtil=function(){};morpheus.DatasetUtil.min=function(dataset,seriesIndex){seriesIndex=seriesIndex||0;var min=Number.MAX_VALUE;for(var i=0,rows=dataset.getRowCount();i<rows;i++){for(var j=0,columns=dataset.getColumnCount();j<columns;j++){var d=dataset.getValue(i,j,seriesIndex);if(isNaN(d)){continue}min=Math.min(min,d)}}return min};morpheus.DatasetUtil.slicedView=function(dataset,rows,columns){return new morpheus.SlicedDatasetView(dataset,rows,columns)};morpheus.DatasetUtil.transposedView=function(dataset){return dataset instanceof morpheus.TransposedDatasetView?dataset.getDataset():new morpheus.TransposedDatasetView(dataset)};morpheus.DatasetUtil.max=function(dataset,seriesIndex){seriesIndex=seriesIndex||0;var max=-Number.MAX_VALUE;for(var i=0,rows=dataset.getRowCount();i<rows;i++){for(var j=0,columns=dataset.getColumnCount();j<columns;j++){var d=dataset.getValue(i,j,seriesIndex);if(isNaN(d)){continue}max=Math.max(max,d)}}return max};morpheus.DatasetUtil.getDatasetReader=function(ext,options){if(options==null){options={}}var datasetReader=null;if(ext==="maf"){datasetReader=new morpheus.MafFileReader;if(options&&options.mafGeneFilter){datasetReader.setGeneFilter(options.mafGeneFilter)}}else if(ext==="gct"){datasetReader=new morpheus.GctReader}else if(ext==="gmt"){datasetReader=new morpheus.GmtDatasetReader}else if(ext==="xlsx"||ext==="xls"){datasetReader=options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.XlsxDatasetReader}else if(ext==="segtab"||ext==="seg"){datasetReader=new morpheus.SegTabReader;if(options&&options.regions){datasetReader.setRegions(options.regions)}}else if(ext==="txt"||ext==="tsv"||ext==="csv"){datasetReader=options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.TxtReader}else if(ext==="json"){datasetReader=new morpheus.JsonDatasetReader}else if(ext==="gct"){datasetReader=new morpheus.GctReader}return datasetReader};morpheus.DatasetUtil.readDatasetArray=function(datasets){var retDef=$.Deferred();var loadedDatasets=[];var promises=[];_.each(datasets,function(url,i){var p=morpheus.DatasetUtil.read(url);p.index=i;p.done(function(dataset){loadedDatasets[this.index]=dataset});p.fail(function(err){var message=["Error opening "+morpheus.Util.getFileName(url)+"."];if(err.message){message.push("<br />Cause: ");message.push(err.message)}retDef.reject(message.join(""))});promises.push(p)});if(promises.length===0){retDef.reject("No datasets specified.")}$.when.apply($,promises).then(function(){retDef.resolve(morpheus.DatasetUtil.join(loadedDatasets,"id"))});return retDef};morpheus.DatasetUtil.annotate=function(options){var retDef=$.Deferred();var promises=[];var functions=[];var isColumns=options.isColumns;_.each(options.annotations,function(ann,annotationIndex){if(morpheus.Util.isArray(ann.file)){functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotate(ann.file,dataset,isColumns,null,ann.datasetField,ann.fileField,ann.include)}}else{var result=morpheus.Util.readLines(ann.file);var fileName=morpheus.Util.getFileName(ann.file);var deferred=$.Deferred();promises.push(deferred);result.fail(function(message){deferred.reject(message)});result.done(function(lines){if(morpheus.Util.endsWith(fileName,".gmt")){var sets=(new morpheus.GmtReader).parseLines(lines);functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotate(null,dataset,isColumns,sets,ann.datasetField,ann.fileField)};deferred.resolve()}else if(morpheus.Util.endsWith(fileName,".cls")){functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotateCls(null,dataset,fileName,isColumns,lines)};deferred.resolve()}else{functions[annotationIndex]=function(dataset){(new morpheus.OpenFileTool).annotate(lines,dataset,isColumns,null,ann.datasetField,ann.fileField,ann.include,ann.transposed)};deferred.resolve()}})}});$.when.apply($,promises).then(function(){retDef.resolve(functions)});return retDef};morpheus.DatasetUtil.read=function(fileOrUrl,options){if(fileOrUrl==null){throw"File is null"}if(options==null){options={}}var isFile=morpheus.Util.isFile(fileOrUrl);var isString=morpheus.Util.isString(fileOrUrl);var ext=options.extension?options.extension:morpheus.Util.getExtension(morpheus.Util.getFileName(fileOrUrl));var datasetReader;var str=fileOrUrl.toString();if(ext===""&&str!=null&&str.indexOf("blob:")===0){datasetReader=options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.TxtReader}else{datasetReader=morpheus.DatasetUtil.getDatasetReader(ext,options);if(datasetReader==null){datasetReader=isFile?options.interactive?new morpheus.Array2dReaderInteractive:new morpheus.TxtReader:new morpheus.GctReader}}if(isString||isFile){var deferred=$.Deferred();if(options.background){var path=morpheus.Util.getScriptPath();var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.path);"+"var ext = morpheus.Util.getExtension(morpheus.Util"+".getFileName(e.data.fileOrUrl));"+"var datasetReader = morpheus.DatasetUtil.getDatasetReader(ext,"+"\te.data.options);"+"datasetReader.read(e.data.fileOrUrl, function(err,dataset) {"+"\tself.postMessage(dataset);"+"\t});"+"}"]);var blobURL=window.URL.createObjectURL(blob);var worker=new Worker(blobURL);worker.addEventListener("message",function(e){deferred.resolve(morpheus.Dataset.fromJSON(e.data));window.URL.revokeObjectURL(blobURL)},false);worker.postMessage({path:path,fileOrUrl:fileOrUrl,options:options})}else{datasetReader.read(fileOrUrl,function(err,dataset){if(err){deferred.reject(err)}else{deferred.resolve(dataset)}})}var pr=deferred.promise();pr.toString=function(){return""+fileOrUrl};return pr}else if(typeof fileOrUrl.done==="function"){return fileOrUrl}else{if(fileOrUrl.promise){return fileOrUrl}var deferred=$.Deferred();if(fileOrUrl.getRowCount){deferred.resolve(fileOrUrl)}else{deferred.resolve(morpheus.Dataset.fromJSON(fileOrUrl))}return deferred.promise()}};morpheus.DatasetUtil.toObjectArray=function(dataset,options){var columns=options.columns||[0];var columnFields=options.columnFields||["value"];if(columnFields.length!==columns.length){throw"columns.length !== columnFields.length"}var metadataFields=options.metadataFields;var rowMetadata=dataset.getRowMetadata();if(!metadataFields){metadataFields=morpheus.MetadataUtil.getMetadataNames(rowMetadata)}var vectors=morpheus.MetadataUtil.getVectors(rowMetadata,metadataFields);var array=[];for(var i=0;i<dataset.getRowCount();i++){var obj={};for(var j=0;j<columns.length;j++){obj[columnFields[j]]=dataset.getValue(i,columns[j])}for(var j=0;j<vectors.length;j++){obj[vectors[j].getName()]=vectors[j].getValue(i)}array.push(obj)}return array};morpheus.DatasetUtil.fixL1K=function(dataset){var names={cell_id:"Cell Line",pert_idose:"Dose (µM)",pert_iname:"Name",pert_itime:"Time (hr)",distil_ss:"Signature Strength",pert_type:"Type",cell_lineage:"Lineage",cell_histology:"Histology",cell_type:"Cell Type"};var fixNames=function(metadata){for(var i=0,count=metadata.getMetadataCount();i<count;i++){var v=metadata.get(i);var name=v.getName();var mapped=names[name];if(mapped){v.setName(mapped)}}};fixNames(dataset.getRowMetadata());fixNames(dataset.getColumnMetadata());var fix666=function(metadata){for(var i=0,count=metadata.getMetadataCount();i<count;i++){var v=metadata.get(i);if(v.getName()=="Dose (µM)"){for(var j=0,size=v.size();j<size;j++){var value=v.getValue(j);if(value!=null){v.setValue(j,parseFloat(value))}}}var isNumber=false;for(var j=0,size=v.size();j<size;j++){var value=v.getValue(j);if(value!=null){isNumber=_.isNumber(value);break}}var newValue=isNumber||v.getName()=="Dose (µM)"?0:"";for(var j=0,size=v.size();j<size;j++){var value=v.getValue(j);if(value!=null&&value=="-666"){v.setValue(j,newValue)}}}};fix666(dataset.getRowMetadata());fix666(dataset.getColumnMetadata());var fixCommas=function(metadata){var regex=/(,)([^ ])/g;_.each(["Lineage","Histology"],function(name){var v=metadata.getByName(name);if(v!=null){for(var i=0,size=v.size();i<size;i++){var val=v.getValue(i);if(val){v.setValue(i,val.replace(regex,", $2"))}}}})};fixCommas(dataset.getRowMetadata());fixCommas(dataset.getColumnMetadata())};morpheus.DatasetUtil.geneSetsToDataset=function(name,sets){var uniqueIds=new morpheus.Map;for(var i=0,length=sets.length;i<length;i++){var ids=sets[i].ids;for(var j=0,nIds=ids.length;j<nIds;j++){uniqueIds.set(ids[j],1)}}var uniqueIdsArray=uniqueIds.keys();var dataset=new morpheus.Dataset({name:name,rows:uniqueIdsArray.length,columns:sets.length});var columnIds=dataset.getColumnMetadata().add("id");for(var i=0,length=sets.length;i<length;i++){columnIds.setValue(i,sets[i].name)}var rowIds=dataset.getRowMetadata().add("id");for(var i=0,size=uniqueIdsArray.length;i<size;i++){rowIds.setValue(i,uniqueIdsArray[i])}var rowIdToIndex=morpheus.VectorUtil.createValueToIndexMap(rowIds);for(var i=0,length=sets.length;i<length;i++){var ids=sets[i].ids;for(var j=0,nIds=ids.length;j<nIds;j++){dataset.setValue(rowIdToIndex.get(ids[j]),i,1)}}return dataset};morpheus.DatasetUtil.getRootDataset=function(dataset){while(dataset.getDataset){dataset=dataset.getDataset()}return dataset};morpheus.DatasetUtil.getSeriesIndex=function(dataset,name){for(var i=0,nseries=dataset.getSeriesCount();i<nseries;i++){if(name===dataset.getName(i)){return i}}return-1};morpheus.DatasetUtil.getSeriesNames=function(dataset){var names=[];for(var i=0,nseries=dataset.getSeriesCount();i<nseries;i++){names.push(dataset.getName(i))}return names};morpheus.DatasetUtil.searchValues=function(options){if(text===""){return}var dataset=options.dataset;var text=options.text;var tokens=morpheus.Util.getAutocompleteTokens(text);if(tokens.length==0){return}var predicates=morpheus.Util.createSearchPredicates({tokens:tokens,defaultMatchMode:options.defaultMatchMode});var matchAllPredicates=options.matchAllPredicates===true;var npredicates=predicates.length;var viewIndices=new morpheus.Set;function isMatch(object,toObject,predicate){if(object!=null){if(toObject){var filterColumnName=predicate.getField();if(filterColumnName!=null){var value=object[filterColumnName];return predicate.accept(value)}else{for(var name in object){var value=object[name];return predicate.accept(value)}}}else{var filterColumnName=predicate.getField();if(filterColumnName==null||filterColumnName===dataset.getName(k)){return predicate.accept(object)}}}}for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var matches=false;itemSearch:if(matchAllPredicates){matches=true;for(var p=0;p<npredicates;p++){var predicate=predicates[p];var pmatch=false;for(var k=0,nseries=dataset.getSeriesCount();k<nseries;k++){var element=dataset.getValue(i,j,k);var isObject=element!=null&&element.toObject!=null;if(isObject){element=element.toObject()}if(isMatch(element,isObject,predicate)){pmatch=true;break}}if(!pmatch){matches=false;break itemSearch}}}else{for(var k=0,nseries=dataset.getSeriesCount();k<nseries;k++){var element=dataset.getValue(i,j,k);var isObject=element!=null&&element.toObject!=null;if(isObject){element=element.toObject()}for(var p=0;p<npredicates;p++){var predicate=predicates[p];if(isMatch(element,isObject,predicate)){matches=true;break itemSearch}}}}if(matches){viewIndices.add(new morpheus.Identifier([i,j]))}}}return viewIndices};morpheus.DatasetUtil.autocompleteValues=function(dataset){return function(tokens,cb){var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);var seriesIndices=[];for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var k=0,nseries=dataset.getSeriesCount();k<nseries;k++){if(dataset.getDataType(i,k)==="Number"){seriesIndices.push([i,k])}}}if(seriesIndices.length===0){return cb()}var _val;elementSearch:for(var k=0,nseries=seriesIndices.length;k<nseries;k++){var pair=seriesIndices[k];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var element=dataset.getValue(pair[0],j,pair[1]);if(element!=null&&element.toObject){_val=element.toObject();break elementSearch}}}var matches=[];var fields=_val==null?[]:_.keys(_val);if(token===""){fields.sort(function(a,b){return a===b?0:a<b?-1:1});fields.forEach(function(field){matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})});return cb(matches)}var field=null;var semi=token.indexOf(":");if(semi>0){if(token.charCodeAt(semi-1)!==92){var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[token.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}var index=fields.indexOf(possibleField);if(index!==-1){token=$.trim(token.substring(semi+1));field=possibleField}}}var set=new morpheus.Set;var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");var max=10;loop:for(var k=0,nseries=seriesIndices.length;k<nseries;k++){var pair=seriesIndices[k];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var element=dataset.getValue(pair[0],j,pair[1]);if(element&&element.toObject){var object=element.toObject();if(field!==null){var val=object[field];if(val!=null){var id=new morpheus.Identifier([val,field]);if(!set.has(id)&&regex.test(val)){set.add(id);if(set.size()===max){break loop}}}}else{for(var name in object){var val=object[name];var id=new morpheus.Identifier([val,name]);if(!set.has(id)&&regex.test(val)){set.add(id);if(set.size()===max){break loop}}}}}}}set.forEach(function(id){var array=id.getArray();var field=array[1];var val=array[0];matches.push({value:field+":"+val,label:'<span style="font-weight:300;">'+field+":</span>"+'<span style="font-weight:900;">'+val+"</span>"})});if(field==null){fields.forEach(function(field){if(regex.test(field)){matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})}})}cb(matches)}};morpheus.DatasetUtil.fill=function(dataset,value,seriesIndex){seriesIndex=seriesIndex||0;for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){dataset.setValue(i,j,value,seriesIndex)}}};morpheus.DatasetUtil.overlay=function(options){var dataset=options.dataset;var newDataset=options.newDataset;var current_dataset_row_annotation_name=options.rowAnnotationName;var current_dataset_column_annotation_name=options.columnAnnotationName;var new_dataset_row_annotation_name=options.newRowAnnotationName;var new_dataset_column_annotation_name=options.newColumnAnnotationName;var rowValueToIndexMap=morpheus.VectorUtil.createValueToIndexMap(dataset.getRowMetadata().getByName(current_dataset_row_annotation_name));var columnValueToIndexMap=morpheus.VectorUtil.createValueToIndexMap(dataset.getColumnMetadata().getByName(current_dataset_column_annotation_name));var seriesIndex=dataset.addSeries({name:newDataset.getName(),dataType:newDataset.getDataType(0)});var rowVector=newDataset.getRowMetadata().getByName(new_dataset_row_annotation_name);var rowIndices=[];var newDatasetRowIndicesSubset=[];for(var i=0,size=rowVector.size();i<size;i++){var index=rowValueToIndexMap.get(rowVector.getValue(i));if(index!==undefined){rowIndices.push(index);newDatasetRowIndicesSubset.push(i)}}var columnVector=newDataset.getColumnMetadata().getByName(new_dataset_column_annotation_name);var columnIndices=[];var newDatasetColumnIndicesSubset=[];for(var i=0,size=columnVector.size();i<size;i++){var index=columnValueToIndexMap.get(columnVector.getValue(i));if(index!==undefined){columnIndices.push(index);newDatasetColumnIndicesSubset.push(i)}}newDataset=new morpheus.SlicedDatasetView(newDataset,newDatasetRowIndicesSubset,newDatasetColumnIndicesSubset);for(var i=0,nrows=newDataset.getRowCount();i<nrows;i++){for(var j=0,ncols=newDataset.getColumnCount();j<ncols;j++){dataset.setValue(rowIndices[i],columnIndices[j],newDataset.getValue(i,j),seriesIndex)}}};morpheus.DatasetUtil.join=function(datasets,field){if(datasets.length===0){throw"No datasets"}if(datasets.length===1){var name=datasets[0].getName();var sourceVector=datasets[0].getRowMetadata().add("Source");for(var i=0,size=sourceVector.size();i<size;i++){sourceVector.setValue(i,name)}return datasets[0]}var ids=new morpheus.Set;for(var i=0;i<datasets.length;i++){var idVector=datasets[i].getColumnMetadata().getByName(field);for(var j=0,size=idVector.size();j<size;j++){ids.add(idVector.getValue(j))}}var dummyDataset=new morpheus.Dataset({rows:0,columns:ids.size(),name:datasets[0].getName()});var dummyIdVector=dummyDataset.getColumnMetadata().add(field);var counter=0;ids.forEach(function(id){dummyIdVector.setValue(counter++,id)});var dataset=new morpheus.JoinedDataset(dummyDataset,datasets[0],field,field);for(var i=1;i<datasets.length;i++){dataset=new morpheus.JoinedDataset(dataset,datasets[i],field,field)}return dataset};morpheus.DatasetUtil.shallowCopy=function(dataset){var rowMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getRowMetadata());var columnMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata());dataset.getRowMetadata=function(){return rowMetadataModel};dataset.getColumnMetadata=function(){return columnMetadataModel};return dataset};morpheus.DatasetUtil.copy=function(dataset){var newDataset=new morpheus.Dataset({name:dataset.getName(),rows:dataset.getRowCount(),columns:dataset.getColumnCount(),dataType:dataset.getDataType(0)});for(var seriesIndex=0,nseries=dataset.getSeriesCount();seriesIndex<nseries;seriesIndex++){if(seriesIndex>0){newDataset.addSeries({name:dataset.getName(seriesIndex),rows:dataset.getRowCount(),columns:dataset.getColumnCount(),dataType:dataset.getDataType(seriesIndex)})}for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){newDataset.setValue(i,j,dataset.getValue(i,j,seriesIndex),seriesIndex)}}}var rowMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getRowMetadata());var columnMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata());newDataset.getRowMetadata=function(){return rowMetadataModel};newDataset.getColumnMetadata=function(){return columnMetadataModel};return newDataset};morpheus.DatasetUtil.toString=function(dataset,value,seriesIndex){seriesIndex=seriesIndex||0;var s=[];for(var i=0,nrows=dataset.getRowCount(),ncols=dataset.getColumnCount();i<nrows;i++){for(var j=0;j<ncols;j++){if(j>0){s.push(", ")}s.push(morpheus.Util.nf(dataset.getValue(i,j,seriesIndex)))}s.push("\n")}return s.join("")};morpheus.DatasetUtil.getNonEmptyRows=function(dataset){var rowsToKeep=[];for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var keep=false;for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(!isNaN(value)){keep=true;break}}if(keep){rowsToKeep.push(i)}}return rowsToKeep};morpheus.Dataset=function(options){morpheus.AbstractDataset.call(this,options.rows,options.columns);if(options.dataType==null){options.dataType="Float32"}this.seriesNames.push(options.name);this.seriesArrays.push(options.array?options.array:morpheus.Dataset.createArray(options));this.seriesDataTypes.push(options.dataType)};morpheus.Dataset.toJSON=function(dataset,options){options=options||{};var seriesArrays=[];var seriesDataTypes=[];var seriesNames=[];var seriesIndices=options.seriesIndices;if(seriesIndices==null){seriesIndices=morpheus.Util.sequ32(dataset.getSeriesCount())}for(var series=0;series<seriesIndices.length;series++){var seriesIndex=seriesIndices[series];seriesNames.push(dataset.getName(seriesIndex));seriesDataTypes.push(dataset.getDataType(seriesIndex));var data=[];seriesArrays.push(data);for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var row=[];data.push(row);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){row[j]=dataset.getValue(i,j,seriesIndex)}}}var vectorToJSON=function(vector){var array=[];for(var i=0,size=vector.size();i<size;i++){array[i]=vector.getValue(i)}var properties=new morpheus.Map;vector.getProperties().forEach(function(value,key){if(morpheus.VectorKeys.JSON_WHITELIST.has(key)){properties.set(key,value)}});return{properties:properties,name:vector.getName(),array:array}};var metadatatoJSON=function(metadata,fields){var vectors=[];var filter;if(fields){filter=new morpheus.Set;fields.forEach(function(field){filter.add(field)})}for(var i=0,count=metadata.getMetadataCount();i<count;i++){var v=metadata.get(i);if(!v.getProperties().has(morpheus.VectorKeys.IS_INDEX)){if(filter){if(filter.has(v.getName())){vectors.push(vectorToJSON(v))}}else{vectors.push(vectorToJSON(v))}}}return vectors};return{rows:dataset.getRowCount(),columns:dataset.getColumnCount(),seriesArrays:seriesArrays,seriesDataTypes:seriesDataTypes,seriesNames:seriesNames,rowMetadataModel:{vectors:metadatatoJSON(dataset.getRowMetadata(),options.rowFields)},columnMetadataModel:{vectors:metadatatoJSON(dataset.getColumnMetadata(),options.columnFields)}}};morpheus.Dataset.fromJSON=function(options){if(options.seriesMappings){for(var seriesIndex=0;seriesIndex<options.seriesMappings.length;seriesIndex++){if(options.seriesMappings[seriesIndex]){var map=options.seriesMappings[seriesIndex];var valueMap=new morpheus.Map;for(var key in map){var value=map[key];valueMap.set(value,morpheus.Util.wrapNumber(value,key))}var array=options.seriesArrays[seriesIndex];for(var i=0;i<options.rows;i++){for(var j=0;j<options.columns;j++){var value=array[i][j];array[i][j]=valueMap.get(value)}}options.seriesDataTypes[seriesIndex]="Number"}}}for(var seriesIndex=0;seriesIndex<options.seriesArrays.length;seriesIndex++){var array=options.seriesArrays[seriesIndex];for(var i=0;i<options.rows;i++){for(var j=0;j<options.columns;j++){var value=array[i][j];if(value==null){array[i][j]=NaN}}}}var dataset=new morpheus.Dataset({name:options.seriesNames[0],dataType:options.seriesDataTypes[0],array:options.seriesArrays[0],rows:options.rows,columns:options.columns});if(options.rowMetadataModel){options.rowMetadataModel.vectors.forEach(function(v){var vector=new morpheus.Vector(v.name,dataset.getRowCount());vector.array=v.array;vector.properties=morpheus.Map.fromJSON(v.properties);dataset.rowMetadataModel.vectors.push(vector)})}if(options.columnMetadataModel){options.columnMetadataModel.vectors.forEach(function(v){var vector=new morpheus.Vector(v.name,dataset.getColumnCount());vector.array=v.array;vector.properties=morpheus.Map.fromJSON(v.properties);dataset.columnMetadataModel.vectors.push(vector)})}for(var i=1;i<options.seriesArrays.length;i++){dataset.addSeries({name:options.seriesNames[i],dataType:options.seriesDataTypes[i],array:options.seriesArrays[i]})}return dataset};morpheus.Dataset.createArray=function(options){var array=[];if(options.dataType==null||options.dataType==="Float32"){for(var i=0;i<options.rows;i++){array.push(new Float32Array(options.columns))}}else if(options.dataType==="Int8"){for(var i=0;i<options.rows;i++){array.push(new Int8Array(options.columns))}}else if(options.dataType==="Int16"){for(var i=0;i<options.rows;i++){array.push(new Int16Array(options.columns))}}else{for(var i=0;i<options.rows;i++){array.push([])}}return array};morpheus.Dataset.prototype={getValue:function(i,j,seriesIndex){seriesIndex=seriesIndex||0;return this.seriesArrays[seriesIndex][i][j]},toString:function(){return this.getName()},setValue:function(i,j,value,seriesIndex){seriesIndex=seriesIndex||0;this.seriesArrays[seriesIndex][i][j]=value},addSeries:function(options){options=$.extend({},{rows:this.getRowCount(),columns:this.getColumnCount(),dataType:"Float32"},options);this.seriesDataTypes.push(options.dataType);this.seriesNames.push(options.name);this.seriesArrays.push(options.array!=null?options.array:morpheus.Dataset.createArray(options));return this.seriesNames.length-1}};morpheus.Util.extend(morpheus.Dataset,morpheus.AbstractDataset);morpheus.ElementSelectionModel=function(project){this.viewIndices=new morpheus.Set;this.project=project};morpheus.ElementSelectionModel.prototype={click:function(rowIndex,columnIndex,add){var id=new morpheus.Identifier([rowIndex,columnIndex]);var isSelected=this.viewIndices.has(id);if(add){isSelected?this.viewIndices.remove(id):this.viewIndices.add(id)}else{this.viewIndices.clear();if(!isSelected){this.viewIndices.add(id)}}this.trigger("selectionChanged")},getProject:function(){return this.project},setViewIndices:function(indices){this.viewIndices=indices;this.trigger("selectionChanged")},clear:function(){this.viewIndices=new morpheus.Set},getViewIndices:function(){return this.viewIndices},count:function(){return this.viewIndices.size()},toModelIndices:function(){var project=this.project;var modelIndices=[];this.viewIndices.forEach(function(id){modelIndices.push(project.convertViewRowIndexToModel(id.getArray()[0]),project.convertViewColumnIndexToModel(id.getArray()[1]))});return modelIndices},save:function(){this.modelIndices=this.toModelIndices()},restore:function(){var project=this.project;this.viewIndices=new morpheus.Set;for(var i=0,length=this.modelIndices.length;i<length;i++){var rowIndex=project.convertModelRowIndexToView(this.modelIndices[i][0]);var columnIndex=project.convertModelColumnIndexToView(this.modelIndices[i][1]);if(rowIndex!==-1&&columnIndex!==-1){this.viewIndices.add(new morpheus.Identifier([rowIndex,columnIndex]))}}}};morpheus.Util.extend(morpheus.ElementSelectionModel,morpheus.Events);morpheus.CombinedFilter=function(isAndFilter){this.filters=[];this.isAndFilter=isAndFilter;this.enabledFilters=[];this.name="combined filter"};morpheus.CombinedFilter.prototype={shallowClone:function(){var f=new morpheus.CombinedFilter(this.isAndFilter);f.filters=this.filters.slice(0);return f},isColumns:function(){return this.filters[0].isColumns()},toString:function(){return this.name},setAnd:function(isAndFilter,notify){this.isAndFilter=isAndFilter;if(notify){this.trigger("and",{})}},isAnd:function(){return this.isAndFilter},equals:function(f){if(!(f instanceof morpheus.CombinedFilter)){return false}if(this.isAndFilter!==f.isAndFilter){return false}if(this.filters.length!==f.filters.length){return false}for(var i=0,length=this.filters.length;i<length;i++){if(!this.filters[i].equals(f.filters[i])){return false}}return true},add:function(filter,notify){this.filters.push(filter);if(notify){this.trigger("add",{filter:filter})}},getFilters:function(){return this.filters},get:function(index){return this.filters[index]},indexOf:function(name,type){for(var i=0,length=this.filters.length;i<length;i++){if(this.filters[i].toString()===name&&(type==null?true:this.filters[i]instanceof type)){return i}}return-1},remove:function(index,notify){this.filters.splice(index,1);if(notify){this.trigger("remove",{index:index})}},set:function(index,filter){this.filters[index]=filter},insert:function(index,filter){this.filters.splice(index,0,filter)},clear:function(){this.filters=[]},init:function(dataset){for(var i=0,nfilters=this.filters.length;i<nfilters;i++){if(this.filters[i].isColumns()){this.filters[i].init(new morpheus.TransposedDatasetView(dataset))}else{this.filters[i].init(dataset)}}this.enabledFilters=this.filters.filter(function(filter){return filter.isEnabled()})},accept:function(index){var filters=this.enabledFilters;if(this.isAndFilter){for(var i=0,nfilters=filters.length;i<nfilters;i++){if(filters[i].accept(index)===false){return false}}return true}else{for(var i=0,nfilters=filters.length;i<nfilters;i++){if(filters[i].accept(index)){return true}}return false}},isEnabled:function(){return this.enabledFilters.length>0}};morpheus.Util.extend(morpheus.CombinedFilter,morpheus.Events);morpheus.IndexFilter=function(acceptIndicesSet,name,isColumns){this.acceptIndicesSet=acceptIndicesSet;this.name=name;this.columns=isColumns};morpheus.IndexFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled},setAcceptIndicesSet:function(acceptIndicesSet){this.acceptIndicesSet=acceptIndicesSet},setEnabled:function(enabled){this.enabled=enabled},equals:function(filter){return filter instanceof morpheus.IndexFilter&&this.acceptIndicesSet.equals(filter.acceptIndicesSet)},init:function(dataset){},toString:function(){return this.name},accept:function(index){return this.acceptIndicesSet.has(index)}};morpheus.VectorFilter=function(set,maxSetSize,name,isColumns){this.set=set;this.name=name;this.maxSetSize=maxSetSize;this.columns=isColumns};morpheus.VectorFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&this.set.size()>0&&this.set.size()!==this.maxSetSize&&this.vector!=null},setEnabled:function(enabled){this.enabled=enabled},equals:function(filter){return filter instanceof morpheus.VectorFilter&&this.name===filter.name},init:function(dataset){this.vector=dataset.getRowMetadata().getByName(this.name)},toString:function(){return this.name},accept:function(index){return this.set.has(this.vector.getValue(index))}};morpheus.NotNullFilter=function(name,isColumns){this.name=name;this.columns=isColumns};morpheus.NotNullFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&this.vector!=null},setEnabled:function(enabled){this.enabled=enabled},equals:function(filter){return filter instanceof morpheus.NotNullFilter&&this.name===filter.name},init:function(dataset){this.vector=dataset.getRowMetadata().getByName(this.name)},toString:function(){return this.name},accept:function(index){return this.vector.getValue(index)!=null}};morpheus.RangeFilter=function(min,max,name,isColumns){this.min=min;this.max=max;this.name=name;this.columns=isColumns};morpheus.RangeFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&(!isNaN(this.min)||!isNaN(this.max))&&this.vector},setEnabled:function(enabled){this.enabled=enabled},setMin:function(value){this.min=isNaN(value)?-Number.MAX_VALUE:value},setMax:function(value){this.max=isNaN(value)?Number.MAX_VALUE:value},equals:function(filter){return filter instanceof morpheus.RangeFilter&&this.name===filter.name},init:function(dataset){this.vector=dataset.getRowMetadata().getByName(this.name)},toString:function(){return this.name},accept:function(index){var value=this.vector.getValue(index);return value>=this.min&&value<=this.max}};morpheus.TopNFilter=function(n,direction,name,isColumns){this.n=n;this.direction=direction;this.name=name;this.columns=isColumns};morpheus.TopNFilter.TOP=0;morpheus.TopNFilter.BOTTOM=1;morpheus.TopNFilter.TOP_BOTTOM=2;morpheus.TopNFilter.prototype={enabled:true,isColumns:function(){return this.columns},isEnabled:function(){return this.enabled&&this.n>0&&this.vector},setEnabled:function(enabled){this.enabled=enabled},setN:function(value){this.n=value},setDirection:function(direction){this.direction=direction},equals:function(filter){return filter instanceof morpheus.TopNFilter&&this.name===filter.name&&this.n===filter.n&&this.direction===filter.direction},init:function(dataset){if(!this.vector||this.vector!==dataset.getRowMetadata().getByName(this.name)){var vector=dataset.getRowMetadata().getByName(this.name);if(vector==null){vector={getValue:function(){},size:function(){return 0}}}this.vector=vector;var set=new morpheus.Set;for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(!isNaN(value)){set.add(value)}}var values=set.values();values.sort(function(a,b){return a===b?0:a<b?-1:1});this.sortedValues=values}var topAndBottomIndices=[this.sortedValues.length-this.n,this.n-1];for(var i=0;i<topAndBottomIndices.length;i++){topAndBottomIndices[i]=Math.max(0,topAndBottomIndices[i]);topAndBottomIndices[i]=Math.min(this.sortedValues.length-1,topAndBottomIndices[i])}var topAndBottomValues=[this.sortedValues[topAndBottomIndices[0]],this.sortedValues[topAndBottomIndices[1]]];if(this.direction===morpheus.TopNFilter.TOP){this.f=function(val){return isNaN(val)?false:val>=topAndBottomValues[0]}}else if(this.direction===morpheus.TopNFilter.BOTTOM){this.f=function(val){return isNaN(val)?false:val<=topAndBottomValues[1]}}else{this.f=function(val){return isNaN(val)?false:val>=topAndBottomValues[0]||val<=topAndBottomValues[1]}}},accept:function(index){return this.f(this.vector.getValue(index))},toString:function(){return this.name}};morpheus.AlwaysTrueFilter=function(){};morpheus.AlwaysTrueFilter.prototype={isEnabled:function(){return false},setEnabled:function(enabled){},equals:function(filter){return filter instanceof morpheus.AlwaysTrueFilter},init:function(dataset){},toString:function(){return"AlwaysTrue"},accept:function(index){return true}};morpheus.CombinedFilter.fromJSON=function(combinedFilter,json){combinedFilter.setAnd(json.isAnd);json.filters.forEach(function(filter){var name=filter.name!=null?filter.name:filter.field;if(filter.type==="set"){var set=new morpheus.Set;filter.values.forEach(function(value){set.add(value)});combinedFilter.add(new morpheus.VectorFilter(set,filter.maxSetSize,name,filter.isColumns))}else if(filter.type==="range"){combinedFilter.add(new morpheus.RangeFilter(filter.min,filter.max,name,filter.isColumns))}else if(filter.type==="top"){if(_.isString(filter.direction)){if(filter.direction==="top"){filter.direction=morpheus.TopNFilter.TOP}else if(filter.direction==="bottom"){filter.direction=morpheus.TopNFilter.BOTTOM}else if(filter.direction==="topAndBottom"){filter.direction=morpheus.TopNFilter.TOP_BOTTOM}}combinedFilter.add(new morpheus.TopNFilter(filter.n,filter.direction,name,filter.isColumns))}else if(filter.type==="index"){var set=new morpheus.Set;filter.indices.forEach(function(value){set.add(value)});combinedFilter.add(new morpheus.IndexFilter(set,name,filter.isColumns))}else{console.log("Unknown filter type")}})};morpheus.CombinedFilter.toJSON=function(filter){var json={isAnd:filter.isAnd(),filters:[]};filter.getFilters().forEach(function(filter){if(filter.isEnabled()){if(filter instanceof morpheus.VectorFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),values:filter.set.values(),maxSetSize:filter.maxSetSize,type:"set"})}else if(filter instanceof morpheus.RangeFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),min:filter.min,max:filter.max,type:"range"})}else if(filter instanceof morpheus.TopNFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),n:filter.n,direction:filter.direction,type:"top"})}else if(filter instanceof morpheus.IndexFilter){json.filters.push({name:filter.name,isColumns:filter.isColumns(),indices:filter.acceptIndicesSet.values(),type:"index"})}}});return json};morpheus.IndexMapper=function(project,isRows){this.project=project;this.isRows=isRows;this.sortKeys=[];this.modelToView=null;this.filteredModelIndices=null;this.filteredSortedModelIndices=null;this.filter=new morpheus.CombinedFilter(true);this._filter();this._sort()};morpheus.IndexMapper.prototype={convertModelIndexToView:function(modelIndex){var index=this.modelToView.get(modelIndex);return index!==undefined?index:-1},convertViewIndexToModel:function(viewIndex){return viewIndex<this.filteredSortedModelIndices.length&&viewIndex>=0?this.filteredSortedModelIndices[viewIndex]:-1},convertToView:function(){return this.filteredSortedModelIndices},setFilter:function(filter){this.filter=filter;this._filter();this._sort()},_filter:function(){var filter=this.filter;var dataset=this.project.getFullDataset();var count=this.isRows?dataset.getRowCount():dataset.getColumnCount();var filteredModelIndices;if(filter!=null){filter.init(dataset);if(filter.isEnabled()){filteredModelIndices=[];for(var i=0;i<count;i++){if(filter.accept(i)){filteredModelIndices.push(i)}}}}this.filteredModelIndices=filteredModelIndices!=null?filteredModelIndices:morpheus.Util.seq(count)},_sort:function(){var sortKeys=this.sortKeys;if(sortKeys.length>0){var dataset=this.project.getFullDataset();var nkeys=sortKeys.length;for(var i=0;i<nkeys;i++){sortKeys[i].init(sortKeys[i].isColumns()?new morpheus.TransposedDatasetView(dataset):dataset,this.filteredSortedModelIndices)}this.filteredSortedModelIndices=this.filteredModelIndices.slice(0);this.filteredSortedModelIndices.sort(function(a,b){for(var i=0;i<nkeys;i++){var key=sortKeys[i];var comparator=key.getComparator();var val1=key.getValue(a);var val2=key.getValue(b);var c=comparator(val1,val2);if(c!==0){return c}}return 0})}else{this.filteredSortedModelIndices=this.filteredModelIndices}var modelToView=new morpheus.Map;for(var i=0,length=this.filteredSortedModelIndices.length;i<length;i++){modelToView.set(this.filteredSortedModelIndices[i],i)}this.modelToView=modelToView},getFilter:function(){return this.filter},getViewCount:function(){if(this.project.getFullDataset()==null){return 0}return this.filteredSortedModelIndices.length},setSelectedModelIndices:function(selectedModelIndices){this.selectionModel.setSelectedModelIndices(selectedModelIndices)},setSortKeys:function(sortKeys){if(sortKeys==null){sortKeys=[]}this.sortKeys=sortKeys;this._sort()}};morpheus.JoinedDataset=function(dataset1,dataset2,dataset1Field,dataset2Field,sourceFieldName){sourceFieldName=sourceFieldName||"Source";this.dataset1Field=dataset1Field;this.dataset2Field=dataset2Field;if(dataset1==null){throw"dataset1 is null"}if(dataset2==null){throw"dataset2 is null"}if(dataset1Field){var v1=dataset1.getColumnMetadata().getByName(dataset1Field);var dataset2ValueToIndex=morpheus.VectorUtil.createValueToIndexMap(dataset2.getColumnMetadata().getByName(dataset2Field));var dataset2ColumnIndices=[];for(var i=0;i<v1.size();i++){dataset2ColumnIndices[i]=dataset2ValueToIndex.get(v1.getValue(i))}dataset2=new morpheus.SlicedDatasetWithNulls(dataset2,dataset2ColumnIndices,dataset1.getColumnCount(),dataset1.getColumnMetadata())}if(!dataset1.getRowMetadata().getByName(sourceFieldName)){var sourceVector=dataset1.getRowMetadata().add(sourceFieldName);var name=dataset1.getName();for(var i=0,nrows=sourceVector.size();i<nrows;i++){sourceVector.setValue(i,name)}}if(!dataset2.getRowMetadata().getByName(sourceFieldName)){var sourceVector=dataset2.getRowMetadata().add(sourceFieldName);var name=dataset2.getName();for(var i=0,nrows=sourceVector.size();i<nrows;i++){sourceVector.setValue(i,name)}}for(var i=0,count=dataset1.getRowMetadata().getMetadataCount();i<count;i++){var name=dataset1.getRowMetadata().get(i).getName();if(dataset2.getRowMetadata().getByName(name)==null){dataset2.getRowMetadata().add(name)}}for(var i=0,count=dataset2.getRowMetadata().getMetadataCount();i<count;i++){var name=dataset2.getRowMetadata().get(i).getName();if(dataset1.getRowMetadata().getByName(name)==null){dataset1.getRowMetadata().add(name)}}var dataset2RowMetadataOrder=[];var metadataInDifferentOrder=false;for(var i=0,count=dataset1.getRowMetadata().getMetadataCount();i<count;i++){var name=dataset1.getRowMetadata().get(i).getName();var index=morpheus.MetadataUtil.indexOf(dataset2.getRowMetadata(),name);dataset2RowMetadataOrder.push(index);if(index!==i){metadataInDifferentOrder=true}}this.dataset1=dataset1;this.dataset2=dataset2;var maxSeriesCount=Math.max(this.dataset1.getSeriesCount(),this.dataset2.getSeriesCount());for(var i=this.dataset1.getSeriesCount();i<maxSeriesCount;i++){this.dataset1.addSeries({name:this.dataset2.getName(i)})}for(var i=this.dataset2.getSeriesCount();i<maxSeriesCount;i++){this.dataset2.addSeries({name:this.dataset1.getName(i)})}this.rowMetadata=new morpheus.JoinedMetadataModel(this.dataset1.getRowMetadata(),!metadataInDifferentOrder?this.dataset2.getRowMetadata():new morpheus.MetadataModelColumnView(this.dataset2.getRowMetadata(),dataset2RowMetadataOrder))};morpheus.JoinedDataset.prototype={getName:function(seriesIndex){return this.dataset1.getName(seriesIndex)},setName:function(seriesIndex,name){this.dataset1.setName(seriesIndex,name)},getDataType:function(seriesIndex){return this.dataset1.getDataType(seriesIndex)},getDatasets:function(){return[this.dataset1,this.dataset2]},getDataset1:function(){return this.dataset1},getRowMetadata:function(){return this.rowMetadata},getColumnMetadata:function(){return this.dataset1.getColumnMetadata()},getRowCount:function(){return this.dataset1.getRowCount()+this.dataset2.getRowCount()},getColumnCount:function(){return this.dataset1.getColumnCount()},getValue:function(i,j,seriesIndex){return i<this.dataset1.getRowCount()?this.dataset1.getValue(i,j,seriesIndex):this.dataset2.getValue(i-this.dataset1.getRowCount(),j,seriesIndex)},setValue:function(i,j,value,seriesIndex){i<this.dataset1.getRowCount()?this.dataset1.setValue(i,j,value,seriesIndex):this.dataset2.setValue(i-this.dataset1.getRowCount(),j,value,seriesIndex)},getSeriesCount:function(){return this.dataset1.getSeriesCount()},addSeries:function(options){this.dataset1.addSeries(options);return this.dataset2.addSeries(options)},removeSeries:function(seriesIndex){this.dataset1.removeSeries(seriesIndex);this.dataset2.removeSeries(seriesIndex)},toString:function(){return this.getName()}};morpheus.SlicedDatasetWithNulls=function(dataset,columnIndices,columnCount,columnMetadata){morpheus.DatasetAdapter.call(this,dataset);this.columnIndices=columnIndices;this.columnCount=columnCount;this.columnMetadata=columnMetadata};morpheus.SlicedDatasetWithNulls.prototype={getColumnMetadata:function(){return this.columnMetadata},getColumnCount:function(){return this.columnCount},getValue:function(i,j,seriesIndex){var index=this.columnIndices[j];return index===undefined?undefined:this.dataset.getValue(i,index,seriesIndex)},setValue:function(i,j,value,seriesIndex){var index=this.columnIndices[j];if(index!==undefined){this.dataset.setValue(i,index,value,seriesIndex)}else{console.log(j+" out of range")}}};morpheus.Util.extend(morpheus.SlicedDatasetWithNulls,morpheus.DatasetAdapter);morpheus.JoinedVector=function(v1,v2){this.v1=v1;this.v2=v2;morpheus.VectorAdapter.call(this,v1);this.properties=new morpheus.Map};morpheus.JoinedVector.prototype={setValue:function(i,value){i<this.v1.size()?this.v1.setValue(i,value):this.v2.setValue(i-this.v1.size(),value)},getValue:function(i){return i<this.v1.size()?this.v1.getValue(i):this.v2.getValue(i-this.v1.size())},size:function(){return this.v1.size()+this.v2.size()},getProperties:function(){return this.properties}};morpheus.Util.extend(morpheus.JoinedVector,morpheus.VectorAdapter);morpheus.JoinedMetadataModel=function(m1,m2){this.m1=m1;this.m2=m2;this.vectors=[];for(var i=0,count=m1.getMetadataCount();i<count;i++){var v1=this.m1.get(i);var v2=this.m2.get(i);var v=new morpheus.JoinedVector(v1,v2);v1.getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){v.properties.set(key,val)}});v2.getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){v.properties.set(key,val)}});this.vectors.push(v)}};morpheus.JoinedMetadataModel.prototype={add:function(name){var index=morpheus.MetadataUtil.indexOf(this,name);var oldVector;if(index!==-1){oldVector=this.remove(index)}var v=new morpheus.Vector(name,this.getItemCount());if(oldVector!=null){oldVector.getProperties().forEach(function(val,key){v.getProperties().set(key,val)});for(var i=0,size=oldVector.size();i<size;i++){v.setValue(i,oldVector.getValue(i))}}this.vectors.push(v);return v},getItemCount:function(){return this.m1.getItemCount()+this.m2.getItemCount()},get:function(index){return this.vectors[index]},remove:function(index){return this.vectors.splice(index,1)[0]},getByName:function(name){for(var i=0,length=this.vectors.length;i<length;i++){if(name===this.vectors[i].getName()){return this.vectors[i]}}},getMetadataCount:function(){return this.vectors.length}};morpheus.MetadataModelAdapter=function(model){this.model=model};morpheus.MetadataModelAdapter.prototype={add:function(name){return this.model.add(name)},getItemCount:function(){return this.model.getItemCount()},get:function(index){return this.model.get(index)},remove:function(index){return this.model.remove(index)},getByName:function(name){return this.model.getByName(name)},getMetadataCount:function(){return this.model.getMetadataCount()}};morpheus.MetadataModelColumnView=function(model,indices){this.model=model;this.indices=indices};morpheus.MetadataModelColumnView.prototype={add:function(name){var vector=this.model.add(name);var index=morpheus.MetadataUtil.indexOf(this.model,name);this.indices.push(index);return vector},getMetadataCount:function(){return this.indices.length},get:function(index){if(index<0||index>=this.indices.length){throw"index out of bounds"}return this.model.get(this.indices[index])},remove:function(index){if(index<0||index>=this.indices.length){throw"index out of bounds"}var v=this.model.remove(this.indices[index]);this.indices.splice(index,1);return v},getByName:function(name){var index=morpheus.MetadataUtil.indexOf(this,name);return index!==-1?this.get(index):undefined}};morpheus.Util.extend(morpheus.MetadataModelColumnView,morpheus.MetadataModelAdapter);morpheus.MetadataModelItemView=function(model,indices){this.model=model;this.indices=indices};morpheus.MetadataModelItemView.prototype={add:function(name){var v=this.model.add(name);return new morpheus.SlicedVector(v,this.indices)},getItemCount:function(){return this.indices.length},get:function(index){var v=this.model.get(index);if(v===undefined){return undefined}return new morpheus.SlicedVector(v,this.indices)},getByName:function(name){var v=this.model.getByName(name);if(v===undefined){return undefined}return new morpheus.SlicedVector(v,this.indices)},getMetadataCount:function(){return this.model.getMetadataCount()}};morpheus.Util.extend(morpheus.MetadataModelItemView,morpheus.MetadataModelAdapter);morpheus.MetadataModel=function(itemCount){this.itemCount=itemCount;this.vectors=[]};morpheus.MetadataModel.prototype={add:function(name,options){var index=morpheus.MetadataUtil.indexOf(this,name);var oldVector;if(index!==-1){oldVector=this.get(index)}var v=new morpheus.Vector(name,this.getItemCount());if(oldVector!=null){for(var i=0,size=oldVector.size();i<size;i++){var val=oldVector.getValue(i);v.setValue(i,val)}}if(index!==-1){this.vectors.splice(index,1,v)}else{this.vectors.push(v)}return v},getItemCount:function(){return this.itemCount},get:function(index){return this.vectors[index]},remove:function(index){return this.vectors.splice(index,1)[0]},getByName:function(name){var index=morpheus.MetadataUtil.indexOf(this,name);return index!==-1?this.get(index):undefined},getMetadataCount:function(){return this.vectors.length}};morpheus.MetadataUtil=function(){};morpheus.MetadataUtil.renameFields=function(dataset,options){_.each(options.rows,function(item){if(item.renameTo){var v=dataset.getRowMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}});_.each(options.columns,function(item){if(item.renameTo){var v=dataset.getColumnMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}})};morpheus.MetadataUtil.search=function(options){var model=options.model;var fullModel=options.fullModel;if(!fullModel){fullModel=model}var text=options.text;var isColumns=options.isColumns;text=$.trim(text);if(text===""){return null}var tokens=morpheus.Util.getAutocompleteTokens(text);if(tokens.length==0){return null}var indexField="#";var fieldNames=morpheus.MetadataUtil.getMetadataNames(fullModel);fieldNames.push(indexField);var predicates=morpheus.Util.createSearchPredicates({tokens:tokens,fields:fieldNames,defaultMatchMode:options.defaultMatchMode});var vectors=[];var nameToVector=new morpheus.Map;for(var j=0;j<fullModel.getMetadataCount();j++){var v=fullModel.get(j);var dataType=morpheus.VectorUtil.getDataType(v);var wrapper={vector:v,dataType:dataType,isArray:dataType.indexOf("[")===0};nameToVector.set(v.getName(),wrapper);if(model.getByName(v.getName())!=null){vectors.push(wrapper)}}var indices=[];var npredicates=predicates.length;for(var p=0;p<npredicates;p++){var predicate=predicates[p];var filterColumnName=predicate.getField();if(filterColumnName!=null&&!predicate.isNumber()){var wrapper=nameToVector.get(filterColumnName);if(wrapper&&(wrapper.dataType==="number"||wrapper.dataType==="[number]")){if(predicate.getText){predicates[p]=new morpheus.Util.EqualsPredicate(filterColumnName,parseFloat(predicate.getText()))}else if(predicate.getValues){var values=[];predicate.getValues().forEach(function(val){values.push(parseFloat(val))});predicate[p]=new morpheus.Util.ExactTermsPredicate(filterColumnName,values)}}}}var matchAllPredicates=options.matchAllPredicates===true;function isPredicateMatch(predicate){var filterColumnName=predicate.getField();if(filterColumnName!=null){var value=null;if(filterColumnName===indexField){value=i+1;if(predicate.accept(value)){return true}}else{var wrapper=nameToVector.get(filterColumnName);if(wrapper){value=wrapper.vector.getValue(i);if(wrapper.isArray){if(value!=null){for(var k=0;k<value.length;k++){if(predicate.accept(value[k])){return true}}}}else{if(predicate.accept(value)){return true}}}}}else{for(var j=0;j<nfields;j++){var wrapper=vectors[j];var value=wrapper.vector.getValue(i);if(wrapper.isArray){if(value!=null){for(var k=0;k<value.length;k++){if(predicate.accept(value[k])){return true}}}}else{if(predicate.accept(value)){return true}}}}}var nfields=vectors.length;for(var i=0,nitems=model.getItemCount();i<nitems;i++){if(!matchAllPredicates){for(var p=0;p<npredicates;p++){var predicate=predicates[p];if(isPredicateMatch(predicate)){indices.push(i);break}}}else{var matches=true;for(var p=0;p<npredicates;p++){var predicate=predicates[p];if(!isPredicateMatch(predicate)){matches=false;break}}if(matches){indices.push(i)}}}return indices};morpheus.MetadataUtil.shallowCopy=function(model){var copy=new morpheus.MetadataModel(model.getItemCount());for(var i=0;i<model.getMetadataCount();i++){var v=model.get(i);var newVector=new morpheus.VectorAdapter(v);newVector.properties=new morpheus.Map;newVector.getProperties=function(){return this.properties};v.getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){newVector.properties.set(key,val)}});copy.vectors.push(newVector)}return copy};morpheus.MetadataUtil.autocomplete=function(model){return function(tokens,cb){var matches=[];var regex=null;var regexMatch=null;var searchModel=model;var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);var fieldSearchFieldName=null;if(token!==""){var semi=token.indexOf(":");if(semi>0){if(token.charCodeAt(semi-1)!==92){var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[token.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}var index=morpheus.MetadataUtil.indexOf(searchModel,possibleField);if(index!==-1){fieldSearchFieldName=possibleField;token=$.trim(token.substring(semi+1));searchModel=new morpheus.MetadataModelColumnView(model,[index])}}}var set=new morpheus.Set;regex=new RegExp(morpheus.Util.escapeRegex(token),"i");regexMatch=new RegExp("("+morpheus.Util.escapeRegex(token)+")","i");var max=10;var vectors=[];var isArray=[];for(var j=0;j<searchModel.getMetadataCount();j++){var v=searchModel.get(j);var dataType=morpheus.VectorUtil.getDataType(v);if(dataType==="string"||dataType==="[string]"){vectors.push(v);isArray.push(dataType==="[string]")}}var nfields=vectors.length;loop:for(var i=0,nitems=searchModel.getItemCount();i<nitems;i++){for(var j=0;j<nfields;j++){var v=vectors[j];var val=v.getValue(i);if(val!=null){if(isArray[j]){for(var k=0;k<val.length;k++){var id=new morpheus.Identifier([val[k],v.getName()]);if(!set.has(id)&&regex.test(val[k])){set.add(id);if(set.size()===max){break loop}}}}else{var id=new morpheus.Identifier([val,v.getName()]);if(!set.has(id)&&regex.test(val)){set.add(id);if(set.size()===max){break loop}}}}}}set.forEach(function(id){var array=id.getArray();var field=array[1];var val=array[0];var quotedField=field;if(quotedField.indexOf(" ")!==-1){quotedField='"'+quotedField+'"'}var quotedValue=val;if(quotedValue.indexOf(" ")!==-1){quotedValue='"'+quotedValue+'"'}matches.push({value:quotedField+":"+quotedValue,label:'<span style="font-weight:300;">'+field+":</span>"+"<span>"+val.replace(regexMatch,"<b>$1</b>")+"</span>"})})}if(regex==null){regex=new RegExp(".*","i")}for(var j=0;j<searchModel.getMetadataCount();j++){var v=searchModel.get(j);var dataType=morpheus.VectorUtil.getDataType(v);var field=v.getName();if(dataType==="number"||dataType==="string"||dataType==="[string]"){if(regex.test(field)&&field!==fieldSearchFieldName){var quotedField=field;if(quotedField.indexOf(" ")!==-1){quotedField='"'+quotedField+'"'}matches.push({value:quotedField+":",label:'<span style="font-weight:300;">'+(regexMatch==null?field:field.replace(regexMatch,"<b>$1</b>"))+":</span>"+(dataType==="number"?"<span"+' style="font-weight:300;font-size:85%;">.., >, <, >=, <=,'+" =</span>":""),show:true})}}}cb(matches)}};morpheus.MetadataUtil.getMetadataNames=function(metadataModel){var names=[];for(var i=0,count=metadataModel.getMetadataCount();i<count;i++){names.push(metadataModel.get(i).getName(i))}names.sort(function(a,b){a=a.toLowerCase();b=b.toLowerCase();return a<b?-1:a===b?0:1});return names};morpheus.MetadataUtil.getVectors=function(metadataModel,names){var vectors=[];names.forEach(function(name){var v=metadataModel.getByName(name);if(!v){throw name+" not found. Available fields are "+morpheus.MetadataUtil.getMetadataNames(metadataModel)}vectors.push(v)});return vectors};morpheus.MetadataUtil.indexOf=function(metadataModel,name){for(var i=0,length=metadataModel.getMetadataCount();i<length;i++){if(name===metadataModel.get(i).getName()){return i}}return-1};morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS=["target","gene_target","moa"];morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS=new morpheus.Set;["pr_analyte_id","pr_gene_title","pr_gene_id","pr_analyte_num","pr_bset_id","pr_lua_id","pr_pool_id","pr_is_bing","pr_is_inf","pr_is_lmark","qc_slope","qc_f_logp","qc_iqr","bead_batch","bead_revision","bead_set","det_mode","det_plate","det_well","mfc_plate_dim","mfc_plate_id","mfc_plate_name","mfc_plate_quad","mfc_plate_well","pert_dose_unit","pert_id_vendor","pert_mfc_desc","pert_mfc_id","pert_time","pert_time_unit","pert_univ_id","pert_vehicle","pool_id","rna_plate","rna_well","count_mean","count_cv","provenance_code"].forEach(function(name){morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS.add(name)});morpheus.MetadataUtil.maybeConvertStrings=function(metadata,metadataStartIndex){for(var i=metadataStartIndex,count=metadata.getMetadataCount();i<count;i++){morpheus.VectorUtil.maybeConvertStringToNumber(metadata.get(i))}morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS.forEach(function(field){if(metadata.getByName(field)){morpheus.VectorUtil.maybeConvertToStringArray(metadata.getByName(field),",")}})};morpheus.MetadataUtil.copy=function(src,dest){if(src.getItemCount()!=dest.getItemCount()){throw"Item count not equal in source and destination. "+src.getItemCount()+" != "+dest.getItemCount()}var itemCount=src.getItemCount();var metadataColumns=src.getMetadataCount();for(var j=0;j<metadataColumns;j++){var srcVector=src.get(j);var destVector=dest.getByName(srcVector.getName());if(destVector==null){destVector=dest.add(srcVector.getName())}for(var i=0;i<itemCount;i++){destVector.setValue(i,srcVector.getValue(i))}}};morpheus.MetadataUtil.addVectorIfNotExists=function(metadataModel,name){var v=metadataModel.getByName(name);if(!v){v=metadataModel.add(name)}return v};morpheus.MetadataUtil.getMatchingIndices=function(metadataModel,tokens){var indices={};for(var itemIndex=0,nitems=metadataModel.getItemCount();itemIndex<nitems;itemIndex++){var matches=false;for(var metadataIndex=0,metadataCount=metadataModel.getMetadataCount();metadataIndex<metadataCount&&!matches;metadataIndex++){var vector=metadataModel.get(metadataModel.getColumnName(metadataIndex));var value=vector.getValue(itemIndex);for(var i=0,length=tokens.length;i<length;i++){if(tokens[i]==value){matches=true;break}}}if(matches){indices[itemIndex]=1}}return indices};morpheus.MolarConcentration=function(){};morpheus.MolarConcentration.getMicroMolarConcentration=function(text){text=text.toLowerCase();for(var i=0;i<morpheus.MolarConcentration.CONCENTRATIONS.length;i++){var pair=morpheus.MolarConcentration.CONCENTRATIONS[i];var key=pair[0];var factorToMolar=pair[1];var index=text.indexOf(key);if(index!=-1){var value=text.substring(0,index).trim();var factor=factorToMolar/1e7;var conc=parseFloat(value);return conc/factor}}};morpheus.MolarConcentration.CONCENTRATIONS=[["mm",1e4],["um",1e7],["µ"+"m",1e7],["nm",1e10],["pm",1e13],["fm",1e16],["am",1e19],["zm",1e22],["ym",1e25],["m",1]];morpheus.MaximumMeanProbe=function(probes){return morpheus.MaximumUnivariateFunction(probes,morpheus.Mean)};morpheus.MaximumMeanProbe.toString=function(){return"Maximum Mean Probe"};morpheus.MaximumMeanProbe.selectOne=true;morpheus.MaximumMedianProbe=function(probes){return morpheus.MaximumUnivariateFunction(probes,morpheus.Median)};morpheus.MaximumMedianProbe.toString=function(){return"Maximum Median Probe"};morpheus.MaximumMedianProbe.selectOne=true;morpheus.MaximumUnivariateFunction=function(rowView,fun){var curMax=Number.NEGATIVE_INFINITY;var curIndex=-1;for(var i=0;i<rowView.dataset.getRowCount();i++){rowView.setIndex(i);var mean=fun(rowView);if(mean>curMax){curMax=mean;curIndex=i}}return{value:curMax,index:curIndex}};morpheus.Positions=function(){this.spaces=undefined;this.defaultPositionFunction=function(index){return this.size*index};this.squishedPositionFunction=function(index){return this.positions[index]};this.positionFunction=this.defaultPositionFunction;this.squishedIndices={};this.isSquished=false};morpheus.Positions.getBottom=function(rect,rowPositions){var bottom=rowPositions.getLength();if(rect!=null){bottom=1+rowPositions.getIndex(rect.y+rect.height,false);bottom=Math.max(0,bottom);bottom=Math.min(rowPositions.getLength(),bottom)}return bottom};morpheus.Positions.getTop=function(rect,rowPositions){var top=0;if(rect!=null){top=rowPositions.getIndex(rect.y,false)-1;top=Math.max(0,top);top=Math.min(rowPositions.getLength(),top)}return top};morpheus.Positions.getLeft=function(rect,columnPositions){var left=0;if(rect!=null){left=columnPositions.getIndex(rect.x,false)-1;left=Math.max(0,left);left=Math.min(columnPositions.getLength(),left)}return left};morpheus.Positions.getRight=function(rect,columnPositions){var right=columnPositions.getLength();if(rect!=null){right=1+columnPositions.getIndex(rect.x+rect.width,false);right=Math.min(columnPositions.getLength(),right)}return right};morpheus.Positions.prototype={length:0,size:13,squishFactor:.1,compress:true,copy:function(){var copy=new morpheus.Positions;if(this.spaces){copy.spaces=this.spaces.slice()}copy.compress=this.compress;copy.squishFactor=this.squishFactor;copy.size=this.size;copy.length=this.length;if(this.isSquished){copy.positionFunction=copy.squishedPositionFunction;copy.squishedIndices=_.clone(this.squishedIndices);copy.isSquished=true}return copy},getIndex:function(position,exact){if(this.getLength()===0){return-1}if(exact){return this.binaryExactSearch(position)}else{return this.binaryInExactSearch(position)}},getLength:function(){return this.length},getPosition:function(index){return this.positionFunction(index)+(this.spaces!==undefined?this.spaces[index]:0)},getItemSize:function(index){return this.squishedIndices[index]===true?this.size*this.squishFactor:this.size},getSize:function(){return this.size},setSpaces:function(spaces){this.spaces=spaces},setLength:function(length){this.length=length;this.trigger("change",{source:this,value:"length"})},setSize:function(size){this.size=size;if(this.isSquished){this.setSquishedIndices(this.squishedIndices)}this.trigger("change",{source:this,value:"size"})},setSquishedIndices:function(squishedIndices){if(squishedIndices!=null){var compress=this.compress;this.squishedIndices=squishedIndices;var positions=[];var squishFactor=this.squishFactor;var size=this.size;var position=0;for(var i=0,length=this.getLength();i<length;i++){var itemSize;if(squishedIndices[i]===true){positions.push(position);itemSize=size*squishFactor;position+=itemSize}else{if(!compress){position=size*i}positions.push(position);position+=size}}this.isSquished=true;this.positions=positions;this.positionFunction=this.squishedPositionFunction}else{this.squishedIndices={};this.isSquished=false;this.positionFunction=this.defaultPositionFunction}this.trigger("change",{source:this,value:"squishedIndices"})},setSquishFactor:function(f){if(this.squishFactor!==f){this.squishFactor=f;if(this.isSquished){this.setSquishedIndices(this.squishedIndices)}this.trigger("change",{source:this,value:"squishFactor"})}},getSquishFactor:function(){return this.squishFactor},binaryExactSearch:function(position){var low=0;var high=this.length-1;while(low<=high){var mid=low+high>>1;var midVal=this.getPosition(mid);var size=this.getItemSize(mid);if(midVal<=position&&position<midVal+size){return mid}if(midVal<position){low=mid+1}else if(midVal>position){high=mid-1}else{return mid}}return-1},binaryInExactSearch:function(position){var low=0;var high=this.getLength()-1;var maxIndex=this.getLength()-1;if(position<=this.getPosition(0)){return 0}while(low<=high){var mid=low+high>>1;var midVal=this.getPosition(mid);var size=this.getItemSize(mid);var nextStart=maxIndex===mid?midVal+size:this.getPosition(mid+1);if(midVal<=position&&position<nextStart){return mid}if(midVal<position){low=mid+1}else if(midVal>position){high=mid-1}else{return mid}}return low-1}};morpheus.Util.extend(morpheus.Positions,morpheus.Events);morpheus.Project=function(dataset){this.originalDataset=dataset;this.rowIndexMapper=new morpheus.IndexMapper(this,true);this.columnIndexMapper=new morpheus.IndexMapper(this,false);this.groupRows=[];this.groupColumns=[];this.rowColorModel=new morpheus.VectorColorModel;this.columnColorModel=new morpheus.VectorColorModel;this.rowShapeModel=new morpheus.VectorShapeModel;this.columnShapeModel=new morpheus.VectorShapeModel;this.rowFontModel=new morpheus.VectorFontModel;this.columnFontModel=new morpheus.VectorFontModel;this.hoverColumnIndex=-1;this.hoverRowIndex=-1;this.columnSelectionModel=new morpheus.SelectionModel(this,true);this.rowSelectionModel=new morpheus.SelectionModel(this,false);this.elementSelectionModel=new morpheus.ElementSelectionModel(this);this.symmetricProjectListener=null;morpheus.Project._recomputeCalculatedColumnFields(this.originalDataset,morpheus.VectorKeys.RECOMPUTE_FUNCTION_NEW_HEAT_MAP);morpheus.Project._recomputeCalculatedColumnFields(new morpheus.TransposedDatasetView(this.originalDataset),morpheus.VectorKeys.RECOMPUTE_FUNCTION_NEW_HEAT_MAP)};morpheus.Project.Events={DATASET_CHANGED:"datasetChanged",ROW_GROUP_BY_CHANGED:"rowGroupByChanged",COLUMN_GROUP_BY_CHANGED:"columnGroupByChanged",ROW_FILTER_CHANGED:"rowFilterChanged",COLUMN_FILTER_CHANGED:"columnFilterChanged",ROW_SORT_ORDER_CHANGED:"rowSortOrderChanged",COLUMN_SORT_ORDER_CHANGED:"columnSortOrderChanged",ROW_TRACK_REMOVED:"rowTrackRemoved",COLUMN_TRACK_REMOVED:"columnTrackRemoved"};morpheus.Project._recomputeCalculatedColumnFields=function(dataset,key){var metadata=dataset.getColumnMetadata();var view=new morpheus.DatasetColumnView(dataset);var nfound=0;for(var metadataIndex=0,count=metadata.getMetadataCount();metadataIndex<count;metadataIndex++){var vector=metadata.get(metadataIndex);if(vector.getProperties().get(morpheus.VectorKeys.FUNCTION)!=null&&vector.getProperties().get(key)){var f=morpheus.VectorUtil.jsonToFunction(vector,morpheus.VectorKeys.FUNCTION);for(var j=0,size=vector.size();j<size;j++){view.setIndex(j);vector.setValue(j,f(view,dataset,j))}nfound++}}return nfound};morpheus.Project.prototype={isSymmetric:function(){return this.symmetricProjectListener!=null},setSymmetric:function(heatMap){if(heatMap!=null){if(this.symmetricProjectListener==null){this.symmetricProjectListener=new morpheus.SymmetricProjectListener(heatMap.getProject(),heatMap.vscroll,heatMap.hscroll)}}else{if(this.symmetricProjectListener!=null){this.symmetricProjectListener.dispose()}this.symmetricProjectListener=null}},getHoverColumnIndex:function(){return this.hoverColumnIndex},setHoverColumnIndex:function(index){this.hoverColumnIndex=index},getHoverRowIndex:function(){return this.hoverRowIndex},setHoverRowIndex:function(index){this.hoverRowIndex=index},getRowColorModel:function(){return this.rowColorModel},getRowShapeModel:function(){return this.rowShapeModel},getColumnShapeModel:function(){return this.columnShapeModel},getRowFontModel:function(){return this.rowFontModel},getColumnFontModel:function(){return this.columnFontModel},getGroupRows:function(){return this.groupRows},getGroupColumns:function(){return this.groupColumns},getFullDataset:function(){return this.originalDataset},getColumnSelectionModel:function(){return this.columnSelectionModel},getRowSelectionModel:function(){return this.rowSelectionModel},getFilteredSortedRowIndices:function(){return this.rowIndexMapper.convertToView()},getFilteredSortedColumnIndices:function(){return this.columnIndexMapper.convertToView()},getElementSelectionModel:function(){return this.elementSelectionModel},setFullDataset:function(dataset,notify){this.originalDataset=dataset;this.rowIndexMapper.setFilter(this.rowIndexMapper.getFilter());this.columnIndexMapper.setFilter(this.columnIndexMapper.getFilter());this.columnSelectionModel.clear();this.rowSelectionModel.clear();this.elementSelectionModel.clear();if(notify){this.trigger(morpheus.Project.Events.DATASET_CHANGED)}},setGroupRows:function(keys,notify){this.groupRows=keys;for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(false)}}if(notify){this.trigger(morpheus.Project.Events.ROW_GROUP_BY_CHANGED)}},setGroupColumns:function(keys,notify){this.groupColumns=keys;for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(true)}}if(notify){this.trigger(morpheus.Project.Events.COLUMN_GROUP_BY_CHANGED)}},setRowFilter:function(filter,notify){this._saveSelection(false);this.rowIndexMapper.setFilter(filter);this._restoreSelection(false);if(notify){this.trigger(morpheus.Project.Events.ROW_FILTER_CHANGED)}},getRowFilter:function(){return this.rowIndexMapper.getFilter()},getColumnFilter:function(){return this.columnIndexMapper.getFilter()},setColumnFilter:function(filter,notify){this._saveSelection(true);this.columnIndexMapper.setFilter(filter);this._restoreSelection(true);if(notify){this.trigger(morpheus.Project.Events.COLUMN_FILTER_CHANGED)}},getColumnColorModel:function(){return this.columnColorModel},getSortedFilteredDataset:function(){return morpheus.DatasetUtil.slicedView(this.getFullDataset(),this.rowIndexMapper.convertToView(),this.columnIndexMapper.convertToView())},getSelectedDataset:function(options){options=$.extend({},{selectedRows:true,selectedColumns:true,emptyToAll:true},options);var dataset=this.getSortedFilteredDataset();var rows=null;if(options.selectedRows){rows=this.rowSelectionModel.getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(rows.length===0&&options.emptyToAll){rows=null}}var columns=null;if(options.selectedColumns){columns=this.columnSelectionModel.getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(columns.length===0&&options.emptyToAll){columns=null}}return rows==null&&columns==null?dataset:new morpheus.SlicedDatasetView(dataset,rows,columns)},_saveSelection:function(isColumns){this.elementSelectionModel.save();if(isColumns){this.columnSelectionModel.save()}else{this.rowSelectionModel.save()}},_restoreSelection:function(isColumns){if(isColumns){this.columnSelectionModel.restore()}else{this.rowSelectionModel.restore()}this.elementSelectionModel.restore()},setRowSortKeys:function(keys,notify){this._saveSelection(false);for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(false)}}this.rowIndexMapper.setSortKeys(keys);this._restoreSelection(false);if(notify){this.trigger(morpheus.Project.Events.ROW_SORT_ORDER_CHANGED)}},setColumnSortKeys:function(keys,notify){this._saveSelection(true);for(var i=0,nkeys=keys.length;i<nkeys;i++){if(keys[i].isColumns()===undefined){keys[i].setColumns(true)}}this.columnIndexMapper.setSortKeys(keys);this._restoreSelection(true);if(notify){this.trigger(morpheus.Project.Events.COLUMN_SORT_ORDER_CHANGED)}},getRowSortKeys:function(){return this.rowIndexMapper.sortKeys},getColumnSortKeys:function(){return this.columnIndexMapper.sortKeys},convertViewColumnIndexToModel:function(viewIndex){return this.columnIndexMapper.convertViewIndexToModel(viewIndex)},convertViewRowIndexToModel:function(viewIndex){return this.rowIndexMapper.convertViewIndexToModel(viewIndex)},convertModelRowIndexToView:function(modelIndex){return this.rowIndexMapper.convertModelIndexToView(modelIndex)},convertModelColumnIndexToView:function(modelIndex){return this.columnIndexMapper.convertModelIndexToView(modelIndex)},isColumnViewIndexSelected:function(index){return this.columnSelectionModel.isViewIndexSelected(index)},isRowViewIndexSelected:function(index){return this.rowSelectionModel.isViewIndexSelected(index)}};morpheus.Util.extend(morpheus.Project,morpheus.Events);morpheus.QNorm=function(){};morpheus.QNorm.execute=function(data){var rows=data.getRowCount();var cols=data.getColumnCount();var i,j,ind;var dimat;var row_mean=new Float32Array(rows);var ranks=new Float32Array(rows);dimat=morpheus.QNorm.get_di_matrix(data);for(j=0;j<cols;j++){dimat[j].sort(function(s1,s2){if(s1.data<s2.data){return-1}if(s1.data>s2.data){return 1}return 0})}for(i=0;i<rows;i++){var sum=0;var numNonMissing=0;for(j=0;j<cols;j++){var f=dimat[j][i].data;if(!isNaN(f)){sum+=f;numNonMissing++}}row_mean[i]=sum/numNonMissing}for(j=0;j<cols;j++){morpheus.QNorm.get_ranks(ranks,dimat[j],rows);for(i=0;i<rows;i++){ind=dimat[j][i].rank;if(ranks[i]-Math.floor(ranks[i])>.4){data.setValue(ind,j,.5*(row_mean[Math.floor(ranks[i])-1]+row_mean[Math.floor(ranks[i])]))}else{data.setValue(ind,j,row_mean[Math.floor(ranks[i])-1])}}}};morpheus.QNorm.get_di_matrix=function(data){var i,j;var rows=data.getRowCount();var cols=data.getColumnCount();var dimat=[];for(j=0;j<cols;j++){dimat.push([]);for(i=0;i<rows;i++){dimat[j][i]={};dimat[j][i].data=data.getValue(i,j);dimat[j][i].rank=i}}return dimat};morpheus.QNorm.get_ranks=function(rank,x,n){var i,j,k;i=0;while(i<n){j=i;while(j<n-1&&x[j].data==x[j+1].data){j++}if(i!=j){for(k=i;k<=j;k++){rank[k]=(i+j+2)/2}}else{rank[i]=i+1}i=j+1}};morpheus.SelectionModel=function(project,isColumns){this.viewIndices=new morpheus.Set;this.project=project;this.isColumns=isColumns};morpheus.SelectionModel.prototype={setViewIndices:function(indices,notify){this.viewIndices=indices;if(notify){this.trigger("selectionChanged")}},isViewIndexSelected:function(index){return this.viewIndices.has(index)},clear:function(){this.viewIndices=new morpheus.Set},getViewIndices:function(){return this.viewIndices},count:function(){return this.viewIndices.size()},toModelIndices:function(){var project=this.project;var f=this.isColumns?project.convertViewColumnIndexToModel:project.convertViewRowIndexToModel;f=_.bind(f,project);var modelIndices=[];this.viewIndices.forEach(function(index){var m=f(index);modelIndices.push(m)});return modelIndices},save:function(){this.modelIndices=this.toModelIndices()},restore:function(){var project=this.project;this.viewIndices=new morpheus.Set;var f=this.isColumns?project.convertModelColumnIndexToView:project.convertModelRowIndexToView;f=_.bind(f,project);for(var i=0,length=this.modelIndices.length;i<length;i++){var index=f(this.modelIndices[i]);if(index!==-1){this.viewIndices.add(index)}}}};morpheus.Util.extend(morpheus.SelectionModel,morpheus.Events);morpheus.SlicedDatasetView=function(dataset,rowIndices,columnIndices){morpheus.DatasetAdapter.call(this,dataset);if(rowIndices==null){rowIndices=null}if(columnIndices==null){columnIndices=null}this.rowIndices=rowIndices;this.columnIndices=columnIndices};morpheus.SlicedDatasetView.prototype={getRowCount:function(){return this.rowIndices!==null?this.rowIndices.length:this.dataset.getRowCount()},getColumnCount:function(){return this.columnIndices!==null?this.columnIndices.length:this.dataset.getColumnCount()},getValue:function(i,j,seriesIndex){return this.dataset.getValue(this.rowIndices!==null?this.rowIndices[i]:i,this.columnIndices!==null?this.columnIndices[j]:j,seriesIndex)},setValue:function(i,j,value,seriesIndex){this.dataset.setValue(this.rowIndices!==null?this.rowIndices[i]:i,this.columnIndices!==null?this.columnIndices[j]:j,value,seriesIndex)},getRowMetadata:function(){return this.rowIndices!==null?new morpheus.MetadataModelItemView(this.dataset.getRowMetadata(),this.rowIndices):this.dataset.getRowMetadata()},getColumnMetadata:function(){return this.columnIndices!==null?new morpheus.MetadataModelItemView(this.dataset.getColumnMetadata(),this.columnIndices):this.dataset.getColumnMetadata()},toString:function(){return this.getName()}};morpheus.Util.extend(morpheus.SlicedDatasetView,morpheus.DatasetAdapter);morpheus.SlicedVector=function(v,indices){morpheus.VectorAdapter.call(this,v);this.indices=indices};morpheus.SlicedVector.prototype={setValue:function(i,value){this.v.setValue(this.indices[i],value)},getValue:function(i){return this.v.getValue(this.indices[i])},size:function(){return this.indices.length}};morpheus.Util.extend(morpheus.SlicedVector,morpheus.VectorAdapter);morpheus.AbstractSortKey=function(name,columns){this.name=name;this.columns=columns};morpheus.AbstractSortKey.prototype={lockOrder:0,columns:true,preservesDendrogram:false,unlockable:true,isColumns:function(){return this.columns},setColumns:function(columns){this.columns=columns},isPreservesDendrogram:function(){return this.preservesDendrogram},setPreservesDendrogram:function(preservesDendrogram){this.preservesDendrogram=preservesDendrogram},getLockOrder:function(){return this.lockOrder},isUnlockable:function(){return this.unlockable},setUnlockable:function(unlockable){this.unlockable=unlockable},setLockOrder:function(lockOrder){this.lockOrder=lockOrder},setSortOrder:function(sortOrder){this.sortOrder=sortOrder},getSortOrder:function(){return this.sortOrder},init:function(){}};morpheus.MatchesOnTopSortKey=function(project,modelIndices,name,columns){morpheus.AbstractSortKey.call(this,name,columns);var highlightedModelIndices={};var p=project;var viewIndices=[];for(var i=0,j=modelIndices.length,length=modelIndices.length;i<length;i++,j--){highlightedModelIndices[modelIndices[i]]=-1;viewIndices.push(i)}this.comparator=function(i1,i2){var a=highlightedModelIndices[i1];if(a===undefined){a=0}var b=highlightedModelIndices[i2];if(b===undefined){b=0}return a===b?0:a<b?-1:1};this.indices=viewIndices};morpheus.MatchesOnTopSortKey.prototype={toString:function(){return this.name},getSortOrder:function(){return 2},getComparator:function(){return this.comparator},getValue:function(i){return i}};morpheus.Util.extend(morpheus.MatchesOnTopSortKey,morpheus.AbstractSortKey);morpheus.SortKey=function(field,sortOrder,columns){morpheus.AbstractSortKey.call(this,field,columns);if(typeof sortOrder==="string"){sortOrder=morpheus.SortKey.SortOrder[sortOrder.toUpperCase()];if(sortOrder===undefined){sortOrder=0}}this.v=null;this.c=null;this.setSortOrder(sortOrder)};morpheus.SortKey.prototype={toString:function(){return this.name},init:function(dataset,visibleModelIndices){this.v=dataset.getRowMetadata().getByName(this.name);if(!this.v){this.v={};this.v.getValue=function(){return 0};this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.ASCENDING_COMPARATOR:morpheus.SortKey.DESCENDING_COMPARATOR}else{var dataType=morpheus.VectorUtil.getDataType(this.v);if(dataType==="number"){this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR:morpheus.SortKey.NUMBER_DESCENDING_COMPARATOR}else if(dataType==="[number]"){var summary=this.v.getProperties().get(morpheus.VectorKeys.ARRAY_SUMMARY_FUNCTION)||morpheus.SortKey.ARRAY_MAX_SUMMARY_FUNCTION;this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.ARRAY_ASCENDING_COMPARATOR(summary):morpheus.SortKey.ARRAY_DESCENDING_COMPARATOR(summary)}else{this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.ASCENDING_COMPARATOR:morpheus.SortKey.DESCENDING_COMPARATOR}if(this.customComparator!=null){var oldC=this.c;var customComparator=this.customComparator;if(this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING){this.c=function(a,b){var val=customComparator(a,b);return val===0?oldC(a,b):val}}else{this.c=function(a,b){var val=customComparator(b,a);return val===0?oldC(a,b):val}}}}if(this.sortOrder===morpheus.SortKey.SortOrder.TOP_N){var pairs=[];var missingIndices=[];for(var i=0,nrows=visibleModelIndices.length;i<nrows;i++){var index=visibleModelIndices[i];var value=this.v.getValue(index);if(!isNaN(value)){pairs.push({index:index,value:value})}else{missingIndices.push(index)}}var c=this.c;this.c=morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR;pairs.sort(function(pair1,pair2){return c(pair1.value,pair2.value)});var modelIndexToValue=[];var nInGroup=Math.min(pairs.length,10);var counter=0;var topIndex=0;var half=Math.floor(pairs.length/2);var topPairs=pairs.slice(0,half);var bottomPairs=pairs.slice(half);var bottomIndex=bottomPairs.length-1;var ntop=topPairs.length;var npairs=pairs.length;while(counter<npairs){for(var i=0;i<nInGroup&&topIndex<ntop;i++,topIndex++,counter++){modelIndexToValue[topPairs[topIndex].index]=counter}var indexCounterPairs=[];for(var i=0;i<nInGroup&&bottomIndex>=0;i++,bottomIndex--,counter++){indexCounterPairs.push([bottomPairs[bottomIndex].index,counter])}for(var i=indexCounterPairs.length-1,j=0;i>=0;i--,j++){var item_i=indexCounterPairs[i];var item_j=indexCounterPairs[j];modelIndexToValue[item_i[0]]=item_j[1]}}for(var i=0,length=missingIndices.length;i<length;i++,counter++){modelIndexToValue[missingIndices[i]]=counter}this.modelIndexToValue=modelIndexToValue}else{delete this.modelIndexToValue}},getComparator:function(){return this.c},getValue:function(i){return this.modelIndexToValue?this.modelIndexToValue[i]:this.v.getValue(i)}};morpheus.Util.extend(morpheus.SortKey,morpheus.AbstractSortKey);morpheus.SortByValuesKey=function(modelIndices,sortOrder,isColumnSort){morpheus.AbstractSortKey.call(this,"values",isColumnSort);this.bothCount=10;this.modelIndices=modelIndices;this.sortOrder=sortOrder;this.setSortOrder(sortOrder)};morpheus.SortByValuesKey.prototype={toString:function(){return this.name},init:function(dataset,visibleModelIndices){this.dataset=morpheus.DatasetUtil.slicedView(dataset,null,this.modelIndices);this.rowView=new morpheus.DatasetRowView(this.dataset);this.summaryFunction=this.modelIndices.length>1?morpheus.Median:function(row){return row.getValue(0)};if(this.sortOrder===morpheus.SortKey.SortOrder.TOP_N){var pairs=[];var missingIndices=[];for(var i=0,nrows=visibleModelIndices.length;i<nrows;i++){var index=visibleModelIndices[i];var value=this.summaryFunction(this.rowView.setIndex(index));if(!isNaN(value)){pairs.push({index:index,value:value})}else{missingIndices.push(index)}}pairs.sort(function(a,b){return a.value<b.value?1:a.value===b.value?0:-1});var modelIndexToValue=[];var nInGroup=Math.min(pairs.length,this.bothCount);var counter=0;var topIndex=0;var half=Math.floor(pairs.length/2);var topPairs=pairs.slice(0,half);var bottomPairs=pairs.slice(half);var bottomIndex=bottomPairs.length-1;var ntop=topPairs.length;var npairs=pairs.length;while(counter<npairs){for(var i=0;i<nInGroup&&topIndex<ntop;i++,topIndex++,counter++){modelIndexToValue[topPairs[topIndex].index]=counter}var indexCounterPairs=[];for(var i=0;i<nInGroup&&bottomIndex>=0;i++,bottomIndex--,counter++){indexCounterPairs.push([bottomPairs[bottomIndex].index,counter])}for(var i=indexCounterPairs.length-1,j=0;i>=0;i--,j++){var item_i=indexCounterPairs[i];var item_j=indexCounterPairs[j];modelIndexToValue[item_i[0]]=item_j[1]}}for(var i=0,length=missingIndices.length;i<length;i++,counter++){modelIndexToValue[missingIndices[i]]=counter}this.modelIndexToValue=modelIndexToValue}else{delete this.modelIndexToValue}},getComparator:function(){return this.c},getValue:function(i){return this.modelIndexToValue?this.modelIndexToValue[i]:this.summaryFunction(this.rowView.setIndex(i))},setSortOrder:function(sortOrder){if(typeof sortOrder==="string"){sortOrder=morpheus.SortKey.SortOrder[sortOrder.toUpperCase()]}this.sortOrder=sortOrder;if(this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING){this.c=morpheus.SortKey.ELEMENT_ASCENDING_COMPARATOR}else if(this.sortOrder===morpheus.SortKey.SortOrder.DESCENDING){this.c=morpheus.SortKey.ELEMENT_DESCENDING_COMPARATOR}else{this.c=morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR}}};morpheus.Util.extend(morpheus.SortByValuesKey,morpheus.AbstractSortKey);morpheus.SpecifiedModelSortOrder=function(modelIndices,nvisible,name,columns){morpheus.AbstractSortKey.call(this,name,columns);this.nvisible=nvisible;var modelIndexToValue=[];for(var i=0,length=modelIndices.length;i<length;i++){modelIndexToValue[modelIndices[i]]=i}this.modelIndices=modelIndices;this.modelIndexToValue=modelIndexToValue;this.c=morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR};morpheus.SpecifiedModelSortOrder.prototype={toString:function(){return this.name},getComparator:function(a,b){return this.c},getValue:function(i){return this.modelIndexToValue[i]},setSortOrder:function(sortOrder){this.sortOrder=sortOrder;this.c=this.sortOrder===morpheus.SortKey.SortOrder.ASCENDING?morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR:morpheus.SortKey.NUMBER_DESCENDING_COMPARATOR}};morpheus.Util.extend(morpheus.SpecifiedModelSortOrder,morpheus.AbstractSortKey);morpheus.SpecifiedGroupByKey=function(clusterIds,columns){morpheus.AbstractSortKey.call(this,"Dendrogram Cut",columns);this.clusterIds=clusterIds;this.c=function(a,b){return a===b?0:a<b?-1:1}};morpheus.SpecifiedGroupByKey.prototype={toString:function(){return this.name},getComparator:function(a,b){return this.c},getValue:function(i){return this.clusterIds[i]}};morpheus.Util.extend(morpheus.SpecifiedGroupByKey,morpheus.AbstractSortKey);morpheus.SortKey.SortOrder={ASCENDING:0,DESCENDING:1,UNSORTED:2,CUSTOM:3,TOP_N:4};morpheus.SortKey.ASCENDING_COMPARATOR=function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=(""+a).toLowerCase();b=(""+b).toLowerCase();return a===b?0:a<b?-1:1};morpheus.SortKey.DESCENDING_COMPARATOR=function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=(""+a).toLowerCase();b=(""+b).toLowerCase();return a===b?0:a<b?1:-1};morpheus.SortKey.NUMBER_ASCENDING_COMPARATOR=function(a,b){var aNaN=a==null||isNaN(a);var bNaN=b==null||isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?-1:1};morpheus.SortKey.NUMBER_DESCENDING_COMPARATOR=function(a,b){var aNaN=a==null||isNaN(a);var bNaN=b==null||isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?1:-1};morpheus.SortKey.STRING_ASCENDING_COMPARATOR=function(a,b){a=a==null||a.toLowerCase===undefined?null:a.toLowerCase();b=b==null||b.toLowerCase===undefined?null:b.toLowerCase();return a===b?0:a<b?-1:1};morpheus.SortKey.STRING_DESCENDING_COMPARATOR=function(a,b){a=a==null||a.toLowerCase===undefined?null:a.toLowerCase();b=b==null||b.toLowerCase===undefined?null:b.toLowerCase();return a===b?0:a<b?1:-1};morpheus.SortKey.ELEMENT_ASCENDING_COMPARATOR=function(obj1,obj2){var a=+obj1;var b=+obj2;var aNaN=isNaN(a);var bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}if(a===b){if(obj1!=null&&obj1.toObject&&obj2!=null&&obj2.toObject){var a1=obj1.toObject();var b1=obj2.toObject();for(var name in a1){a=a1[name];b=b1[name];var c=a===b?0:a<b?-1:1;if(c!==0){return c}}}}return a===b?0:a<b?-1:1};morpheus.SortKey.ELEMENT_DESCENDING_COMPARATOR=function(obj1,obj2){var a=+obj1;var b=+obj2;var aNaN=isNaN(a);var bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}if(a===b){if(obj1!=null&&obj1.toObject&&obj2!=null&&obj2.toObject){var a1=obj1.toObject();var b1=obj2.toObject();for(var name in a1){a=a1[name];b=b1[name];var c=a===b?0:a<b?1:-1;if(c!==0){return c}}}}return a===b?0:a<b?1:-1};morpheus.SortKey.BOX_PLOT_SUMMARY_FUNCTION=function(array){var box=array.box;if(box==null){var v=morpheus.VectorUtil.arrayAsVector(array);box=morpheus.BoxPlotItem(this.indices!=null?new morpheus.SlicedVector(v,this.indices):v);array.box=box}return box.q3};morpheus.SortKey.ARRAY_MAX_SUMMARY_FUNCTION=function(array){var a=0;if(array!=null){var aPosMax=-Number.MAX_VALUE;var aNegMax=Number.MAX_VALUE;for(var i=0,length=array.length;i<length;i++){var value=array[i];if(!isNaN(value)){if(value>=0){aPosMax=value>aPosMax?value:aPosMax}else{aNegMax=value<aNegMax?value:aNegMax}}}if(aPosMax!==-Number.MAX_VALUE){a=aPosMax}if(aNegMax!==Number.MAX_VALUE){a=Math.abs(aNegMax)>a?aNegMax:a}}return a};morpheus.SortKey.ARRAY_ASCENDING_COMPARATOR=function(summary){return function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=summary(a);b=summary(b);aNaN=isNaN(a);bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?-1:1}};morpheus.SortKey.ARRAY_DESCENDING_COMPARATOR=function(summary){return function(a,b){var aNaN=a==null;var bNaN=b==null;if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}a=summary(a);b=summary(b);aNaN=isNaN(a);bNaN=isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}return a===b?0:a<b?1:-1}};morpheus.SortKey.reverseComparator=function(c){return function(a,b){return c(b,a)}};morpheus.SortKey.keepExistingSortKeys=function(newSortKeys,existingSortKeys){for(var i=0,length=existingSortKeys.length;i<length;i++){var key=existingSortKeys[i];if(key.getLockOrder()>0){var existingIndex=-1;for(var j=0;j<newSortKeys.length;j++){if(newSortKeys[j]===key){existingIndex=j;break}}if(existingIndex!==-1){newSortKeys.splice(existingIndex,1)}newSortKeys.splice(key.getLockOrder()===1?0:newSortKeys.length,0,key)}}return newSortKeys};morpheus.SortKey.fromJSON=function(project,json){var sortKeys=[];json.forEach(function(key){var sortKey=null;if(key.type==="annotation"){sortKey=new morpheus.SortKey(key.field,key.order,key.isColumns);if(key.customSortOrder!=null){var customSortOrderMap=new morpheus.Map;for(var i=0,size=key.customSortOrder.length;i<size;i++){customSortOrderMap.set(key.customSortOrder[i],i)}var comparator=function(a,b){var v1=customSortOrderMap.get(a);var v2=customSortOrderMap.get(b);if(v1===undefined&&v2===undefined){return 0}if(v1===undefined){v1=Infinity}if(v2===undefined){v2=Infinity}return v1<v2?-1:1};sortKey.customComparator=comparator;if(key.preservesDendrogram){sortKey.nvisible=key.customSortOrder.length}}}else if(key.type==="byValues"){sortKey=new morpheus.SortByValuesKey(key.modelIndices,key.order,key.isColumns)}else if(key.type==="specified"){sortKey=new morpheus.SpecifiedModelSortOrder(key.modelIndices,key.nvisible,key.name,key.isColumns)}else if(key.type==="matchesOnTop"){sortKey=new morpheus.MatchesOnTopSortKey(project,key.modelIndices,key.name,key.isColumns)}else{if(key.field!=null){sortKey=new morpheus.SortKey(key.field,key.order)}else{console.log("Unknown key: "+key)}}if(sortKey!=null){if(key.preservesDendrogram!=null){sortKey.setPreservesDendrogram(key.preservesDendrogram)}if(key.lockOrder!=null&&key.lockOrder!==0){sortKey.setLockOrder(key.lockOrder);sortKey.setUnlockable(key.unlockable)}sortKeys.push(sortKey)}});return sortKeys};morpheus.SortKey.toJSON=function(sortKeys){var json=[];sortKeys.forEach(function(key){var sortKey=null;if(key instanceof morpheus.SortKey){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"annotation",field:""+key}}else if(key instanceof morpheus.SortByValuesKey){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"byValues",modelIndices:key.modelIndices}}else if(key instanceof morpheus.SpecifiedModelSortOrder){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"specified",modelIndices:key.modelIndices,name:key.name,nvisible:key.nvisible}}else if(key instanceof morpheus.MatchesOnTopSortKey){sortKey={isColumns:key.isColumns(),order:key.getSortOrder(),type:"matchesOnTop",modelIndices:key.modelIndices,name:key.name}}if(sortKey!=null){sortKey.preservesDendrogram=key.isPreservesDendrogram();if(key.getLockOrder&&key.getLockOrder()!==0){sortKey.lockOrder=key.getLockOrder();sortKey.unlockable=key.isUnlockable?key.isUnlockable():false}json.push(sortKey)}else{console.log("Unknown sort key type")}});return json};morpheus.SymmetricProjectListener=function(project,vscroll,hscroll){var ignoreEvent=false;var rowGroupBy;var columnGroupBy;var rowFilter;var columnFilter;var rowSortOrder;var columnSortOrder;var columnSelection;var rowSelection;var vscrollFunction;var hscrollFunction;project.on(morpheus.Project.Events.ROW_GROUP_BY_CHANGED,rowGroupBy=function(){if(ignoreEvent){return}ignoreEvent=true;project.setGroupColumns(project.getGroupRows(),true);ignoreEvent=false});project.on(morpheus.Project.Events.COLUMN_GROUP_BY_CHANGED,columnGroupBy=function(){if(ignoreEvent){return}ignoreEvent=true;project.setGroupRows(project.getGroupColumns(),true);ignoreEvent=false});project.on(morpheus.Project.Events.ROW_FILTER_CHANGED,rowFilter=function(){if(ignoreEvent){return}ignoreEvent=true;project.setColumnFilter(project.getRowFilter(),true);ignoreEvent=false});project.on(morpheus.Project.Events.COLUMN_FILTER_CHANGED,columnFilter=function(){if(ignoreEvent){return}ignoreEvent=true;project.setRowFilter(project.getColumnFilter(),true);ignoreEvent=false});project.on(morpheus.Project.Events.ROW_SORT_ORDER_CHANGED,rowSortOrder=function(){if(ignoreEvent){return}ignoreEvent=true;project.setColumnSortKeys(project.getRowSortKeys(),true);ignoreEvent=false});project.on(morpheus.Project.Events.COLUMN_SORT_ORDER_CHANGED,columnSortOrder=function(){if(ignoreEvent){return}ignoreEvent=true;project.setRowSortKeys(project.getColumnSortKeys(),true);ignoreEvent=false});project.getColumnSelectionModel().on("selectionChanged",columnSelection=function(){if(ignoreEvent){return}ignoreEvent=true;project.getRowSelectionModel().setViewIndices(project.getColumnSelectionModel().getViewIndices(),true);ignoreEvent=false});project.getRowSelectionModel().on("selectionChanged",rowSelection=function(){if(ignoreEvent){return}ignoreEvent=true;project.getColumnSelectionModel().setViewIndices(project.getRowSelectionModel().getViewIndices(),true);ignoreEvent=false});vscroll.on("scroll",vscrollFunction=function(){if(ignoreEvent){return}ignoreEvent=true;var f=vscroll.getMaxValue()===0?0:vscroll.getValue()/vscroll.getMaxValue();hscroll.setValue(f*hscroll.getMaxValue(),true);ignoreEvent=false});hscroll.on("scroll",hscrollFunction=function(){if(ignoreEvent){return}ignoreEvent=true;var f=hscroll.getMaxValue()===0?0:hscroll.getValue()/hscroll.getMaxValue();vscroll.setValue(f*vscroll.getMaxValue(),true);ignoreEvent=false});this.dispose=function(){project.off(morpheus.Project.Events.ROW_GROUP_BY_CHANGED,rowGroupBy);project.off(morpheus.Project.Events.COLUMN_GROUP_BY_CHANGED,columnGroupBy);project.off(morpheus.Project.Events.ROW_FILTER_CHANGED,rowFilter);project.off(morpheus.Project.Events.COLUMN_FILTER_CHANGED,columnFilter);project.off(morpheus.Project.Events.ROW_SORT_ORDER_CHANGED,rowSortOrder);project.off(morpheus.Project.Events.COLUMN_SORT_ORDER_CHANGED,columnSortOrder);project.getColumnSelectionModel().off("selectionChanged",columnSelection);project.getRowSelectionModel().off("selectionChanged",rowSelection);vscroll.off("scroll",vscrollFunction);hscroll.off("scroll",hscrollFunction)}};morpheus.TransposedDatasetView=function(dataset){morpheus.DatasetAdapter.call(this,dataset)};morpheus.TransposedDatasetView.prototype={getRowCount:function(){return this.dataset.getColumnCount()},getColumnCount:function(){return this.dataset.getRowCount()},getValue:function(i,j,seriesIndex){return this.dataset.getValue(j,i,seriesIndex)},setValue:function(i,j,value,seriesIndex){this.dataset.setValue(j,i,value,seriesIndex)},getRowMetadata:function(){return this.dataset.getColumnMetadata()},getColumnMetadata:function(){return this.dataset.getRowMetadata()}};morpheus.Util.extend(morpheus.TransposedDatasetView,morpheus.DatasetAdapter);morpheus.Percentile=function(vector,p,isSorted){return morpheus.ArrayPercentile(morpheus.RemoveNaN(vector),p,isSorted)};morpheus.Percentile.toString=function(){return"Percentile"};morpheus.RemoveNaN=function(values){var array=[];for(var i=0,size=values.size();i<size;i++){var value=values.getValue(i);if(!isNaN(value)){array.push(value)}}return array};morpheus.Median=function(vector){return morpheus.ArrayPercentile(morpheus.RemoveNaN(vector),50,false)};morpheus.Median.toString=function(){return"Median"};morpheus.ArrayPercentile=function(values,p,isSorted){if(!isSorted){values.sort(function(a,b){return a<b?-1:a===b?0:1})}return d3.quantile(values,p/100)};morpheus.MaxPercentiles=function(percentiles){var f=function(vector){var values=[];for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(!isNaN(value)){values.push(value)}}if(values.length===0){return NaN}values.sort(function(a,b){return a<b?-1:a===b?0:1});var max=0;for(var i=0;i<percentiles.length;i++){var p=morpheus.ArrayPercentile(values,percentiles[i],true);if(Math.abs(p)>Math.abs(max)){max=p}}return max};f.toString=function(){var s=["Maximum of "];for(var i=0,length=percentiles.length;i<length;i++){if(i>0&&length>2){s.push(", ")}if(i===length-1){s.push(length==2?" and ":"and ")}s.push(percentiles[i])}s.push(" percentiles");return s.join("")};return f};morpheus.CountIf=function(vector,criteria){if(!/[<>=!]/.test(criteria)){criteria='=="'+criteria+'"'}var matches=0;for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(eval(value+criteria)){matches++}}return matches};morpheus.Mean=function(vector){var sum=0;var count=0;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){sum+=val;count++}}return count===0?NaN:sum/count};morpheus.Mean.toString=function(){return"Mean"};morpheus.Sum=function(vector){var sum=0;var found=false;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){found=true;sum+=val}}return!found?NaN:sum};morpheus.Sum.toString=function(){return"Sum"};morpheus.CountNonNaN=function(vector){var count=0;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){count++}}return count};morpheus.CountNonNaN.toString=function(){return"Count non-NaN"};morpheus.Max=function(vector){var max=-Number.MAX_VALUE;var found=false;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){found=true;max=Math.max(max,val)}}return!found?NaN:max};morpheus.Max.toString=function(){return"Max"};morpheus.Min=function(vector){var min=Number.MAX_VALUE;var found=false;for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(!isNaN(val)){found=true;min=Math.min(min,val)}}return!found?NaN:min};morpheus.Min.toString=function(){return"Min"};morpheus.Variance=function(list,mean){if(mean==undefined){mean=morpheus.Mean(list)}var sum=0;var n=0;for(var j=0,size=list.size();j<size;j++){var x=list.getValue(j);if(!isNaN(x)){var diff=x-mean;diff=diff*diff;sum+=diff;n++}}if(n<=1){return NaN}n=n-1;if(n<1){n=1}var variance=sum/n;return variance};morpheus.Variance.toString=function(){return"Variance"};morpheus.StandardDeviation=function(list,mean){return Math.sqrt(morpheus.Variance(list,mean))};morpheus.StandardDeviation.toString=function(){return"Standard deviation"};var LOG_10=Math.log(10);morpheus.Log10=function(x){return x<=0?0:Math.log(x)/LOG_10};var LOG_2=Math.log(2);morpheus.Log2=function(x){return x<=0?0:Math.log(x)/LOG_2};morpheus.FDR_BH=function(nominalPValues){var size=nominalPValues.length;var fdr=[];var pValueIndices=morpheus.Util.indexSort(nominalPValues,true);var ranks=morpheus.Util.rankIndexArray(pValueIndices);for(var i=pValueIndices.length-1;i>0;i--){var bigPValue=nominalPValues[pValueIndices[i]];var smallPValue=nominalPValues[pValueIndices[i-1]];if(bigPValue==smallPValue){ranks[pValueIndices[i-1]]=ranks[pValueIndices[i]]}}for(var i=0;i<size;i++){var rank=ranks[i];var p=nominalPValues[i];fdr[i]=p*size/rank}var pIndices=morpheus.Util.indexSort(nominalPValues,false);for(var i=0;i<pIndices.length-1;i++){var highIndex=pIndices[i];var lowIndex=pIndices[i+1];fdr[lowIndex]=Math.min(fdr[lowIndex],fdr[highIndex])}for(var i=0;i<size;i++){fdr[i]=Math.min(fdr[i],1)}return fdr};morpheus.FDR_BH.tString=function(){return"FDR(BH)"};morpheus.MAD=function(list,median){if(median==null){median=morpheus.Percentile(list,50)}var temp=[];for(var j=0,size=list.size();j<size;j++){var value=list.getValue(j);if(!isNaN(value)){temp.push(Math.abs(value-median))}}var r=morpheus.Percentile(new morpheus.Vector("",temp.length).setArray(temp),50);return 1.4826*r};morpheus.MAD.toString=function(){return"Median absolute deviation"};morpheus.CV=function(list){var mean=morpheus.Mean(list);var stdev=Math.sqrt(morpheus.Variance(list,mean));return stdev/mean};morpheus.CV.toString=function(){return"Coefficient of variation"};morpheus.BoxPlotItem=function(list){var values=morpheus.RemoveNaN(list);values.sort(function(a,b){return a===b?0:a<b?-1:1});if(values.length===0){return{median:NaN,q1:NaN,q3:NaN,lowerAdjacentValue:NaN,upperAdjacentValue:NaN}}return morpheus.BoxPlotArrayItem(values)};morpheus.BoxPlotArrayItem=function(values){var median=morpheus.ArrayPercentile(values,50,true);var q1=morpheus.ArrayPercentile(values,25,true);var q3=morpheus.ArrayPercentile(values,75,true);var w=1.5;var upperAdjacentValue=-Number.MAX_VALUE;var lowerAdjacentValue=Number.MAX_VALUE;var upperOutlier=q3+w*(q3-q1);var lowerOutlier=q1-w*(q3-q1);var sum=0;for(var i=0,length=values.length;i<length;i++){var value=values[i];if(value<=upperOutlier){upperAdjacentValue=Math.max(upperAdjacentValue,value)}if(value>=lowerOutlier){lowerAdjacentValue=Math.min(lowerAdjacentValue,value)}sum+=value}var mean=sum/values.length;if(lowerAdjacentValue>q1){lowerAdjacentValue=q1}if(upperAdjacentValue<q3){upperAdjacentValue=q3}return{mean:mean,median:median,q1:q1,q3:q3,lowerAdjacentValue:lowerAdjacentValue,upperAdjacentValue:upperAdjacentValue}};morpheus.VectorColorModel=function(){this.vectorNameToColorMap=new morpheus.Map;this.vectorNameToColorScheme=new morpheus.Map;this.colors=morpheus.VectorColorModel.TWENTY_COLORS};morpheus.VectorColorModel.YES_COLOR="#d8b365";morpheus.VectorColorModel.FEMALE="#ff99ff";morpheus.VectorColorModel.MALE="#66ccff";morpheus.VectorColorModel.TWENTY_COLORS=["#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b","#c49c94","#e377c2","#f7b6d2","#7f7f7f","#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"];morpheus.VectorColorModel.CATEGORY_20A=morpheus.VectorColorModel.TWENTY_COLORS;morpheus.VectorColorModel.CATEGORY_20B=["#393b79","#5254a3","#6b6ecf","#9c9ede","#637939","#8ca252","#b5cf6b","#cedb9c","#8c6d31","#bd9e39","#e7ba52","#e7cb94","#843c39","#ad494a","#d6616b","#e7969c","#7b4173","#a55194","#ce6dbd","#de9ed6"];morpheus.VectorColorModel.CATEGORY_20C=["#3182bd","#6baed6","#9ecae1","#c6dbef","#e6550d","#fd8d3c","#fdae6b","#fdd0a2","#31a354","#74c476","#a1d99b","#c7e9c0","#756bb1","#9e9ac8","#bcbddc","#dadaeb","#636363","#969696","#bdbdbd","#d9d9d9"];morpheus.VectorColorModel.CATEGORY_ALL=[].concat(morpheus.VectorColorModel.CATEGORY_20A,morpheus.VectorColorModel.CATEGORY_20B,morpheus.VectorColorModel.CATEGORY_20C);morpheus.VectorColorModel.TABLEAU10=["#1f77b4","#ff7f0e","#2ca02c","#d62728","#9467bd","#8c564b","#e377c2","#7f7f7f","#bcbd22","#17becf"];morpheus.VectorColorModel.STANDARD_COLORS={na:"#c0c0c0",nan:"#c0c0c0","":"#ffffff",wt:"#ffffff",n:"#ffffff",0:"#ffffff",y:morpheus.VectorColorModel.YES_COLOR,1:morpheus.VectorColorModel.YES_COLOR,male:morpheus.VectorColorModel.MALE,m:morpheus.VectorColorModel.MALE,female:morpheus.VectorColorModel.FEMALE,f:morpheus.VectorColorModel.FEMALE,kd:"#C675A8",oe:"#56b4e9",cp:"#FF9933",pcl:"#003B4A","trt_sh.cgs":"#C675A8",trt_oe:"#56b4e9",trt_cp:"#FF9933",a375:"#1490C1",a549:"#AAC8E9",hcc515:"#1C9C2A",hepg2:"#94DC89",ht29:"#946DBE",mcf7:"#C5B2D5",pc3:"#38C697",asc:"#FF8000",cd34:"#FFBB75",ha1e:"#FB4124",neu:"#FF9A94",npc:"#E57AC6",cancer:"#1490C1","immortalized normal":"#FF8000"};morpheus.VectorColorModel.getStandardColor=function(value){if(value==null){return"#ffffff"}var stringValue=value.toString().toLowerCase();return morpheus.VectorColorModel.STANDARD_COLORS[stringValue]};morpheus.VectorColorModel.getColorMapForNumber=function(length){var colors;if(length<3){colors=colorbrewer.Set1[3]}else{colors=colorbrewer.Paired[length]}return colors?colors:morpheus.VectorColorModel.TWENTY_COLORS};morpheus.VectorColorModel.prototype={toJSON:function(tracks){var _this=this;var json={};tracks.forEach(function(track){if(track.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)){var colorMap=_this.vectorNameToColorMap.get(track.getName());if(colorMap!=null){json[track.getName()]=colorMap}}else{var colorScheme=_this.vectorNameToColorScheme.get(track.getName());if(colorScheme!=null){var colorSchemeJSON=morpheus.AbstractColorSupplier.toJSON(colorScheme.getCurrentColorSupplier());json[track.getName()]=colorSchemeJSON}}});return json},fromJSON:function(json){for(var name in json){var obj=json[name];if(obj.colors){obj.scalingMode="fixed";this.vectorNameToColorScheme.set(name,morpheus.AbstractColorSupplier.fromJSON(obj))}else{this.vectorNameToColorMap.set(name,morpheus.Map.fromJSON(obj))}}},clear:function(vector){this.vectorNameToColorMap.remove(vector.getName());this.vectorNameToColorScheme.remove(vector.getName())},copy:function(){var c=new morpheus.VectorColorModel;c.colors=this.colors.slice(0);this.vectorNameToColorMap.forEach(function(colorMap,name){var newColorMap=new morpheus.Map;newColorMap.setAll(colorMap);c.vectorNameToColorMap.set(name,newColorMap)});this.vectorNameToColorScheme.forEach(function(colorScheme,name){c.vectorNameToColorScheme.set(name,colorScheme.copy(new morpheus.Project(new morpheus.Dataset({name:"",rows:1,columns:1}))))});return c},clearAll:function(){this.vectorNameToColorMap=new morpheus.Map;this.vectorNameToColorScheme=new morpheus.Map},containsDiscreteColor:function(vector,value){var metadataValueToColorMap=this.vectorNameToColorMap.get(vector.getName());if(metadataValueToColorMap===undefined){return false}var c=metadataValueToColorMap.get(value);return c!=null},setDiscreteColorMap:function(colors){this.colors=colors},getContinuousColorScheme:function(vector){return this.vectorNameToColorScheme.get(vector.getName())},isContinuous:function(vector){return this.vectorNameToColorScheme.has(vector.getName())},getDiscreteColorScheme:function(vector){return this.vectorNameToColorMap.get(vector.getName())},createContinuousColorMap:function(vector){var minMax=morpheus.VectorUtil.getMinMax(vector);var min=minMax.min;var max=minMax.max;var cs=new morpheus.HeatMapColorScheme(new morpheus.Project(new morpheus.Dataset({name:"",rows:1,columns:1})),{type:"fixed",map:[{value:min,color:colorbrewer.Greens[3][0]},{value:max,color:colorbrewer.Greens[3][2]}]});this.vectorNameToColorScheme.set(vector.getName(),cs);return cs},_getColorForValue:function(value){var color=morpheus.VectorColorModel.getStandardColor(value);if(color==null){var existingMetadataValueToColorMap=this.vectorNameToColorMap.values();for(var i=0,length=existingMetadataValueToColorMap.length;i<length;i++){color=existingMetadataValueToColorMap[i].get(value);if(color!==undefined){return color}}}return color},getContinuousMappedValue:function(vector,value){var cs=this.vectorNameToColorScheme.get(vector.getName());if(cs===undefined){cs=this.createContinuousColorMap(vector)}return cs.getColor(0,0,value)},getMappedValue:function(vector,value){var metadataValueToColorMap=this.vectorNameToColorMap.get(vector.getName());if(metadataValueToColorMap===undefined){metadataValueToColorMap=new morpheus.Map;this.vectorNameToColorMap.set(vector.getName(),metadataValueToColorMap);var values=morpheus.VectorUtil.getValues(vector);var ncolors=0;var colors=null;if(values.length<3){colors=colorbrewer.Dark2[3]}else{colors=colorbrewer.Paired[values.length]}if(!colors){if(values.length<=20){colors=d3.scale.category20().range()}else{colors=morpheus.VectorColorModel.CATEGORY_ALL}}if(colors){var ncolors=colors.length;for(var i=0,nvalues=values.length;i<nvalues;i++){var color=this._getColorForValue(values[i]);if(color==null){color=colors[i%ncolors]}metadataValueToColorMap.set(values[i],color)}}else{var _this=this;_.each(values,function(val){_this.getMappedValue(vector,val)})}}var color=metadataValueToColorMap.get(value);if(color==null){color=this._getColorForValue(value);if(color==null){var index=metadataValueToColorMap.size();color=this.colors[index%this.colors.length]}metadataValueToColorMap.set(value,color)}return color},setMappedValue:function(vector,value,color){var metadataValueToColorMap=this.vectorNameToColorMap.get(vector.getName());if(metadataValueToColorMap===undefined){metadataValueToColorMap=new morpheus.Map;this.vectorNameToColorMap.set(vector.getName(),metadataValueToColorMap)}metadataValueToColorMap.set(value,color)}};morpheus.VectorFontModel=function(){this.vectorNameToMappedValue=new morpheus.Map;this.fonts=morpheus.VectorFontModel.FONTS};morpheus.VectorFontModel.FONTS=[{weight:400},{weight:700},{weight:900}];morpheus.VectorFontModel.prototype={toJSON:function(tracks){var _this=this;var json={};tracks.forEach(function(track){if(track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){var map=_this.vectorNameToMappedValue.get(track.getName());if(map!=null){json[track.getName()]=map}}});return json},fromJSON:function(json){for(var name in json){var obj=json[name];this.vectorNameToMappedValue.set(name,morpheus.Map.fromJSON(obj))}},clear:function(vector){this.vectorNameToMappedValue.remove(vector.getName())},copy:function(){var c=new morpheus.VectorFontModel;c.fonts=this.fonts.slice(0);this.vectorNameToMappedValue.forEach(function(fontMap,name){var newFontMap=new morpheus.Map;newFontMap.setAll(fontMap);c.vectorNameToMappedValue.set(name,newFontMap)});return c},clearAll:function(){this.vectorNameToMappedValue=new morpheus.Map},_getFontForValue:function(value){if(value==null){return morpheus.VectorFontModel.FONTS[0]}var existingMetadataValueToFontMap=this.vectorNameToMappedValue.values();for(var i=0,length=existingMetadataValueToFontMap.length;i<length;i++){var font=existingMetadataValueToFontMap[i].get(value);if(font!==undefined){return font}}},getMap:function(name){return this.vectorNameToMappedValue.get(name)},getMappedValue:function(vector,value){var metadataValueToFontMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToFontMap===undefined){metadataValueToFontMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToFontMap);var values=morpheus.VectorUtil.getValues(vector);for(var i=0,nvalues=values.length;i<nvalues;i++){var font=this._getFontForValue(values[i]);if(font==null){font=this.fonts[0]}metadataValueToFontMap.set(values[i],font)}}var font=metadataValueToFontMap.get(value);if(font==null){font=this._getFontForValue(value);if(font==null){font=this.fonts[0]}metadataValueToFontMap.set(value,font)}return font},setMappedValue:function(vector,value,font){var metadataValueToFontMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToFontMap===undefined){metadataValueToFontMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToFontMap)}metadataValueToFontMap.set(value,font)}};morpheus.VectorKeys={};morpheus.VectorKeys.FIELDS="morpheus.fields";morpheus.VectorKeys.VALUE_TO_INDICES="morpheus.valueToIndices";morpheus.VectorKeys.VISIBLE_FIELDS="morpheus.visibleFields";morpheus.VectorKeys.DATA_TYPE="morpheus.dataType";morpheus.VectorKeys.ARRAY_SUMMARY_FUNCTION="morpheus.arraySummaryFunct";morpheus.VectorKeys.HEADER_SUMMARY="morpheus.headerSummary";morpheus.VectorKeys.SHOW_HEADER_SUMMARY="morpheus.showHeaderSummary";morpheus.VectorKeys.TITLE="morpheus.title";morpheus.VectorKeys.FUNCTION="morpheus.funct";morpheus.VectorKeys.SELECTION="morpheus.selection";morpheus.VectorKeys.RECOMPUTE_FUNCTION_NEW_HEAT_MAP="morpheus.recompute.funct.new.heat.map";morpheus.VectorKeys.RECOMPUTE_FUNCTION_SELECTION="morpheus.recompute.funct.selection";morpheus.VectorKeys.FORMATTER="morpheus.formatter";morpheus.VectorKeys.IS_INDEX="morpheus.isIndex";morpheus.VectorKeys.DISCRETE="morpheus.discrete";morpheus.VectorKeys.COPY_IGNORE=new morpheus.Set;morpheus.VectorKeys.COPY_IGNORE.add(morpheus.VectorKeys.HEADER_SUMMARY);morpheus.VectorKeys.COPY_IGNORE.add(morpheus.VectorKeys.DATA_TYPE);morpheus.VectorKeys.COPY_IGNORE.add(morpheus.VectorKeys.VALUE_TO_INDICES);morpheus.VectorKeys.JSON_WHITELIST=new morpheus.Set;morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.FIELDS);morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.FORMATTER);morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.DATA_TYPE);morpheus.VectorKeys.JSON_WHITELIST.add(morpheus.VectorKeys.TITLE);morpheus.VectorShapeModel=function(){this.shapes=morpheus.VectorShapeModel.SHAPES;this.vectorNameToMappedValue=new morpheus.Map};morpheus.VectorShapeModel.SHAPES=["circle","square","plus","x","asterisk","diamond","triangle-up","triangle-down","triangle-left","triangle-right","circle-minus"];morpheus.VectorShapeModel.FILLED_SHAPES=["circle","square","diamond","triangle-up","triangle-down","triangle-left","triangle-right"];morpheus.VectorShapeModel.prototype={toJSON:function(tracks){var _this=this;var json={};tracks.forEach(function(track){if(track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){var map=_this.vectorNameToMappedValue.get(track.getName());if(map!=null){json[track.getName()]=map}}});return json},fromJSON:function(json){for(var name in json){var obj=json[name];this.vectorNameToMappedValue.set(name,morpheus.Map.fromJSON(obj))}},clear:function(vector){this.vectorNameToMappedValue.remove(vector.getName())},copy:function(){var c=new morpheus.VectorShapeModel;c.shapes=this.shapes.slice(0);this.vectorNameToMappedValue.forEach(function(shapeMap,name){var newShapeMap=new morpheus.Map;newShapeMap.setAll(shapeMap);c.vectorNameToMappedValue.set(name,newShapeMap)});return c},clearAll:function(){this.vectorNameToMappedValue=new morpheus.Map},_getShapeForValue:function(value){if(value==null){return"none"}var existingMetadataValueToShapeMap=this.vectorNameToMappedValue.values();for(var i=0,length=existingMetadataValueToShapeMap.length;i<length;i++){var shape=existingMetadataValueToShapeMap[i].get(value);if(shape!==undefined){return shape}}},getMap:function(name){return this.vectorNameToMappedValue.get(name)},getMappedValue:function(vector,value){var metadataValueToShapeMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToShapeMap===undefined){metadataValueToShapeMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToShapeMap);var values=morpheus.VectorUtil.getValues(vector);for(var i=0,nvalues=values.length;i<nvalues;i++){var shape=this._getShapeForValue(values[i]);if(shape==null){shape=this.shapes[i%this.shapes.length]}metadataValueToShapeMap.set(values[i],shape)}}var shape=metadataValueToShapeMap.get(value);if(shape==null){shape=this._getShapeForValue(value);if(shape==null){var index=metadataValueToShapeMap.size();shape=this.shapes[index%this.shapes.length]}metadataValueToShapeMap.set(value,shape)}return shape},setMappedValue:function(vector,value,shape){var metadataValueToShapeMap=this.vectorNameToMappedValue.get(vector.getName());if(metadataValueToShapeMap===undefined){metadataValueToShapeMap=new morpheus.Map;this.vectorNameToMappedValue.set(vector.getName(),metadataValueToShapeMap)}metadataValueToShapeMap.set(value,shape)}};morpheus.VectorUtil=function(){};morpheus.VectorUtil.jsonToFunction=function(vector,key){var f=vector.getProperties().get(key);if(typeof f==="object"){var binSize=f.binSize;var min=f.domain[0];var max=f.domain[1];var numberOfBins=Math.ceil((max-min)/binSize);var percent=f.percent;var cumulative=f.cumulative;var histogramFunction=function(view,selectedDataset,columnIndex){var total=0;var binNumberToOccurences=new Uint32Array(numberOfBins);for(var i=0,nrows=selectedDataset.getRowCount();i<nrows;i++){var value=selectedDataset.getValue(i,columnIndex);if(!isNaN(value)){if(value>=min&&value<=max){var bin=Math.floor((value-min)/binSize);if(bin<0){bin=0}else if(bin>=numberOfBins){bin=numberOfBins-1}binNumberToOccurences[bin]++}total++}}if(cumulative){for(var i=numberOfBins-2;i>=0;i--){binNumberToOccurences[i]+=binNumberToOccurences[i+1]}}if(percent){var percents=new Float32Array(numberOfBins);for(var i=0;i<numberOfBins;i++){percents[i]=100*(binNumberToOccurences[i]/total)}return percents}return binNumberToOccurences};vector.getProperties().set(key,histogramFunction);var jsonSpec=f;f=histogramFunction;f.toJSON=function(){return jsonSpec}}return f};morpheus.VectorUtil.createValueToIndexMap=function(vector,splitArrayValues){var map=new morpheus.Map;var isArray=splitArrayValues&&morpheus.VectorUtil.getDataType(vector)[0]==="[";for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(isArray){if(val!=null){for(var k=0;k<val.length;k++){map.set(val[k],j)}}}else{map.set(val,j)}}return map};morpheus.VectorUtil.createValueToIndicesMap=function(vector,splitArrayValues){if(!vector){throw"vector is null"}var isArray=splitArrayValues&&morpheus.VectorUtil.getDataType(vector)[0]==="[";var map=new morpheus.Map;for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(isArray){if(val!=null){for(var k=0;k<val.length;k++){var list=map.get(val[k]);if(list===undefined){list=[];map.set(val[k],list)}list.push(j)}}}else{var list=map.get(val);if(list===undefined){list=[];map.set(val,list)}list.push(j)}}return map};morpheus.VectorUtil.createValueToCountMap=function(vector){if(!vector){throw"vector is null"}var map=new morpheus.Map;var dataType=morpheus.VectorUtil.getDataType(vector);var isArray=dataType[0]==="[";for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(val!=null){if(isArray){for(var k=0;k<val.length;k++){var count=map.get(val[k])||0;map.set(val[k],count+1)}}else{var count=map.get(val)||0;map.set(val,count+1)}}}return map};morpheus.VectorUtil.createValuesToIndicesMap=function(vectors){var map=new morpheus.Map;var nvectors=vectors.length;if(vectors[0]==null){throw"no vectors found"}for(var i=0,nitems=vectors[0].size();i<nitems;i++){var array=[];for(var j=0;j<nvectors;j++){var vector=vectors[j];var val=vector.getValue(i);array.push(val)}var key=new morpheus.Identifier(array);var list=map.get(key);if(list===undefined){list=[];map.set(key,list)}list.push(i)}return map};morpheus.VectorUtil.createValuesToIndexMap=function(vectors){var map=new morpheus.Map;var nvectors=vectors.length;if(vectors[0]==null){throw"no vectors found"}for(var i=0,nitems=vectors[0].size();i<nitems;i++){var array=[];for(var j=0;j<nvectors;j++){var vector=vectors[j];var val=vector.getValue(i);array.push(val)}var key=new morpheus.Identifier(array);map.set(key,i)}return map};morpheus.VectorUtil.createValuesToCountMap=function(vectors){var map=new morpheus.Map;var nvectors=vectors.length;if(vectors[0]==null){throw"no vectors found"}for(var i=0,nitems=vectors[0].size();i<nitems;i++){var array=[];for(var j=0;j<nvectors;j++){var vector=vectors[j];var val=vector.getValue(i);array.push(val)}var key=new morpheus.Identifier(array);var count=map.get(key)||0;map.set(key,count+1)}return map};morpheus.VectorUtil.getValues=function(vector,excludeNull){var set=new morpheus.Set;for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);if(excludeNull&&val==null){continue}set.add(val)}var array=set.values();array.sort(morpheus.SortKey.ASCENDING_COMPARATOR);return array};morpheus.VectorUtil.getSet=function(vector,splitArrayValues){var set=new morpheus.Set;var isArray=splitArrayValues&&morpheus.VectorUtil.getDataType(vector)[0]==="[";for(var j=0,size=vector.size();j<size;j++){var value=vector.getValue(j);if(isArray){if(value!=null){for(var k=0,nvalues=value.length;k<nvalues;k++){set.add(value[k])}}}else{set.add(value)}}return set};morpheus.VectorUtil.maybeConvertToStringArray=function(vector,delim){var newValues=[];var regex=new RegExp(delim);var found=false;for(var i=0,nrows=vector.size();i<nrows;i++){var s=vector.getValue(i);if(s!=null){if(!s.split){return false}var tokens=s.split(regex);newValues.push(tokens);if(!found&&tokens.length>1){found=true}}}if(found){for(var i=0,nrows=newValues.length;i<nrows;i++){vector.setValue(i,newValues[i])}vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"[string]")}return found};morpheus.VectorUtil.maybeConvertStringToNumber=function(vector){var newValues=[];var found=false;for(var i=0,nrows=vector.size();i<nrows;i++){var s=vector.getValue(i);if(s!=null&&s!==""&&s!=="NA"&&s!=="NaN"){if(!$.isNumeric(s)){return false}else{found=true}}newValues.push(parseFloat(s))}if(!found){return false}for(var i=0,nrows=newValues.length;i<nrows;i++){vector.setValue(i,newValues[i])}vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,"number");return true};morpheus.VectorUtil.containsMoreThanOneValue=function(vector){return morpheus.VectorUtil.containsMoreThanNValues(vector,1)};morpheus.VectorUtil.containsMoreThanNValues=function(vector,n){var s=new morpheus.Set;for(var j=0,size=vector.size();j<size;j++){var val=vector.getValue(j);s.add(val);if(s.size()>n){return true}}return false};morpheus.VectorUtil.createSpanMap=function(vector){var previous=vector.getValue(0);var startIndexToEndIndex=new morpheus.Map;var start=0;for(var i=1,nrows=vector.size();i<nrows;i++){var val=vector.getValue(i);if(previous!==val){previous=val;startIndexToEndIndex.set(start,i);start=i}}startIndexToEndIndex.set(start,vector.size());return startIndexToEndIndex};morpheus.VectorUtil.toArray=function(vector){var array=[];for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);array.push(val)}return array};morpheus.VectorUtil.arrayAsVector=function(array,name){var v=new morpheus.Vector(name,array.length);v.array=array;return v};morpheus.VectorUtil.toString=function(vector){var array=[];for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);array.push(val)}return array.join(", ")};morpheus.VectorUtil.getDataType=function(vector){var dataType=vector.getProperties().get(morpheus.VectorKeys.DATA_TYPE);if(dataType===undefined){var firstNonNull=morpheus.VectorUtil.getFirstNonNull(vector);dataType=morpheus.Util.getDataType(firstNonNull);vector.getProperties().set(morpheus.VectorKeys.DATA_TYPE,dataType)}return dataType};morpheus.VectorUtil.getMinMax=function(vector){var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;var fields=vector.getProperties().get(morpheus.VectorKeys.FIELDS);var isArray=morpheus.VectorUtil.getDataType(vector)[0]==="[";if(fields!=null){var nvalues=fields.length;for(var i=0,size=vector.size();i<size;i++){var array=vector.getValue(i);if(array){for(var j=0;j<nvalues;j++){var value=array[j];if(!isNaN(value)){min=value<min?value:min;max=value>max?value:max}}}}}else if(isArray){for(var i=0,size=vector.size();i<size;i++){var array=vector.getValue(i);if(array!=null){for(var j=0,nvalues=array.length;j<nvalues;j++){var value=array[j];if(!isNaN(value)){min=value<min?value:min;max=value>max?value:max}}}}}else{for(var i=0,size=vector.size();i<size;i++){var value=vector.getValue(i);if(!isNaN(value)){min=value<min?value:min;max=value>max?value:max}}}return{min:min,max:max}};morpheus.VectorUtil.getFirstNonNull=function(vector){for(var i=0,length=vector.size();i<length;i++){var val=vector.getValue(i);if(val!=null){return val}}return null};morpheus.VectorUtil.isNumber=function(vector){return morpheus.VectorUtil.getDataType(vector)==="number"};morpheus.Vector=function(name,size){this.array=[];morpheus.AbstractVector.call(this,name,size)};morpheus.Vector.fromArray=function(name,array){var v=new morpheus.Vector(name,array.length);v.array=array;return v};morpheus.Vector.prototype={push:function(value){this.array.push(value)},setValue:function(index,value){this.array[index]=value},getValue:function(index){return this.array[index]},setName:function(name){this.name=name},setArray:function(array){this.array=array;return this}};morpheus.Util.extend(morpheus.Vector,morpheus.AbstractVector);morpheus.LandingPage=function(pageOptions){pageOptions=$.extend({},{el:$("#vis")},pageOptions);this.pageOptions=pageOptions;var _this=this;var html=[];html.push('<div style="display:none;" class="container-fluid">');html.push('<div style="min-height:78vh" class="row">');html.push('<div class="col-xs-12 col-md-offset-1 col-md-7"><div'+' data-name="input"></div>');html.push('<div class="clearfix"></div>');html.push("</div>");html.push('<div data-name="desc" class="col-xs-12 col-md-3"><p><img'+' src="https://software.broadinstitute.org/morpheus/css/images/morpheus_landing_img.png" style="width:100%;"></p></div>');html.push("</div>");html.push('<div class="row"><div class="col-xs-12 morpheus-footer"></div></div>');html.push("</div>");var $el=$(html.join(""));(new morpheus.HelpMenu).$el.appendTo($el.find(".morpheus-footer"));this.$el=$el;var $description=$el.find("[data-name=desc]");morpheus.Util.createMorpheusHeader().appendTo($description);$("<p>Versatile matrix visualization and analysis software</p><p>View your dataset as a heat"+" map,"+" then explore"+" the"+' interactive tools in Morpheus. Cluster, create new annotations, search, filter, sort, display charts, and more.</p><p style="color:#586069;">30,000+ users <br />100,000+'+" matrices analyzed</p>").appendTo($description);var $input=$el.find("[data-name=input]");$('<svg width="32px" height="32px"><g><rect x="0" y="0" width="32" height="14" style="fill:#ca0020;stroke:none"/><rect x="0" y="18" width="32" height="14" style="fill:#0571b0;stroke:none"/></g></svg><h2 style="padding-left: 4px; display:inline-block;">Open</h2>').appendTo($input);$('<div style="margin-bottom:20px;"><small>All'+" data is"+" processed in the"+" browser and never sent to any server.</small></div>").appendTo($input);var filePicker=new morpheus.FilePicker({fileCallback:function(file){_this.openFile(file)},optionsCallback:function(opt){_this.open(opt)}});filePicker.$el.appendTo($input);if(pageOptions.tabManager){this.tabManager=pageOptions.tabManager}else{this.tabManager=new morpheus.TabManager({landingPage:this});this.tabManager.on("change rename add remove",function(e){var title=_this.tabManager.getTabText(_this.tabManager.getActiveTabId());if(title==null||title===""){title="Morpheus"}document.title=title});this.tabManager.$nav.appendTo($(this.pageOptions.el));this.tabManager.$tabContent.appendTo($(this.pageOptions.el))}};morpheus.LandingPage.prototype={open:function(openOptions){this.dispose();var optionsArray=_.isArray(openOptions)?openOptions:[openOptions];var _this=this;for(var i=0;i<optionsArray.length;i++){var options=optionsArray[i];options.tabManager=_this.tabManager;options.focus=i===0;options.standalone=true;options.landingPage=_this;new morpheus.HeatMap(options)}},dispose:function(){this.$el.hide()},show:function(){var _this=this;this.$el.show();$(window).on("beforeunload.morpheus",function(){if(_this.tabManager.getTabCount()>0){return"Are you sure you want to close Morpheus?"}})},openFile:function(value){var _this=this;var fileName=morpheus.Util.getFileName(value);if(fileName.toLowerCase().indexOf(".json")===fileName.length-5){morpheus.Util.getText(value).done(function(text){_this.open(JSON.parse(text))}).fail(function(err){morpheus.FormBuilder.showMessageModal({title:"Error",message:"Unable to load session"})})}else{var options={dataset:{file:value,options:{interactive:true}}};morpheus.OpenDatasetTool.fileExtensionPrompt(fileName,function(readOptions){if(readOptions){for(var key in readOptions){options.dataset.options[key]=readOptions[key]}}_this.open(options)})}}};morpheus.SampleDatasets=function(options){var _this=this;var $el=options.$el;this.callback=options.callback;$el.on("click","[name=ccle]",function(e){var $this=$(this);var obj={};$this.parents(".collapse").find("input:checked").each(function(i,c){obj[$(c).data("type")]=true});_this.openCCLE(obj);e.preventDefault()});$el.on("click","[name=tcgaLink]",function(e){e.preventDefault();var $this=$(this);var type=$this.data("disease-type");var obj={};$this.parents(".collapse").find("input:checked").each(function(i,c){obj[$(c).data("type")]=true});var disease;for(var i=0;i<_this.diseases.length;i++){if(_this.diseases[i].type===type){disease=_this.diseases[i];break}}obj.type=type;obj.name=disease.name;_this.openTcga(obj)});$el.on("click","[data-toggle=dataTypeToggle]",function(e){var $this=$(this);var $button=$this.parents(".collapse").find("button");var isDisabled=$this.parents(".collapse").find("input:checked").length===0;$button.prop("disabled",isDisabled)});fetch("https://software.broadinstitute.org/morpheus/preloaded-datasets/tcga/tcga_index.txt").then(function(response){if(response.ok){return response.text()}}).then(function(text){var exampleHtml=[];var id=_.uniqueId("morpheus");exampleHtml.push('<a data-toggle="collapse" href="#'+id+'" aria-expanded="false" aria-controls="'+id+'">Cancer Cell Line Encyclopedia (CCLE), Project Achilles</a>');exampleHtml.push('<div class="collapse" id="'+id+'">');exampleHtml.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align:'+' top;">');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;"'+' data-toggle="dataTypeToggle"'+' data-type="mrna">GENE EXPRESSION</label>');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle"'+' data-type="cn">COPY NUMBER BY GENE</label>');exampleHtml.push("</div>");exampleHtml.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align: top;">');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle"'+' data-type="sig_genes">MUTATIONS</label>');exampleHtml.push('<label><input type="checkbox" style="margin-left:4px;" data-toggle="dataTypeToggle"'+' data-type="ach">GENE ESSENTIALITY</label>');exampleHtml.push("</div>");exampleHtml.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align: top;">');exampleHtml.push('<button disabled type="button" class="btn btn-default" name="ccle">Open</button>');exampleHtml.push("</div>");exampleHtml.push("</div>");exampleHtml.push("<hr>");exampleHtml.push('<div>TCGA data <a target="_blank" href="https://confluence.broadinstitute.org/display/GDAC/Dashboard-Stddata">(Broad GDAC 1/28/2016)</a></div><span>Please adhere to the'+' <a target="_blank"'+' href="http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines">TCGA'+" publication guidelines</a></u> when using TCGA data in your publications.</span>");exampleHtml.push("<br />");exampleHtml.push('<div data-name="tcga"></div>');$(exampleHtml.join("")).appendTo($el);if(options.show){$el.css("display","")}var lines=text.split("\n");var diseases=[];for(var i=0;i<lines.length;i++){var line=lines[i];if(line===""){continue}var tokens=line.split("\t");var type=tokens[0];var dataTypes=tokens[1].split(",");var name=morpheus.TcgaUtil.DISEASE_STUDIES[type];var disease={mrna:dataTypes.indexOf("mRNAseq_RSEM_normalized_log2.txt")!==-1,sig_genes:dataTypes.indexOf("sig_genes.txt")!==-1,gistic:dataTypes.indexOf("all_lesions.conf_99.txt")!==-1,sample_info:dataTypes.indexOf("All_CDEs.txt")!==-1,mutation:dataTypes.indexOf("mutations_merged.maf.txt")!==-1,rppa:dataTypes.indexOf("rppa.txt")!==-1,methylation:dataTypes.indexOf("meth.by_mean.data.txt")!==-1,name:name,type:type,dataTypes:dataTypes};if(disease.mrna||disease.gistic||disease.sig_genes||disease.rppa||disease.methylation){diseases.push(disease)}}diseases.sort(function(a,b){a=a.name.toLowerCase();b=b.name.toLowerCase();return a===b?0:a<b?-1:1});var tcga=[];_this.diseases=diseases;for(var i=0;i<diseases.length;i++){var id=_.uniqueId("morpheus");var disease=diseases[i];tcga.push("<div>");tcga.push('<a data-toggle="collapse" href="#'+id+'" aria-expanded="false"'+' aria-controls="'+id+'">'+disease.name+" ("+disease.type+")</a>");tcga.push('<div class="collapse" id="'+id+'">');for(var j=0;j<morpheus.SampleDatasets.TCGA_DISEASE_TYPES_INFO.length;j++){var info=morpheus.SampleDatasets.TCGA_DISEASE_TYPES_INFO[j];if(j%2===0){if(j>0){tcga.push("</div>")}tcga.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align:top;">')}tcga.push('<label><input type="checkbox" style="margin-left:4px;"'+' data-toggle="dataTypeToggle"'+' data-type="'+info.type+'"'+(!disease[info.id]?" disabled":"")+">"+info.name+"</label>")}tcga.push("</div>");tcga.push('<div style="margin: 6px 0 0 20px;display: inline-block;vertical-align:top;">');tcga.push('<button disabled type="button" class="btn btn-default" name="tcgaLink"'+' data-disease-type="'+disease.type+'">Open</button>');tcga.push("</div>");tcga.push("</div>");tcga.push("</div>")}$(tcga.join("")).appendTo($el.find("[data-name=tcga]"))}).catch(function(error){console.log(error)})};morpheus.SampleDatasets.getTcgaDataset=function(options){var baseUrl="https://software.broadinstitute.org/morpheus/preloaded-datasets/tcga/"+options.type+"/";var datasetOptions={};if(options.mrna){datasetOptions.mrna=baseUrl+"mRNAseq_RSEM_normalized_log2.txt"}if(options.methylation){datasetOptions.methylation=baseUrl+"meth.by_mean.data.txt"}if(options.sig_genes){datasetOptions.mutation=baseUrl+"mutations_merged.maf.txt";datasetOptions.sigGenes=baseUrl+"sig_genes.txt"}if(options.rppa){datasetOptions.rppa=baseUrl+"rppa.txt"}if(options.gistic){datasetOptions.gistic=baseUrl+"all_lesions.conf_99.txt"}if(options.gisticGene){datasetOptions.gisticGene=baseUrl+"all_data_by_genes.txt"}datasetOptions.mrnaClust=baseUrl+"bestclus.txt";datasetOptions.columnAnnotations=[{file:baseUrl+"All_CDEs.txt",datasetField:"participant_id",fileField:"patient_id",transposed:false}];return morpheus.TcgaUtil.getDataset(datasetOptions)};morpheus.SampleDatasets.getCCLEDataset=function(options){var datasets=[];if(options.sig_genes){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/ccle2maf_081117.maf.txt")}if(options.cn){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/CCLE_copynumber_byGene_2013-12-03.gct")}if(options.mrna){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/CCLE_expression_081117.rpkm.gct")}if(options.ach){datasets.push("https://software.broadinstitute.org/morpheus/preloaded-datasets/Achilles_v2.20.2_GeneSolutions.gct")}var d=$.Deferred();var datasetPromise=morpheus.DatasetUtil.readDatasetArray(datasets);datasetPromise.done(function(dataset){var idVector=dataset.getColumnMetadata().get(0);var siteVector=dataset.getColumnMetadata().add("site");for(var j=0,ncols=siteVector.size();j<ncols;j++){var id=idVector.getValue(j);var index=id.indexOf("_");if(index!==-1){idVector.setValue(j,id.substring(0,index));siteVector.setValue(j,id.substring(index+1))}}d.resolve(dataset)}).fail(function(err){d.reject(err)});return d};morpheus.SampleDatasets.prototype={openTcga:function(options){this.callback({name:options.name,renderReady:function(heatMap){var whitelist=["age_at_initial_pathologic_diagnosis","breast_carcinoma_estrogen_receptor_status","breast_carcinoma_progesterone_receptor_status","lab_proc_her2_neu_immunohistochemistry_receptor_status","days_to_death","ethnicity","gender","histological_type","pathologic_stage"];var columnMetadata=heatMap.getProject().getFullDataset().getColumnMetadata();for(var i=0;i<whitelist.length;i++){if(columnMetadata.getByName(whitelist[i])){heatMap.addTrack(whitelist[i],true,"color")}}if(options.sig_genes){if(heatMap.getTrackIndex("q_value",false)===-1){heatMap.addTrack("q_value",false,"text")}}},columns:[{field:"participant_id",display:"text"},{field:"sample_type",display:"color"},{field:"mutation_summary",display:"stacked_bar"},{field:"mutation_summary_selection",display:"stacked_bar"},{field:"mRNAseq_cluster",display:"color, highlight"}],dataset:morpheus.SampleDatasets.getTcgaDataset(options)})},openCCLE:function(options){var name=[];if(options.sig_genes){name.push("Mut")}if(options.cn){name.push("CN")}if(options.mrna){name.push("Exp")}if(options.ach){name.push("Ach")}this.callback({rows:[{field:"id",display:"text"},{field:"Description",display:"text, tooltip"},{field:"mutation_summary",display:"stacked_bar"},{field:"Source",display:"color"}],columns:[{field:"id",display:"text,tooltip"},{field:"mutation_summary",display:"stacked_bar"},{field:"site",display:"color, highlight"}],dataset:morpheus.SampleDatasets.getCCLEDataset(options),name:"CCLE - "+name.join(", ")})}};morpheus.SampleDatasets.TCGA_DISEASE_TYPES_INFO=[{id:"mrna",name:"GENE EXPRESSION",type:"mrna"},{id:"gistic",name:"GISTIC COPY NUMBER",type:"gistic"},{id:"gistic",name:"COPY NUMBER BY GENE",type:"gisticGene"},{id:"sig_genes",name:"MUTATION",type:"sig_genes"},{id:"rppa",name:"PROTEOMICS",type:"rppa"},{id:"methylation",name:"METHYLATION",type:"methylation"}];morpheus.AdjustDataTool=function(){};morpheus.AdjustDataTool.prototype={toString:function(){return"Adjust"},init:function(project,form){var _this=this;form.$form.find("[name=scale_column_sum]").on("change",function(e){form.setVisible("column_sum",form.getValue("scale_column_sum"))});form.setVisible("column_sum",false)},gui:function(){return[{name:"scale_column_sum",type:"checkbox",help:"Whether to scale each column sum to a specified value"},{name:"column_sum",type:"text",style:"max-width:150px;"},{name:"log_2",type:"checkbox"},{name:"inverse_log_2",type:"checkbox"},{name:"quantile_normalize",type:"checkbox"},{name:"z-score",type:"checkbox",help:"Subtract mean, divide by standard deviation"},{name:"robust_z-score",type:"checkbox",help:"Subtract median, divide by median absolute deviation"},{name:"use_selected_rows_and_columns_only",type:"checkbox"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;if(options.input.log_2||options.input.inverse_log_2||options.input["z-score"]||options.input["robust_z-score"]||options.input.quantile_normalize||options.input.scale_column_sum){var sortedFilteredDataset=morpheus.DatasetUtil.copy(project.getSortedFilteredDataset());var rowIndices=project.getRowSelectionModel().getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(rowIndices.length===0){rowIndices=null}var columnIndices=project.getColumnSelectionModel().getViewIndices().values().sort(function(a,b){return a===b?0:a<b?-1:1});if(columnIndices.length===0){columnIndices=null}var dataset=options.input.use_selected_rows_and_columns_only?new morpheus.Slice:sortedFilteredDataset;var rowView=new morpheus.DatasetRowView(dataset);var functions=[];if(options.input.scale_column_sum){var scaleToValue=parseFloat(options.input.column_sum);if(!isNaN(scaleToValue)){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var sum=0;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var value=dataset.getValue(i,j);if(!isNaN(value)){sum+=value}}var ratio=scaleToValue/sum;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var value=dataset.getValue(i,j);dataset.setValue(i,j,value*ratio)}}}}if(options.input.log_2){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){dataset.setValue(i,j,morpheus.Log2(dataset.getValue(i,j)))}}}if(options.input.inverse_log_2){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(value>=0){dataset.setValue(i,j,Math.pow(2,value))}}}}if(options.input.quantile_normalize){morpheus.QNorm.execute(dataset)}if(options.input["z-score"]){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){rowView.setIndex(i);var mean=morpheus.Mean(rowView);var stdev=Math.sqrt(morpheus.Variance(rowView));for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){dataset.setValue(i,j,(dataset.getValue(i,j)-mean)/stdev)}}}if(options.input["robust_z-score"]){for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){rowView.setIndex(i);var median=morpheus.Median(rowView);var mad=morpheus.MAD(rowView,median);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){dataset.setValue(i,j,(dataset.getValue(i,j)-median)/mad)}}}return new morpheus.HeatMap({name:heatMap.getName(),dataset:dataset,parent:heatMap,symmetric:project.isSymmetric()&&dataset.getColumnCount()===dataset.getRowCount()})}}};morpheus.AnnotateDendrogramTool=function(isColumns){this._isColumns=isColumns};morpheus.AnnotateDendrogramTool.prototype={toString:function(){return"Annotate Dendrogram"},gui:function(){return[{name:"file",value:"",type:"file",required:true,help:"an xlsx file or a tab-delimitted text file"}]},execute:function(options){var fileOrUrl=options.input.file;var isColumns=this._isColumns;var heatMap=options.heatMap;var result=morpheus.Util.readLines(fileOrUrl);var fileName=morpheus.Util.getFileName(fileOrUrl);var dendrogram=isColumns?heatMap.columnDendrogram:heatMap.rowDendrogram;var nameToNode=new morpheus.Map;morpheus.DendrogramUtil.dfs(dendrogram.tree.rootNode,function(node){nameToNode.set(node.name,node);return true});var tab=/\t/;result.done(function(lines){var header=lines[0].split(tab);var promptTool={};promptTool.execute=function(options){var nodeIdField=options.input.node_id_field;var nodeIdIndex=_.indexOf(header,nodeIdField);var numberOfMatchingNodes=0;for(var i=1;i<lines.length;i++){var array=lines[i].split(tab);var nodeName=array[nodeIdIndex];var node=nameToNode.get(nodeName);if(node!==undefined){numberOfMatchingNodes++;var info=node.info||(node.info={});for(var j=0;j<array.length;j++){if(j===nodeIdIndex){continue}var vals=info[header[j]];if(vals===undefined){vals=[];info[header[j]]=vals}vals.push(array[j])}}}heatMap.trigger("dendrogramAnnotated",{isColumns:isColumns});dendrogram.setInvalid(true);dendrogram.repaint()};promptTool.toString=function(){return"Select Node Id Field"};promptTool.gui=function(){return[{name:"node_id_field",type:"select",options:_.map(header,function(item){return{name:item,value:item}}),required:true}]};morpheus.HeatMap.showTool(promptTool,heatMap)})}};morpheus.ChartTool=function(chartOptions){var _this=this;this.project=chartOptions.project;this.heatmap=chartOptions.heatmap;var project=this.project;this.$el=$('<div class="container-fluid">'+'<div class="row">'+'<div data-name="configPane" class="col-xs-2"></div>'+'<div class="col-xs-10"><div style="position:relative;" data-name="chartDiv"></div></div>'+"</div></div>");var formBuilder=new morpheus.FormBuilder({formStyle:"vertical"});this.formBuilder=formBuilder;formBuilder.append({name:"chart_type",type:"bootstrap-select",options:["boxplot","row profile","column profile","row scatter matrix","column scatter"+" matrix"]});var rowOptions=[];var columnOptions=[];var numericRowOptions=[];var numericColumnOptions=[];var options=[];var numericOptions=[];var updateOptions=function(){var dataset=project.getFullDataset();rowOptions=[{name:"(None)",value:""}];columnOptions=[{name:"(None)",value:""}];numericRowOptions=[{name:"(None)",value:""}];numericColumnOptions=[{name:"(None)",value:""}];options=[{name:"(None)",value:""}];numericOptions=[{name:"(None)",value:""}];morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata()).forEach(function(name){var dataType=morpheus.VectorUtil.getDataType(dataset.getRowMetadata().getByName(name));if(dataType==="number"||dataType==="[number]"){numericRowOptions.push({name:name+" (row)",value:name+"_r"})}rowOptions.push({name:name+" (row)",value:name+"_r"})});morpheus.MetadataUtil.getMetadataNames(dataset.getColumnMetadata()).forEach(function(name){var dataType=morpheus.VectorUtil.getDataType(dataset.getColumnMetadata().getByName(name));if(dataType==="number"||dataType==="[number]"){numericColumnOptions.push({name:name+" (column)",value:name+"_c"})}columnOptions.push({name:name+" (column)",value:name+"_c"})});options=options.concat(rowOptions.slice(1));options=options.concat(columnOptions.slice(1));numericOptions=numericOptions.concat(numericRowOptions.slice(1));numericOptions=numericOptions.concat(numericColumnOptions.slice(1))};updateOptions();formBuilder.append({name:"group_by",type:"bootstrap-select",options:options});formBuilder.append({name:"axis_label",type:"bootstrap-select",options:rowOptions});formBuilder.append({name:"show_outliers",type:"checkbox",value:true});formBuilder.append({name:"color",type:"bootstrap-select",options:options});formBuilder.append({name:"tooltip",type:"bootstrap-select",multiple:true,search:true,options:options.slice(1)});formBuilder.append({name:"chart_width",type:"range",value:400,min:60,max:800,step:10});formBuilder.append({name:"chart_height",type:"range",value:400,min:20,max:800,step:10});var chartTypeToParameter={"row profile":{axis_label:"columns",tooltip:"columns",color:"rows"},"column profile":{axis_label:"rows",tooltip:"rows",color:"columns"},"row scatter matrix":{axis_label:"rows",color:"columns",tooltip:"columns"},"column scatter matrix":{axis_label:"columns",color:"rows",tooltip:"rows"},boxplot:{group_by:true,show_outliers:true,tooltip:"both"}};function setVisibility(){var chartType=formBuilder.getValue("chart_type");var chartOptions=chartTypeToParameter[chartType];if(chartOptions.axis_label!=null){formBuilder.setOptions("axis_label",chartOptions.axis_label==="rows"?rowOptions:columnOptions,true)}formBuilder.setVisible("color",chartOptions.color!=null);formBuilder.setVisible("axis_label",chartOptions.axis_label!=null);formBuilder.setVisible("group_by",chartOptions.group_by);formBuilder.setVisible("show_outliers",chartOptions.show_outliers);formBuilder.setOptions("tooltip",chartOptions.tooltip==="rows"?rowOptions.slice(1):chartOptions.tooltip==="columns"?columnOptions.slice(1):options);formBuilder.setOptions("color",chartOptions.color==="rows"?rowOptions:chartOptions.color==="columns"?columnOptions:options)}this.tooltip=[];var draw=function(){_.debounce(_this.draw(),100)};formBuilder.$form.on("change","select,input[type=range]",function(e){if($(this).attr("name")==="tooltip"){var tooltipVal=_this.formBuilder.getValue("tooltip");_this.tooltip.length=0;if(tooltipVal!=null){tooltipVal.forEach(function(tip){_this.tooltip.push(morpheus.ChartTool.getVectorInfo(tip))})}}else{setVisibility();draw()}});formBuilder.$form.on("click","input[type=checkbox]",function(e){draw()});formBuilder.$form.on("keypress","input[type=text]",function(e){if(e.which===13){draw()}});setVisibility();var trackChanged=function(){updateOptions();setVisibility();formBuilder.setOptions("group_by",options,true)};project.getColumnSelectionModel().on("selectionChanged.chart",draw);project.getRowSelectionModel().on("selectionChanged.chart",draw);project.on("trackChanged.chart",trackChanged);this.$chart=this.$el.find("[data-name=chartDiv]");var $dialog=$('<div style="background:white;" title="Chart"></div>');var $configPane=this.$el.find("[data-name=configPane]");formBuilder.$form.appendTo($configPane);this.$el.appendTo($dialog);$dialog.dialog({dialogClass:"morpheus",close:function(event,ui){project.off("trackChanged.chart",trackChanged);project.getRowSelectionModel().off("selectionChanged.chart",draw);project.getColumnSelectionModel().off("selectionChanged.chart",draw);_this.$el.empty()},resizable:true,height:600,width:900});this.$dialog=$dialog;this.draw()};morpheus.ChartTool.getVectorInfo=function(value){var field=value.substring(0,value.length-2);var isColumns=value.substring(value.length-2)==="_c";return{field:field,isColumns:isColumns}};morpheus.ChartTool.prototype={_createScatter:function(options){var _this=this;var dataset=options.dataset;var colorByVector=options.colorByVector;var colorModel=options.colorModel;var heatmap=this.heatmap;var chartWidth=options.chartWidth;var chartHeight=options.chartHeight;var axisLabelVector=options.axisLabelVector;var transpose=options.transpose;var chart={animation:false,toolbox:{feature:{brush:{title:{rect:"Rectangle selection",polygon:"Polygon selection",clear:"Clear Selection",keep:"Keep previous selection"}}}},brush:{brushLink:"all",xAxisIndex:[],yAxisIndex:[],inBrush:{opacity:1}},tooltip:{trigger:"item"},grid:[],xAxis:[],yAxis:[],series:[]};var index=0;var GAP=20;var BASE_LEFT=40;var BASE_TOP=40;for(var rowIndexOne=1,nrows=dataset.getRowCount();rowIndexOne<nrows;rowIndexOne++){for(var rowIndexTwo=0;rowIndexTwo<rowIndexOne;rowIndexTwo++){(function(){var data=[];var color=[];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){data.push([dataset.getValue(rowIndexOne,j),dataset.getValue(rowIndexTwo,j),j])}if(colorByVector){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var colorByValue=colorByVector.getValue(j);color.push(colorModel.getMappedValue(colorByVector,colorByValue))}}chart.grid.push({left:GAP+(rowIndexOne-1)*(chartWidth+GAP),top:BASE_TOP+rowIndexTwo*(chartHeight+GAP),width:chartWidth,height:chartHeight});chart.brush.xAxisIndex&&chart.brush.xAxisIndex.push(index);chart.brush.yAxisIndex&&chart.brush.yAxisIndex.push(index);chart.xAxis.push({splitNumber:3,position:"top",name:axisLabelVector!=null&&rowIndexTwo===0?axisLabelVector.getValue(rowIndexOne):"",nameGap:25,nameLocation:"middle",axisLine:{show:false,onZero:false},axisTick:{show:rowIndexTwo===0,inside:true},axisLabel:{show:rowIndexTwo===0},type:"value",gridIndex:index,scale:true});chart.yAxis.push({splitNumber:3,nameGap:50,name:axisLabelVector!=null&&rowIndexOne===nrows-1?axisLabelVector.getValue(rowIndexTwo):"",nameLocation:"middle",position:"right",axisLine:{show:false,onZero:false},axisTick:{show:rowIndexOne===nrows-1,inside:true},axisLabel:{show:rowIndexOne===nrows-1},type:"value",gridIndex:index,scale:true});chart.series.push({symbolSize:4,tooltip:{formatter:function(obj){var value=obj.value;var s=[];s.push("x: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[0]));s.push("<br>");s.push("y "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[1]));if(transpose){morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:new morpheus.TransposedDatasetView(dataset),rowIndex:value[2],columnIndex:-1})}else{morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:dataset,rowIndex:-1,columnIndex:value[2]})}return s.join("")}},itemStyle:{normal:{color:function(param){return color.length===0?"#1f78b4":color[param.dataIndex]}}},type:"scatter",xAxisIndex:index,yAxisIndex:index,data:data});index++})()}}var myChart=echarts.init(options.el);myChart.setOption(chart)},_createProfile:function(options){var _this=this;var dataset=options.dataset;var colorByVector=options.colorByVector;var colorModel=options.colorModel;var heatmap=this.heatmap;var chartWidth=options.chartWidth;var chartHeight=options.chartHeight;var axisLabelVector=options.axisLabelVector;var transpose=options.transpose;var axisLabel=[];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){axisLabel.push(axisLabelVector!=null?axisLabelVector.getValue(j):""+j)}var series=[];var colorMap=morpheus.VectorColorModel.getColorMapForNumber(dataset.getRowCount());for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){var colorByValue=colorByVector!=null?colorByVector.getValue(i):""+i;var color=colorByVector!=null?colorModel.getMappedValue(colorByVector,colorByValue):colorMap[i%colorMap.length];var data=[];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){data.push([j,dataset.getValue(i,j),i])}series.push({name:colorByValue,type:"line",data:data,tooltip:{formatter:function(obj){var value=obj.value;var s=[];s.push(_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[1]));morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:dataset,rowIndex:value[2],columnIndex:value[0]});return s.join("")}}})}var chart={legend:{orient:"vertical",left:"right",top:2,itemWidth:14,height:dataset.getRowCount()*20,data:series.map(function(s){return s.name})},animation:false,tooltip:{trigger:"item"},xAxis:{type:"category",data:axisLabel},yAxis:{axisLine:{show:true,onZero:false},type:"value",name:""},grid:{right:120},series:series};var myChart=echarts.init(options.el);myChart.setOption(chart)},_createBoxPlot:function(options){var _this=this;var showPoints=options.showPoints;var datasets=options.datasets;var ids=options.ids;var heatmap=this.heatmap;var size=6;var boxData=[];var outliers=[];for(var k=0,ndatasets=datasets.length;k<ndatasets;k++){var dataset=datasets[k];var id=ids[k];var values=new Float32Array(dataset.getRowCount()*dataset.getColumnCount());var counter=0;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(!isNaN(value)){values[counter]=value;counter++}}}if(counter!==values.length){values=values.slice(0,counter)}values.sort();var item=morpheus.BoxPlotArrayItem(values);boxData.push([item.lowerAdjacentValue,item.q1,item.median,item.q3,item.upperAdjacentValue]);if(options.showOutliers){var w=1.5;var upperOutlier=item.q3+w*(item.q3-item.q1);var lowerOutlier=item.q1-w*(item.q3-item.q1);for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(value>upperOutlier||value<lowerOutlier){outliers.push([id,value,i,j])}}}}}var chart={animation:false,tooltip:{trigger:"item"},xAxis:{type:"category",data:ids},yAxis:{axisLine:{show:true,onZero:false},type:"value",name:""},series:[{animationDuration:0,hoverAnimation:false,name:"boxplot",type:"boxplot",data:boxData,tooltip:{formatter:function(param){var text=[];if(param.name!==""){text.push(param.name)}text=text.concat(["upper: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[4]),"Q3: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[3]),"median: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[2]),"Q1: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[1]),"lower: "+_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(param.data[0])]);return text.join("<br/>")}}},{name:"outlier",type:"scatter",data:outliers,symbolSize:5,itemStyle:{normal:{borderWidth:1,borderColor:"black",opacity:.8}},tooltip:{formatter:function(obj){var value=obj.value;var s=[];if(value[0]!==""){s.push(value[0]);s.push("<br>")}s.push(_this.heatmap.getHeatMapElementComponent().getDrawValuesFormat()(value[1]));morpheus.ChartTool.getTooltip({text:s,tooltip:_this.tooltip,dataset:dataset,rowIndex:value[2],columnIndex:value[3]});return s.join("")}}}]};var myChart=echarts.init(options.el);myChart.setOption(chart)},draw:function(){var _this=this;this.$chart.empty();var gridWidth=parseInt(this.formBuilder.getValue("chart_width"));var gridHeight=parseInt(this.formBuilder.getValue("chart_height"));var showOutliers=this.formBuilder.getValue("show_outliers");var groupBy=this.formBuilder.getValue("group_by");var axisLabel=this.formBuilder.getValue("axis_label");var chartType=this.formBuilder.getValue("chart_type");var dataset=this.project.getSelectedDataset({emptyToAll:false});this.dataset=dataset;if(dataset.getRowCount()===0&&dataset.getColumnCount()===0){$("<h4>Please select rows and columns in the heat map.</h4>").appendTo(this.$chart);return}else if(dataset.getRowCount()===0){$("<h4>Please select rows in the heat map.</h4>").appendTo(this.$chart);return}if(dataset.getColumnCount()===0){$("<h4>Please select columns in the heat map.</h4>").appendTo(this.$chart);return}var heatmap=this.heatmap;var axisLabelInfo=morpheus.ChartTool.getVectorInfo(axisLabel);var axisLabelVector=axisLabelInfo.isColumns?dataset.getColumnMetadata().getByName(axisLabelInfo.field):dataset.getRowMetadata().getByName(axisLabelInfo.field);var rowIds=[undefined];var columnIds=[undefined];var colorBy=this.formBuilder.getValue("color");var colorByVector=null;var colorModel=null;if(colorBy!=null){var colorByInfo=morpheus.ChartTool.getVectorInfo(colorBy);colorModel=!colorByInfo.isColumns?this.project.getRowColorModel():this.project.getColumnColorModel();colorByVector=colorByInfo.isColumns?dataset.getColumnMetadata().getByName(colorByInfo.field):dataset.getRowMetadata().getByName(colorByInfo.field)}if(chartType==="row profile"||chartType==="column profile"){var transpose=chartType==="column profile";if(transpose){dataset=new morpheus.TransposedDatasetView(dataset)}if(dataset.getRowCount()>100){$("<h4>Maximum chart size exceeded.</h4>").appendTo(this.$chart);return}var $chart=$('<div style="width: '+(gridWidth+120)+"px;height:"+gridHeight+'px;"></div>');$chart.appendTo(this.$chart);this._createProfile({width:gridWidth,el:$chart[0],dataset:dataset,chartWidth:gridWidth,chartHeight:gridHeight,transpose:transpose,colorModel:colorModel,colorByVector:colorByVector,axisLabelVector:axisLabelVector})}else if(chartType==="row scatter matrix"||chartType==="column scatter matrix"){var transpose=chartType==="column scatter matrix";if(transpose){dataset=new morpheus.TransposedDatasetView(dataset)}if(dataset.getRowCount()>20){$("<h4>Maximum chart size exceeded.</h4>").appendTo(this.$chart);return}var $chart=$('<div style="width:'+(80+(dataset.getRowCount()-1)*(gridWidth+20))+"px;height:"+(80+dataset.getRowCount()*(gridHeight+20))+'px;"></div>');$chart.appendTo(this.$chart);this._createScatter({el:$chart[0],dataset:dataset,chartWidth:gridWidth,chartHeight:gridHeight,transpose:transpose,colorModel:colorModel,colorByVector:colorByVector,axisLabelVector:axisLabelVector})}else if(chartType==="boxplot"){var datasets=[];var ids=[];if(groupBy){var groupByInfo=morpheus.ChartTool.getVectorInfo(groupBy);var vector=groupByInfo.isColumns?dataset.getColumnMetadata().getByName(groupByInfo.field):dataset.getRowMetadata().getByName(groupByInfo.field);var isArray=morpheus.VectorUtil.getDataType(vector)[0]==="[";var valueToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector,true);valueToIndices.forEach(function(indices,value){datasets.push(new morpheus.SlicedDatasetView(dataset,groupByInfo.isColumns?null:indices,groupByInfo.isColumns?indices:null));ids.push(value)})}else{datasets.push(dataset);ids.push("")}var $chartEl=$('<div style="width: '+gridWidth+"px;height:"+gridHeight+'px;"></div>');$chartEl.appendTo(this.$chart);this._createBoxPlot({showOutliers:showOutliers,el:$chartEl[0],datasets:datasets,ids:ids})}}};morpheus.ChartTool.getTooltip=function(options){for(var tipIndex=0;tipIndex<options.tooltip.length;tipIndex++){var tip=options.tooltip[tipIndex];var metadata;var index;if(tip.isColumns){metadata=options.dataset.getColumnMetadata();index=options.columnIndex}else{metadata=options.dataset.getRowMetadata();index=options.rowIndex}if(index!==-1){var v=metadata.getByName(tip.field);morpheus.HeatMapTooltipProvider.vectorToString(v,index,options.text,"<br>")}}};morpheus.CollapseDatasetTool=function(){};morpheus.CollapseDatasetTool.Functions=[morpheus.Mean,morpheus.Median,new morpheus.MaxPercentiles([25,75]),morpheus.Min,morpheus.Max,morpheus.Percentile,morpheus.Sum,morpheus.MaximumMeanProbe,morpheus.MaximumMedianProbe];morpheus.CollapseDatasetTool.Functions.fromString=function(s){for(var i=0;i<morpheus.CollapseDatasetTool.Functions.length;i++){if(morpheus.CollapseDatasetTool.Functions[i].toString()===s){return morpheus.CollapseDatasetTool.Functions[i]}}throw new Error(s+" not found")};morpheus.CollapseDatasetTool.prototype={toString:function(){return"Collapse"},init:function(project,form){var setValue=function(val){var isRows=val==="Rows";var names=morpheus.MetadataUtil.getMetadataNames(isRows?project.getFullDataset().getRowMetadata():project.getFullDataset().getColumnMetadata());form.setOptions("collapse_to_fields",names)};form.$form.find("[name=collapse]").on("change",function(e){setValue($(this).val())});form.setVisible("percentile",false);form.$form.find("[name=collapse_method]").on("change",function(e){form.setVisible("percentile",$(this).val()===morpheus.Percentile.toString());form.setVisible("collapse",!morpheus.CollapseDatasetTool.Functions.fromString($(this).val()).selectOne)});setValue("Rows")},gui:function(){return[{name:"collapse_method",options:morpheus.CollapseDatasetTool.Functions,value:morpheus.CollapseDatasetTool.Functions[1].toString(),type:"select"},{name:"percentile",value:75,type:"text"},{name:"collapse",options:["Columns","Rows"],value:"Rows",type:"radio"},{name:"collapse_to_fields",options:[],type:"select",multiple:true}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var f=morpheus.CollapseDatasetTool.Functions.fromString(options.input.collapse_method);if(f.toString()===morpheus.Percentile.toString()){var p=parseFloat(options.input.percentile);f=function(vector){return morpheus.Percentile(vector,p)}}var collapseToFields=options.input.collapse_to_fields;if(collapseToFields.length===0){throw new Error("Please select one or more fields to collapse to")}var dataset=project.getFullDataset();var rows=options.input.collapse=="Rows";if(!rows){dataset=new morpheus.TransposedDatasetView(dataset)}var allFields=morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata());var collapseMethod=f.selectOne?morpheus.SelectRow:morpheus.CollapseDataset;dataset=collapseMethod(dataset,collapseToFields,f,true);if(!rows){dataset=new morpheus.TransposedDatasetView(dataset)}var set=new morpheus.Map;_.each(allFields,function(field){set.set(field,true)});_.each(collapseToFields,function(field){set.remove(field)});return new morpheus.HeatMap({name:heatMap.getName(),dataset:dataset,parent:heatMap,symmetric:false})}};morpheus.CreateAnnotation=function(){};morpheus.CreateAnnotation.prototype={toString:function(){return"Create Calculated Annotation"},gui:function(){return[{name:"annotate",options:["Columns","Rows"],value:"Rows",type:"radio"},{name:"annotation_name",value:"",type:"text",required:true,autocomplete:"off"},{name:"formula",value:"",type:"textarea",placeholder:"e.g MAD()",required:true,help:"JavaScript formula. Built-in functions (case-sensitive): COUNTIF(expression),"+" MAD(), MAX(),"+" MEAN(), MEDIAN(), MIN(), PERCENTILE(p), SUM(), VARIANCE(). Refer to a field using FIELD(name)"},{name:"use_selected_rows_and_columns_only",type:"checkbox"}]},execute:function(options){var __project=options.project;var isColumns=options.input.annotate=="Columns";var __formula=options.input.formula;var __dataset=options.input.use_selected_rows_and_columns_only?__project.getSelectedDataset():__project.getSortedFilteredDataset();if(isColumns){__dataset=morpheus.DatasetUtil.transposedView(__dataset)}var __rowView=new morpheus.DatasetRowView(__dataset);var __vector=__dataset.getRowMetadata().add(options.input.annotation_name);var COUNTIF=function(val){return morpheus.CountIf(__rowView,val)};var MAD=function(){return morpheus.MAD(__rowView)};var MAX=function(){return morpheus.Max(__rowView)};var MEAN=function(){return morpheus.Mean(__rowView)};var MEDIAN=function(p){return morpheus.Percentile(__rowView,50)};var MIN=function(){return morpheus.Min(__rowView)};var PERCENTILE=function(p){return morpheus.Percentile(__rowView,p)};var SUM=function(){return morpheus.Sum(__rowView)};var VARIANCE=function(){return morpheus.Variance(__rowView)};var __index=0;var FIELD=function(field){var vector=__dataset.getRowMetadata().getByName(field);return vector?vector.getValue(__index):undefined};for(var size=__dataset.getRowCount();__index<size;__index++){__rowView.setIndex(__index);var __val=eval(__formula);if(typeof __val==="function"){__val=""}__vector.setValue(__index,__val)}morpheus.VectorUtil.maybeConvertStringToNumber(__vector);__project.trigger("trackChanged",{vectors:[__vector],display:["text"],columns:isColumns})}};morpheus.DendrogramEnrichmentTool=function(isColumns){this.isColumns=isColumns};morpheus.DendrogramEnrichmentTool.prototype={toString:function(){return"Dendrogram Enrichment"},gui:function(project){var dataset=project.getSortedFilteredDataset();var fields=morpheus.MetadataUtil.getMetadataNames(this.isColumns?dataset.getColumnMetadata():dataset.getRowMetadata());return[{name:"field",options:fields,type:"bootstrap-select",multiple:false},{name:"min_p-value_for_enrichment",type:"text",value:"0.05"},{name:"minimum_number_of_total_members_in_group",type:"text",value:"5"},{name:"minimum_number_of_members_in_group",type:"text",value:"3"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var pValue=options.input["min_p-value_for_enrichment"];var minTotalGroupSize=options.input.minimum_number_of_total_members_in_group;var minGroupSize=options.input.minimum_number_of_members_in_group;var dataset=project.getSortedFilteredDataset();var dendrogram=this.isColumns?heatMap.columnDendrogram:heatMap.rowDendrogram;var vector=this.isColumns?dataset.getColumnMetadata().getByName(options.input.field):dataset.getRowMetadata().getByName(options.input.field);var valueToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector);var valueToGlobalCount=new morpheus.Map;var values=[];valueToIndices.forEach(function(indices,value){valueToGlobalCount.set(value,indices.length);values.push(value)});var nvalues=values.length;var N=vector.size();morpheus.DendrogramUtil.dfs(dendrogram.tree.rootNode,function(node){delete node.info;var valueToCount=new morpheus.Map;for(var i=0;i<nvalues;i++){valueToCount.set(values[i],0)}var min=node.minIndex;var max=node.maxIndex;var n=max-min+1;if(n>1&&n>=minTotalGroupSize){for(var i=min;i<=max;i++){var value=vector.getValue(i);valueToCount.set(value,valueToCount.get(value)+1)}for(var i=0;i<nvalues;i++){var K=valueToGlobalCount.get(values[i]);var k=valueToCount.get(values[i]);if(k>=minGroupSize){var a=k;var b=K-k;var c=n-k;var d=N+k-n-K;var p=morpheus.FisherExact.fisherTest(a,b,c,d);if(p<=pValue){if(!node.info){node.info={}}node.info[values[i]]=p}}}}return true});dendrogram.setInvalid(true);dendrogram.repaint()}};morpheus.DevAPI=function(){};morpheus.DevAPI.prototype={toString:function(){return"API"},gui:function(){return[{name:"code",value:"",type:"textarea",required:true,help:"Enter your code"}]},execute:function(options){var heatMap=options.heatMap;var code=options.input.code;eval(code);heatMap.getProject().setFullDataset(heatMap.getProject().getFullDataset(),true)}};morpheus.HClusterTool=function(){};morpheus.HClusterTool.PRECOMPUTED_DIST="Matrix values (for a precomputed distance matrix)";morpheus.HClusterTool.PRECOMPUTED_SIM="Matrix values (for a precomputed similarity matrix)";morpheus.HClusterTool.Functions=[morpheus.Euclidean,morpheus.Jaccard,new morpheus.OneMinusFunction(morpheus.Cosine),new morpheus.OneMinusFunction(morpheus.KendallsCorrelation),new morpheus.OneMinusFunction(morpheus.Pearson),new morpheus.OneMinusFunction(morpheus.Spearman),morpheus.HClusterTool.PRECOMPUTED_DIST,morpheus.HClusterTool.PRECOMPUTED_SIM];morpheus.HClusterTool.Functions.fromString=function(s){for(var i=0;i<morpheus.HClusterTool.Functions.length;i++){if(morpheus.HClusterTool.Functions[i].toString()===s){return morpheus.HClusterTool.Functions[i]}}throw new Error(s+" not found")};morpheus.HClusterTool.createLinkageMethod=function(linkageString){var linkageMethod;if(linkageString==="Average"){linkageMethod=morpheus.AverageLinkage}else if(linkageString==="Complete"){linkageMethod=morpheus.CompleteLinkage}else if(linkageString==="Single"){linkageMethod=morpheus.SingleLinkage}else{throw new Error("Unknown linkage method "+linkageString)}return linkageMethod};morpheus.HClusterTool.execute=function(dataset,input){var linkageMethod=morpheus.HClusterTool.createLinkageMethod(input.linkage_method);var f=morpheus.HClusterTool.Functions.fromString(input.metric);if(f===morpheus.HClusterTool.PRECOMPUTED_DIST){f=0}else if(f===morpheus.HClusterTool.PRECOMPUTED_SIM){f=1}var rows=input.cluster=="Rows"||input.cluster=="Rows and columns";var columns=input.cluster=="Columns"||input.cluster=="Rows and columns";var doCluster=function(d,groupByFields){return groupByFields&&groupByFields.length>0?new morpheus.HClusterGroupBy(d,groupByFields,f,linkageMethod):new morpheus.HCluster(morpheus.HCluster.computeDistanceMatrix(d,f),linkageMethod)};var rowsHcl;var columnsHcl;if(rows){rowsHcl=doCluster(input.selectedColumnsToUseForClusteringRows?new morpheus.SlicedDatasetView(dataset,null,input.selectedColumnsToUseForClusteringRows):dataset,input.group_rows_by)}if(columns){columnsHcl=doCluster(morpheus.DatasetUtil.transposedView(input.selectedRowsToUseForClusteringColumns?new morpheus.SlicedDatasetView(dataset,input.selectedRowsToUseForClusteringColumns,null):dataset),input.group_columns_by)}return{rowsHcl:rowsHcl,columnsHcl:columnsHcl}};morpheus.HClusterTool.prototype={toString:function(){return"Hierarchical Clustering"},init:function(project,form){form.setOptions("group_rows_by",morpheus.MetadataUtil.getMetadataNames(project.getFullDataset().getRowMetadata()));form.setOptions("group_columns_by",morpheus.MetadataUtil.getMetadataNames(project.getFullDataset().getColumnMetadata()));form.setVisible("group_rows_by",false);form.setVisible("cluster_rows_in_space_of_selected_columns_only",false);form.$form.find("[name=cluster]").on("change",function(e){var val=$(this).val();var showGroupColumns=false;var showGroupRows=false;if(val==="Columns"){showGroupColumns=true}else if(val==="Rows"){showGroupRows=true}else{showGroupColumns=true;showGroupRows=true}form.setVisible("group_columns_by",showGroupColumns);form.setVisible("group_rows_by",showGroupRows);form.setVisible("cluster_columns_in_space_of_selected_rows_only",showGroupColumns);form.setVisible("cluster_rows_in_space_of_selected_columns_only",showGroupRows)})},gui:function(){return[{name:"metric",options:morpheus.HClusterTool.Functions,value:morpheus.HClusterTool.Functions[4].toString(),type:"select"},{name:"linkage_method",options:["Average","Complete","Single"],value:"Average",type:"select"},{name:"cluster",options:["Columns","Rows","Rows and columns"],value:"Columns",type:"select"},{name:"group_columns_by",options:[],type:"bootstrap-select",multiple:true},{name:"group_rows_by",options:[],type:"bootstrap-select",multiple:true},{name:"cluster_columns_in_space_of_selected_rows_only",type:"checkbox"},{name:"cluster_rows_in_space_of_selected_columns_only",type:"checkbox"}]},execute:function(options){var project=options.project;var heatmap=options.heatMap;var selectedRowsToUseForClusteringColumns=options.input.cluster_columns_in_space_of_selected_rows_only?project.getRowSelectionModel().getViewIndices().values():null;if(selectedRowsToUseForClusteringColumns!=null&&selectedRowsToUseForClusteringColumns.length===0){selectedRowsToUseForClusteringColumns=null}var selectedColumnsToUseForClusteringRows=options.input.cluster_rows_in_space_of_selected_columns_only?project.getColumnSelectionModel().getViewIndices().values():null;if(selectedColumnsToUseForClusteringRows!=null&&selectedColumnsToUseForClusteringRows.length===0){selectedColumnsToUseForClusteringRows=null}var rows=options.input.cluster=="Rows"||options.input.cluster=="Rows and columns";var columns=options.input.cluster=="Columns"||options.input.cluster=="Rows and columns";options.input.selectedRowsToUseForClusteringColumns=selectedRowsToUseForClusteringColumns;options.input.selectedColumnsToUseForClusteringRows=selectedColumnsToUseForClusteringRows;var dataset=project.getSortedFilteredDataset();if(options.input.background===undefined){options.input.background=true}options.input.background=options.input.background&&typeof Worker!=="undefined";var rowModelOrder;var columnModelOrder;if(rows){rowModelOrder=[];for(var i=0;i<dataset.getRowCount();i++){rowModelOrder[i]=project.convertViewRowIndexToModel(i)}}if(columns){columnModelOrder=[];for(var i=0;i<dataset.getColumnCount();i++){columnModelOrder[i]=project.convertViewColumnIndexToModel(i)}}if(options.input.background===false){var result=morpheus.HClusterTool.execute(dataset,options.input);if(result.rowsHcl){var modelOrder=[];for(var i=0;i<result.rowsHcl.reorderedIndices.length;i++){modelOrder[i]=rowModelOrder[result.rowsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.rowsHcl.tree,false,modelOrder)}if(result.columnsHcl){var modelOrder=[];for(var i=0;i<result.columnsHcl.reorderedIndices.length;i++){modelOrder[i]=columnModelOrder[result.columnsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.columnsHcl.tree,true,modelOrder)}}else{var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.HClusterTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:options.input.group_columns_by||[],rowFields:options.input.group_rows_by||[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){var result=e.data;if(result.rowsHcl){var modelOrder=[];for(var i=0;i<result.rowsHcl.reorderedIndices.length;i++){modelOrder[i]=rowModelOrder[result.rowsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.rowsHcl.tree,false,modelOrder)}if(result.columnsHcl){var modelOrder=[];for(var i=0;i<result.columnsHcl.reorderedIndices.length;i++){modelOrder[i]=columnModelOrder[result.columnsHcl.reorderedIndices[i]]}heatmap.setDendrogram(result.columnsHcl.tree,true,modelOrder)}worker.terminate();window.URL.revokeObjectURL(url)};return worker}}};morpheus.KMeansTool=function(){};morpheus.KMeansTool.execute=function(dataset,input){var f=morpheus.HClusterTool.Functions.fromString(input.metric);if(f===morpheus.HClusterTool.PRECOMPUTED_DIST){f=0}else if(f===morpheus.HClusterTool.PRECOMPUTED_SIM){f=1}var rows=input.cluster=="Rows"||input.cluster=="Rows and columns";var columns=input.cluster=="Columns"||input.cluster=="Rows and columns";var doCluster=function(d){var kmeans=new morpheus.KMeansPlusPlusClusterer(input.number_of_clusters,input.maximum_iterations,f);var vectors=[];for(var i=0;i<d.getRowCount();i++){vectors.push(new morpheus.DatasetRowView(d).setIndex(i))}var clusters=kmeans.execute(vectors);var assignments=[];for(var i=0;i<clusters.length;i++){clusters[i].getPoints().forEach(function(p){assignments[p.i]=i+1})}return assignments};var rowAssignments;var columnAssignments;if(rows){rowAssignments=doCluster(input.selectedColumnsToUseForClusteringRows?new morpheus.SlicedDatasetView(dataset,null,input.selectedColumnsToUseForClusteringRows):dataset)}if(columns){columnAssignments=doCluster(morpheus.DatasetUtil.transposedView(input.selectedRowsToUseForClusteringColumns?new morpheus.SlicedDatasetView(dataset,input.selectedRowsToUseForClusteringColumns,null):dataset))}return{rowAssignments:rowAssignments,columnAssignments:columnAssignments}};morpheus.KMeansTool.prototype={toString:function(){return"KMeans Clustering"},init:function(project,form){form.setVisible("cluster_rows_in_space_of_selected_columns_only",false);form.$form.find("[name=cluster]").on("change",function(e){var val=$(this).val();var val=$(this).val();var showGroupColumns=false;var showGroupRows=false;if(val==="Columns"){showGroupColumns=true}else if(val==="Rows"){showGroupRows=true}else{showGroupColumns=true;showGroupRows=true}form.setVisible("cluster_columns_in_space_of_selected_rows_only",showGroupColumns);form.setVisible("cluster_rows_in_space_of_selected_columns_only",showGroupRows)})},gui:function(){return[{name:"metric",options:morpheus.HClusterTool.Functions,value:morpheus.HClusterTool.Functions[4].toString(),type:"select"},{name:"cluster",options:["Columns","Rows","Rows and columns"],value:"Columns",type:"select"},{name:"number_of_clusters",value:"2",type:"text"},{name:"cluster_columns_in_space_of_selected_rows_only",type:"checkbox"},{name:"cluster_rows_in_space_of_selected_columns_only",type:"checkbox"},{name:"maximum_iterations",value:"1000",type:"text"}]},execute:function(options){var project=options.project;var heatmap=options.heatMap;options.input.number_of_clusters=parseInt(options.input.number_of_clusters);options.input.maximum_iterations=parseInt(options.input.maximum_iterations);var selectedRowsToUseForClusteringColumns=options.input.cluster_columns_in_space_of_selected_rows_only?project.getRowSelectionModel().getViewIndices().values():null;if(selectedRowsToUseForClusteringColumns!=null&&selectedRowsToUseForClusteringColumns.length===0){selectedRowsToUseForClusteringColumns=null}var selectedColumnsToUseForClusteringRows=options.input.cluster_rows_in_space_of_selected_columns_only?project.getColumnSelectionModel().getViewIndices().values():null;if(selectedColumnsToUseForClusteringRows!=null&&selectedColumnsToUseForClusteringRows.length===0){selectedColumnsToUseForClusteringRows=null}var rows=options.input.cluster=="Rows"||options.input.cluster=="Rows and columns";var columns=options.input.cluster=="Columns"||options.input.cluster=="Rows and columns";options.input.selectedRowsToUseForClusteringColumns=selectedRowsToUseForClusteringColumns;options.input.selectedColumnsToUseForClusteringRows=selectedColumnsToUseForClusteringRows;var dataset=project.getSortedFilteredDataset();options.input.background=options.input.background&&typeof Worker!=="undefined";function addAssignments(d,assignments,k){var v=d.getColumnMetadata().add("k_means_"+k);for(var i=0;i<assignments.length;i++){v.setValue(i,assignments[i])}}if(options.input.background===false){var result=morpheus.KMeansTool.execute(dataset,options.input);if(result.columnAssignments){addAssignments(dataset,result.columnAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,true,{highlightMatchingValues:true,discreteAutoDetermined:true,display:["color"]})}if(result.rowAssignments){addAssignments(new morpheus.TransposedDatasetView(dataset),result.rowAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,false,{highlightMatchingValues:true,discreteAutoDetermined:true,display:["color"]})}heatmap.revalidate()}else{var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.KMeansTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){var result=e.data;if(result.columnAssignments){addAssignments(dataset,result.columnAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,true,{highlightMatchingValues:true,discrete:true,display:["color"]})}if(result.rowAssignments){addAssignments(new morpheus.TransposedDatasetView(dataset),result.rowAssignments,options.input.number_of_clusters);heatmap.addTrack("k_means_"+options.input.number_of_clusters,false,{highlightMatchingValues:true,discrete:true,display:["color"]})}heatmap.revalidate();worker.terminate();window.URL.revokeObjectURL(url)};return worker}}};morpheus.MarkerSelection=function(){};morpheus.MarkerSelection.Functions=[morpheus.FisherExact,morpheus.FoldChange,morpheus.MeanDifference,morpheus.SignalToNoise,morpheus.createSignalToNoiseAdjust(),morpheus.TTest];morpheus.MarkerSelection.Functions.fromString=function(s){for(var i=0;i<morpheus.MarkerSelection.Functions.length;i++){if(morpheus.MarkerSelection.Functions[i].toString()===s){return morpheus.MarkerSelection.Functions[i]}}throw s+" not found"};morpheus.MarkerSelection.execute=function(dataset,input){var aIndices=[];var bIndices=[];for(var i=0;i<input.numClassA;i++){aIndices[i]=i}for(var i=input.numClassA;i<dataset.getColumnCount();i++){bIndices[i]=i}var f=morpheus.MarkerSelection.Functions.fromString(input.metric);var permutations=new morpheus.PermutationPValues(dataset,aIndices,bIndices,input.npermutations,f);return{rowSpecificPValues:permutations.rowSpecificPValues,k:permutations.k,fdr:permutations.fdr,scores:permutations.scores}};morpheus.MarkerSelection.prototype={toString:function(){return"Marker Selection"},init:function(project,form){var _this=this;var updateAB=function(fieldNames){var ids=[];if(fieldNames!=null){var vectors=morpheus.MetadataUtil.getVectors(project.getFullDataset().getColumnMetadata(),fieldNames);var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);idToIndices.forEach(function(indices,id){ids.push(id)})}ids.sort();form.setOptions("class_a",ids);form.setOptions("class_b",ids)};var $field=form.$form.find("[name=field]");$field.on("change",function(e){updateAB($(this).val())});if($field[0].options.length>0){$field.val($field[0].options[0].value)}updateAB($field.val());var $metric=form.$form.find("[name=metric]");$metric.on("change",function(e){var isFishy=$(this).val()==="Fisher Exact Test";form.setVisible("grouping_value",isFishy);form.setVisible("permutations",!isFishy);form.setVisible("number_of_markers",!isFishy)});form.setVisible("grouping_value",false)},gui:function(project){var dataset=project.getSortedFilteredDataset();var fields=morpheus.MetadataUtil.getMetadataNames(dataset.getColumnMetadata());return[{name:"metric",options:morpheus.MarkerSelection.Functions,value:morpheus.SignalToNoise.toString(),type:"select",help:""},{name:"grouping_value",value:"1",help:"Class values are categorized into two groups based on whether dataset values are greater than or equal to this value"},{name:"field",options:fields,type:"select",multiple:true},{name:"class_a",title:"Class A",options:[],value:"",type:"checkbox-list",multiple:true},{name:"class_b",title:"Class B",options:[],value:"",type:"checkbox-list",multiple:true},{name:"number_of_markers",value:"100",type:"text",help:"The initial number of markers to show in each direction."},{name:"permutations",value:"0",type:"text"}]},execute:function(options){var project=options.project;var classA=options.input.class_a;var classB=options.input.class_b;if(classA.length===0&&classB.length===0){throw"No samples in class A and class B"}if(classA.length===0){throw"No samples in class A"}if(classB.length===0){throw"No samples in class B"}for(var i=0;i<classA.length;i++){var val=classA[i];if(!(val instanceof morpheus.Identifier)){classA[i]=new morpheus.Identifier(morpheus.Util.isArray(val)?val:[val])}}for(var i=0;i<classB.length;i++){var val=classB[i];if(!(val instanceof morpheus.Identifier)){classB[i]=new morpheus.Identifier(morpheus.Util.isArray(val)?val:[val])}}var npermutations=parseInt(options.input.permutations);var dataset=project.getSortedFilteredDataset();var fieldNames=options.input.field;if(!morpheus.Util.isArray(fieldNames)){fieldNames=[fieldNames]}var vectors=morpheus.MetadataUtil.getVectors(dataset.getColumnMetadata(),fieldNames);var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);var aIndices=[];var bIndices=[];classA.forEach(function(id){var indices=idToIndices.get(id);if(indices===undefined){throw new Error(id+" not found in "+idToIndices.keys())}aIndices=aIndices.concat(indices)});classB.forEach(function(id){var indices=idToIndices.get(id);if(indices===undefined){throw new Error(id+" not found in "+idToIndices.keys())}bIndices=bIndices.concat(indices)});var f=morpheus.MarkerSelection.Functions.fromString(options.input.metric);var classASet={};for(var i=0;i<aIndices.length;i++){classASet[aIndices[i]]=true}for(var i=0;i<bIndices.length;i++){if(classASet[bIndices[i]]){throw"The sample was found in class A and class B"}}var isFishy=f.toString()===morpheus.FisherExact.toString();if((aIndices.length===1||bIndices.length===1)&&!isFishy&&f.toString()!==morpheus.MeanDifference.toString()){f=morpheus.FoldChange}var list1=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,aIndices));var list2=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,bIndices));var markerSelectionFields=morpheus.MarkerSelection.Functions.map(function(f){return f.toString()}).concat(["odds_ratio","FDR(BH)","p_value"]);markerSelectionFields.forEach(function(name){var index=morpheus.MetadataUtil.indexOf(dataset.getRowMetadata(),name);if(index!==-1){dataset.getRowMetadata().remove(index);options.heatMap.removeTrack(name,false)}});var v=dataset.getRowMetadata().add(f.toString());var vectors=[v];var comparisonVector=dataset.getColumnMetadata().add("Comparison");for(var i=0;i<aIndices.length;i++){comparisonVector.setValue(aIndices[i],"A")}for(var i=0;i<bIndices.length;i++){comparisonVector.setValue(bIndices[i],"B")}function done(result){if(result){var pvalueVector=dataset.getRowMetadata().add("p_value");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var kVector=dataset.getRowMetadata().add("k");for(var i=0,size=pvalueVector.size();i<size;i++){pvalueVector.setValue(i,result.rowSpecificPValues[i]);fdrVector.setValue(i,result.fdr[i]);kVector.setValue(i,result.k[i]);v.setValue(i,result.scores[i])}kVector.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});vectors.push(pvalueVector);vectors.push(fdrVector);vectors.push(kVector)}if(project.getRowFilter().getFilters().length>0){project.getRowFilter().setAnd(true,true)}var rowFilters=project.getRowFilter().getFilters();for(var i=0;i<rowFilters.length;i++){if(rowFilters[i]instanceof morpheus.TopNFilter){project.getRowFilter().remove(i,true);i--}}if(!isFishy){project.getRowFilter().add(new morpheus.TopNFilter(parseInt(options.input.number_of_markers),morpheus.TopNFilter.TOP_BOTTOM,vectors[0].getName()),true)}project.setRowFilter(project.getRowFilter(),true);project.setRowSortKeys([new morpheus.SortKey(vectors[0].getName(),isFishy?morpheus.SortKey.SortOrder.ASCENDING:morpheus.SortKey.SortOrder.DESCENDING)],true);var selectedColumnIndices=new morpheus.Set;aIndices.forEach(function(index){selectedColumnIndices.add(index)});bIndices.forEach(function(index){selectedColumnIndices.add(index)});project.getColumnSelectionModel().setViewIndices(selectedColumnIndices,true);project.setColumnSortKeys([new morpheus.SortKey(comparisonVector.getName(),morpheus.SortKey.SortOrder.ASCENDING)],true);project.trigger("trackChanged",{vectors:vectors,display:vectors.map(function(){return"text"}),columns:false});project.trigger("trackChanged",{vectors:[comparisonVector],display:["color"],columns:true})}if(isFishy){var groupingValue=parseFloat(options.input.grouping_value);var oddsRatioVector=dataset.getRowMetadata().add("odds_ratio");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var contingencyTableVector=dataset.getRowMetadata().add("contingency_table");var pvalues=[];for(var i=0,size=dataset.getRowCount();i<size;i++){var abcd=morpheus.createContingencyTable(list1.setIndex(i),list2.setIndex(i),groupingValue);contingencyTableVector.setValue(i,"[["+abcd[0]+", "+abcd[1]+"], ["+abcd[2]+", "+abcd[3]+"]]");var ratio=abcd[0]*abcd[3]/(abcd[1]*abcd[2]);if(isNaN(ratio)||ratio===Number.POSITIVE_INFINITY){ratio=0}oddsRatioVector.setValue(i,ratio);v.setValue(i,morpheus.FisherExact.fisherTest(abcd[0],abcd[1],abcd[2],abcd[3]));pvalues.push(v.getValue(i))}var fdr=morpheus.FDR_BH(pvalues);for(var i=0,size=dataset.getRowCount();i<size;i++){fdrVector.setValue(i,fdr[i])}vectors.push(oddsRatioVector);vectors.push(fdrVector);vectors.push(contingencyTableVector);done()}else{if(npermutations>0){var subset=new morpheus.SlicedDatasetView(dataset,null,aIndices.concat(bIndices));options.input.background=options.input.background&&typeof Worker!=="undefined";options.input.numClassA=aIndices.length;options.input.npermutations=npermutations;if(options.input.background){var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.MarkerSelection.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(subset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){done(e.data);worker.terminate();window.URL.revokeObjectURL(url)};return worker}else{done(morpheus.MarkerSelection.execute(subset,options.input))}}else{for(var i=0,size=dataset.getRowCount();i<size;i++){v.setValue(i,f(list1.setIndex(i),list2.setIndex(i)))}if(f.toString()===morpheus.TTest.toString()&&typeof jStat!=="undefined"){var pvalueVector=dataset.getRowMetadata().add("p_value");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var rowSpecificPValues=new Float32Array(dataset.getRowCount());for(var i=0,size=dataset.getRowCount();i<size;i++){list1.setIndex(i);list2.setIndex(i);var m1=morpheus.Mean(list1);var m2=morpheus.Mean(list2);var v1=morpheus.Variance(list1,m1);var v2=morpheus.Variance(list2,m2);var n1=morpheus.CountNonNaN(list1);var n2=morpheus.CountNonNaN(list2);var df=morpheus.DegreesOfFreedom(v1,v2,n1,n2);var t=v.getValue(i);var p=2*(1-jStat.studentt.cdf(Math.abs(t),df));rowSpecificPValues[i]=p;pvalueVector.setValue(i,p)}vectors.push(pvalueVector);var fdr=morpheus.FDR_BH(rowSpecificPValues);for(var i=0,size=dataset.getRowCount();i<size;i++){fdrVector.setValue(i,fdr[i])}vectors.push(fdrVector)}done()}}}};morpheus.NearestNeighbors=function(){};morpheus.NearestNeighbors.Functions=[morpheus.Cosine,morpheus.Euclidean,morpheus.Jaccard,morpheus.KendallsCorrelation,morpheus.Pearson,morpheus.Spearman,morpheus.WeightedMean];morpheus.NearestNeighbors.Functions.fromString=function(s){for(var i=0;i<morpheus.NearestNeighbors.Functions.length;i++){if(morpheus.NearestNeighbors.Functions[i].toString()===s){return morpheus.NearestNeighbors.Functions[i]}}throw new Error(s+" not found")};morpheus.NearestNeighbors.execute=function(dataset,input){var f=morpheus.NearestNeighbors.Functions.fromString(input.metric);var permutations=new morpheus.PermutationPValues(dataset,null,null,input.npermutations,f,morpheus.Vector.fromArray("",input.listValues));return{rowSpecificPValues:permutations.rowSpecificPValues,k:permutations.k,fdr:permutations.fdr,scores:permutations.scores}};morpheus.NearestNeighbors.prototype={toString:function(){return"Nearest Neighbors"},init:function(project,form){var $selectedOnly=form.$form.find("[name=use_selected_only]").parent();form.$form.find("[name=compute_nearest_neighbors_of]").on("change",function(e){var val=$(this).val();if(val==="selected rows"||val==="column annotation"){$($selectedOnly.contents()[1]).replaceWith(document.createTextNode(" Use selected columns only"))}else{$($selectedOnly.contents()[1]).replaceWith(document.createTextNode(" Use selected rows only"))}form.setVisible("annotation",false);if(val==="column annotation"||val==="row annotation"){var metadata=val==="column annotation"?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata();var names=[];for(var i=0;i<metadata.getMetadataCount();i++){var v=metadata.get(i);if(morpheus.VectorUtil.getDataType(v)==="number"){names.push(v.getName())}}names.sort(function(a,b){a=a.toLowerCase();b=b.toLowerCase();return a<b?-1:a===b?0:1});form.setOptions("annotation",names);form.setVisible("annotation",true)}});$($selectedOnly.contents()[1]).replaceWith(document.createTextNode(" Use selected columns only"));form.setVisible("annotation",false)},gui:function(){return[{name:"metric",options:morpheus.NearestNeighbors.Functions,value:morpheus.Pearson.toString(),type:"select"},{name:"compute_nearest_neighbors_of",options:["selected rows","selected columns","column annotation","row annotation"],value:"selected rows",type:"radio"},{name:"use_selected_only",type:"checkbox"},{name:"annotation",type:"bootstrap-select"},{name:"permutations",value:"0",type:"text"}]},execute:function(options){var project=options.project;var isColumns=options.input.compute_nearest_neighbors_of=="selected columns"||options.input.compute_nearest_neighbors_of=="row annotation";var isAnnotation=options.input.compute_nearest_neighbors_of=="column annotation"||options.input.compute_nearest_neighbors_of=="row annotation";var heatMap=options.heatMap;var f=morpheus.NearestNeighbors.Functions.fromString(options.input.metric);var dataset=project.getSortedFilteredDataset();if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var selectedIndices=(isColumns?project.getColumnSelectionModel():project.getRowSelectionModel()).getViewIndices().values();if(!isAnnotation&&selectedIndices.length===0){throw new Error("No "+(isColumns?"columns":"rows")+" selected")}var spaceIndices=null;if(options.input.use_selected_only){spaceIndices=(!isColumns?project.getColumnSelectionModel():project.getRowSelectionModel()).getViewIndices().values();dataset=morpheus.DatasetUtil.slicedView(dataset,null,spaceIndices)}var d1=morpheus.DatasetUtil.slicedView(dataset,selectedIndices,null);var nearestNeighborsList;if(isAnnotation){nearestNeighborsList=dataset.getColumnMetadata().getByName(options.input.annotation);if(!nearestNeighborsList){throw new Error("No annotation selected.")}}else{if(d1.getRowCount()>1){var columnView=new morpheus.DatasetColumnView(d1);var newDataset=new morpheus.Dataset({name:"",rows:1,columns:d1.getColumnCount()});for(var j=0,ncols=d1.getColumnCount();j<ncols;j++){var v=morpheus.Percentile(columnView.setIndex(j),50);newDataset.setValue(0,j,v)}d1=newDataset}nearestNeighborsList=new morpheus.DatasetRowView(d1)}var npermutations=parseInt(options.input.permutations);var scoreVector=dataset.getRowMetadata().add(f.toString());if(npermutations>0){if(options.input.background===undefined){options.input.background=true}options.input.background=options.input.background&&typeof Worker!=="undefined";options.input.npermutations=npermutations;var done=function(result){var pvalueVector=dataset.getRowMetadata().add("p_value");var fdrVector=dataset.getRowMetadata().add("FDR(BH)");var kVector=dataset.getRowMetadata().add("k");for(var i=0,size=pvalueVector.size();i<size;i++){pvalueVector.setValue(i,result.rowSpecificPValues[i]);fdrVector.setValue(i,result.fdr[i]);kVector.setValue(i,result.k[i]);scoreVector.setValue(i,result.scores[i])}kVector.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});var vectors=[pvalueVector,fdrVector,kVector,scoreVector];project.trigger("trackChanged",{vectors:vectors,display:["text"],columns:isColumns})};var listValues=new Float32Array(nearestNeighborsList.size());for(var i=0,size=listValues.length;i<size;i++){listValues[i]=nearestNeighborsList.getValue(i)}options.input.listValues=listValues;if(options.input.background){var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.NearestNeighbors.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){done(e.data);worker.terminate();window.URL.revokeObjectURL(url)};return worker}else{done(morpheus.NearestNeighbors.execute(dataset,options.input))}}else{var datasetRowView=new morpheus.DatasetRowView(dataset);for(var i=0,size=dataset.getRowCount();i<size;i++){scoreVector.setValue(i,f(nearestNeighborsList,datasetRowView.setIndex(i)))}if(!isColumns){project.setRowSortKeys([new morpheus.SortKey(f.toString(),morpheus.SortKey.SortOrder.DESCENDING)],true)}else{project.setColumnSortKeys([new morpheus.SortKey(f.toString(),morpheus.SortKey.SortOrder.DESCENDING)],true)}project.trigger("trackChanged",{vectors:[scoreVector],display:["text"],columns:isColumns})}}};morpheus.NewHeatMapTool=function(){};morpheus.NewHeatMapTool.prototype={toString:function(){return"New Heat Map"},execute:function(options){var project=options.project;var heatMap=options.heatMap;var dataset=project.getSelectedDataset({selectedRows:true,selectedColumns:true});morpheus.DatasetUtil.shallowCopy(dataset);var heatmap=new morpheus.HeatMap({name:heatMap.getName(),dataset:dataset,parent:heatMap,symmetric:project.isSymmetric()&&dataset.getColumnCount()===dataset.getRowCount()})}};morpheus.OpenDatasetTool=function(){};morpheus.OpenDatasetTool.prototype={toString:function(){return"Open Dataset"},_read:function(options,deferred){var _this=this;var project=options.project;var heatMap=options.heatMap;var file=options.input.file;var action=options.input.open_file_action;var dataset=project.getSortedFilteredDataset();deferred.fail(function(err){var message=["Error opening "+morpheus.Util.getFileName(file)+"."];if(err.message){message.push("<br />Cause: ");message.push(err.message)}morpheus.FormBuilder.showInModal({title:"Error",html:message.join(""),focus:document.activeElement})});deferred.done(function(newDataset){var extension=morpheus.Util.getExtension(morpheus.Util.getFileName(file));var filename=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(file));if(action==="append"||action==="append columns"){var appendRows=action==="append";_.each(heatMap.options.rows,function(item){if(item.renameTo){var v=newDataset.getRowMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}});_.each(heatMap.options.columns,function(item){if(item.renameTo){var v=newDataset.getColumnMetadata().getByName(item.field);if(v){v.setName(item.renameTo)}}});if(heatMap.options.datasetReady){heatMap.options.datasetReady(newDataset)}var currentDatasetMetadataNames=morpheus.MetadataUtil.getMetadataNames(!appendRows?dataset.getRowMetadata():dataset.getColumnMetadata());var newDatasetMetadataNames=morpheus.MetadataUtil.getMetadataNames(!appendRows?newDataset.getRowMetadata():newDataset.getColumnMetadata());if(currentDatasetMetadataNames.length>1||newDatasetMetadataNames.length>1){_this._matchAppend(newDatasetMetadataNames,currentDatasetMetadataNames,heatMap,function(appendOptions){heatMap.getProject().setFullDataset(appendRows?new morpheus.JoinedDataset(dataset,newDataset,appendOptions.current_dataset_annotation_name,appendOptions.new_dataset_annotation_name):new morpheus.TransposedDatasetView(new morpheus.JoinedDataset(new morpheus.TransposedDatasetView(dataset),new morpheus.TransposedDatasetView(newDataset),appendOptions.current_dataset_annotation_name,appendOptions.new_dataset_annotation_name)),true);if(heatMap.options.renderReady){heatMap.options.renderReady(heatMap);heatMap.updateDataset()}if(appendRows){heatMap.getHeatMapElementComponent().getColorScheme().setSeparateColorSchemeForRowMetadataField("Source");var sourcesSet=morpheus.VectorUtil.getSet(heatMap.getProject().getFullDataset().getRowMetadata().getByName("Source"));sourcesSet.forEach(function(source){heatMap.autoDisplay({extension:morpheus.Util.getExtension(source),filename:source})})}heatMap.tabManager.setTabTitle(heatMap.tabId,heatMap.getProject().getFullDataset().getRowCount()+" row"+morpheus.Util.s(heatMap.getProject().getFullDataset().getRowCount())+" x "+heatMap.getProject().getFullDataset().getColumnCount()+" column"+morpheus.Util.s(heatMap.getProject().getFullDataset().getColumnCount()));heatMap.revalidate()})}else{heatMap.getProject().setFullDataset(appendRows?new morpheus.JoinedDataset(dataset,newDataset,currentDatasetMetadataNames[0],newDatasetMetadataNames[0]):new morpheus.TransposedDatasetView(new morpheus.JoinedDataset(new morpheus.TransposedDatasetView(dataset),new morpheus.TransposedDatasetView(newDataset),currentDatasetMetadataNames[0],newDatasetMetadataNames[0])),true);if(heatMap.options.renderReady){heatMap.options.renderReady(heatMap);heatMap.updateDataset()}if(appendRows){heatMap.getHeatMapElementComponent().getColorScheme().setSeparateColorSchemeForRowMetadataField("Source");var sourcesSet=morpheus.VectorUtil.getSet(heatMap.getProject().getFullDataset().getRowMetadata().getByName("Source"));sourcesSet.forEach(function(source){heatMap.autoDisplay({extension:morpheus.Util.getExtension(source),filename:source})})}heatMap.tabManager.setTabTitle(heatMap.tabId,heatMap.getProject().getFullDataset().getRowCount()+" row"+morpheus.Util.s(heatMap.getProject().getFullDataset().getRowCount())+" x "+heatMap.getProject().getFullDataset().getColumnCount()+" column"+morpheus.Util.s(heatMap.getProject().getFullDataset().getColumnCount()));heatMap.revalidate()}}else if(action==="overlay"){_this._matchOverlay(morpheus.MetadataUtil.getMetadataNames(newDataset.getColumnMetadata()),morpheus.MetadataUtil.getMetadataNames(dataset.getColumnMetadata()),morpheus.MetadataUtil.getMetadataNames(newDataset.getRowMetadata()),morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata()),heatMap,function(appendOptions){morpheus.DatasetUtil.overlay({dataset:dataset,newDataset:newDataset,rowAnnotationName:appendOptions.current_dataset_row_annotation_name,newRowAnnotationName:appendOptions.new_dataset_row_annotation_name,columnAnnotationName:appendOptions.current_dataset_column_annotation_name,newColumnAnnotationName:appendOptions.new_dataset_column_annotation_name})})}else if(action==="open"){console.log("open");new morpheus.HeatMap({dataset:newDataset,parent:heatMap,inheritFromParent:false})}else{console.log("Unknown action: "+action)}if(action!=="open"){heatMap.revalidate()}})},execute:function(options){var file=options.input.file;var _this=this;var d=$.Deferred();morpheus.OpenDatasetTool.fileExtensionPrompt(file,function(readOptions){if(!readOptions){readOptions={}}readOptions.interactive=true;var deferred=morpheus.DatasetUtil.read(file,readOptions);deferred.always(function(){d.resolve()});_this._read(options,deferred)});return d},_matchAppend:function(newDatasetMetadataNames,currentDatasetMetadataNames,heatMap,callback){var tool={};tool.execute=function(options){return options.input};tool.toString=function(){return"Select Fields"};tool.gui=function(){var items=[{name:"current_dataset_annotation_name",options:currentDatasetMetadataNames,type:"select",value:"id",required:true}];items.push({name:"new_dataset_annotation_name",type:"select",value:"id",options:newDatasetMetadataNames,required:true});return items};morpheus.HeatMap.showTool(tool,heatMap,callback)},_matchOverlay:function(newDatasetColumnMetadataNames,currentDatasetColumnMetadataNames,newDatasetRowMetadataNames,currentDatasetRowMetadataNames,heatMap,callback){var tool={};tool.execute=function(options){return options.input};tool.toString=function(){return"Select Fields"};tool.gui=function(){var items=[];items.push({name:"current_dataset_column_annotation_name",options:currentDatasetColumnMetadataNames,type:"select",value:"id",required:true});items.push({name:"new_dataset_column_annotation_name",type:"select",value:"id",options:newDatasetColumnMetadataNames,required:true});items.push({name:"current_dataset_row_annotation_name",options:currentDatasetRowMetadataNames,type:"select",value:"id",required:true});items.push({name:"new_dataset_row_annotation_name",type:"select",value:"id",options:newDatasetRowMetadataNames,required:true});return items};morpheus.HeatMap.showTool(tool,heatMap,callback)}};morpheus.OpenDatasetTool.fileExtensionPrompt=function(file,callback){var ext=morpheus.Util.getExtension(morpheus.Util.getFileName(file));var deferred;if(ext==="seg"||ext==="segtab"){this._promptSegtab(function(regions){callback(regions)})}else{callback(null)}};morpheus.OpenDatasetTool._promptMaf=function(promptCallback){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"MAF_gene_symbols",value:"",type:"textarea",required:true,help:"Enter one gene symbol per line to filter genes. Leave blank to show all genes."});morpheus.FormBuilder.showInModal({title:"Gene Symbols",html:formBuilder.$form,close:"OK",onClose:function(){var text=formBuilder.getValue("MAF_gene_symbols");var lines=morpheus.Util.splitOnNewLine(text);var mafGeneFilter=new morpheus.Map;for(var i=0,nlines=lines.length,counter=0;i<nlines;i++){var line=lines[i];if(line!==""){mafGeneFilter.set(line,counter++)}}var readOptions=mafGeneFilter.size()>0?{mafGeneFilter:mafGeneFilter}:null;promptCallback(readOptions)}})};morpheus.OpenDatasetTool._promptSegtab=function(promptCallback){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"regions",value:"",type:"textarea",required:true,help:"Define the regions over which you want to define the CNAs. Enter one region per line. Each line should contain region_id, chromosome, start, and end separated by a tab. Leave blank to use all unique segments in the segtab file as regions."});morpheus.FormBuilder.showInModal({title:"Regions",html:formBuilder.$form,close:"OK",onClose:function(){var text=formBuilder.getValue("regions");var lines=morpheus.Util.splitOnNewLine(text);var regions=[];var tab=/\t/;for(var i=0,nlines=lines.length,counter=0;i<nlines;i++){var line=lines[i];if(line!==""){var tokens=line.split(tab);if(tokens.length>=4){regions.push({id:tokens[0],chromosome:tokens[1],start:parseInt(tokens[2]),end:parseInt(tokens[3])})}}}var readOptions=regions.length>0?{regions:regions}:null;promptCallback(readOptions)}})};morpheus.OpenDendrogramTool=function(file){this._file=file};morpheus.OpenDendrogramTool.prototype={toString:function(){return"Open Dendrogram"},init:function(project,form){var setValue=function(val){var isRows=val==="Rows";var names=morpheus.MetadataUtil.getMetadataNames(isRows?project.getFullDataset().getRowMetadata():project.getFullDataset().getColumnMetadata());names.unshift("Newick file does not contain node ids");form.setOptions("match_leaf_node_ids_to",names)};form.$form.find("[name=orientation]").on("change",function(e){setValue($(this).val())});setValue("Columns")},gui:function(){return[{name:"orientation",options:["Columns","Rows"],value:"Columns",type:"radio"},{name:"match_leaf_node_ids_to",options:[],type:"select"}]},execute:function(options){var fileOrUrl=this._file;var isColumns=options.input.orientation==="Columns";var dendrogramField=options.input.match_leaf_node_ids_to;if(dendrogramField==""||dendrogramField==="Newick file does not contain node ids"){dendrogramField=null}var heatMap=options.heatMap;var dendrogramDeferred=morpheus.Util.getText(fileOrUrl);dendrogramDeferred.done(function(text){var dataset=options.project.getSortedFilteredDataset();if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var tree=morpheus.DendrogramUtil.parseNewick(text);if(tree.leafNodes.length!==dataset.getRowCount()){throw new Error("# leaf nodes in dendrogram "+tree.leafNodes.length+" != "+dataset.getRowCount())}var modelIndices=[];if(dendrogramField!=null){var vector=dataset.getRowMetadata().getByName(dendrogramField);var valueToIndex=morpheus.VectorUtil.createValueToIndexMap(vector);for(var i=0,length=tree.leafNodes.length;i<length;i++){var newickId=tree.leafNodes[i].name;var index=valueToIndex.get(newickId);if(index===undefined){throw new Error("Unable to find dendrogram id "+tree.leafNodes[i].name+" in annotations")}modelIndices.push(index)}}else{for(var i=0,length=tree.leafNodes.length;i<length;i++){var newickId=tree.leafNodes[i].name;newickId=parseInt(newickId);if(!isNaN(newickId)){modelIndices.push(newickId)}else{break}}if(modelIndices.length!==tree.leafNodes.length){modelIndices=[];for(var i=0,length=tree.leafNodes.length;i<length;i++){modelIndices.push(i)}}}heatMap.setDendrogram(tree,isColumns,modelIndices)})}};morpheus.OpenFileTool=function(options){this.options=options||{}};morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS=[{name:"Open session",value:"Open session"},{name:"Open dataset in new tab",value:"open"},{name:"Append rows to current dataset",value:"append"},{name:"Append columns to current dataset",value:"append columns"},{name:"Overlay onto current dataset",value:"overlay"},{divider:true},{name:"Annotate columns",value:"Annotate Columns"},{name:"Annotate rows",value:"Annotate Rows"},{divider:true},{name:"Open dendrogram",value:"Open dendrogram"}];morpheus.OpenFileTool.prototype={toString:function(){return"Open"+(this.options.file!=null?" - "+this.options.file.name:"")},gui:function(){var params=[{name:"open_file_action",value:"open",type:"bootstrap-select",options:morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS}];if(this.options.file==null){params.options={size:"modal-lg",cancel:false,ok:false}}else{var extension=morpheus.Util.getExtension(morpheus.Util.getFileName(this.options.file));if(extension==="json"){params[0].options=params[0].options.filter(function(opt){return opt.value!=null&&(opt.value==="Open session"||opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)})}else if(extension==="gct"){params[0].options=params[0].options.filter(function(opt){return opt.value!=null&&(opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)})}}return params},init:function(project,form,initOptions){var _this=this;if(this.options.file==null){form.setVisible("open_file_action",false);var $div=$("<div></div>");var $ok=$('<div style="display:none;padding:15px;text-align:right;"><button name="action-selected" type="button" class="btn'+' btn-default">OK</button></div>');$ok.find("[name=action-selected]").on("click",function(){_this.ok()});var filePicker=new morpheus.FilePicker({fileCallback:function(fileOrUrl){$div.hide();$ok.show();_this.options.file=fileOrUrl;var extension=morpheus.Util.getExtension(morpheus.Util.getFileName(_this.options.file));if(extension==="json"){form.setOptions("open_file_action",morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS.filter(function(opt){return opt.value!=null&&(opt.value==="Open session"||opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)}))}else if(extension==="gct"){form.setOptions("open_file_action",morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS.filter(function(opt){return opt.value!=null&&(opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)}))}form.setVisible("open_file_action",true)},optionsCallback:function(heatMapOptions){$div.hide();$ok.show();_this.options.file=heatMapOptions.dataset;form.setVisible("open_file_action",true);form.setOptions("open_file_action",morpheus.OpenFileTool.OPEN_FILE_ACTION_OPTIONS.filter(function(opt){return opt.value!=null&&(opt.value==="open"||opt.value==="overlay"||opt.value.indexOf("append")!==-1)}))}});filePicker.$el.appendTo($div);$ok.appendTo(form.$form);$div.appendTo(form.$form)}},execute:function(options){var _this=this;var isInteractive=this.options.file==null;var heatMap=options.heatMap;if(!isInteractive){options.input.file=this.options.file}var project=options.project;if(options.input.open_file_action==="Open session"){return morpheus.Util.getText(options.input.file).done(function(text){var options=JSON.parse(text);options.tabManager=heatMap.getTabManager();options.focus=true;options.inheritFromParent=false;options.landingPage=heatMap.options.landingPage;new morpheus.HeatMap(options)}).fail(function(err){morpheus.FormBuilder.showMessageModal({title:"Error",message:"Unable to load session",focus:document.activeElement})})}else if(options.input.open_file_action==="append columns"||options.input.open_file_action==="append"||options.input.open_file_action==="open"||options.input.open_file_action==="overlay"){return(new morpheus.OpenDatasetTool).execute(options)}else if(options.input.open_file_action==="Open dendrogram"){morpheus.HeatMap.showTool(new morpheus.OpenDendrogramTool(options.input.file),options.heatMap)}else{var d=$.Deferred();var isAnnotateColumns=options.input.open_file_action=="Annotate Columns";var fileOrUrl=options.input.file;var dataset=project.getFullDataset();var fileName=morpheus.Util.getFileName(fileOrUrl);if(morpheus.Util.endsWith(fileName,".cls")){var result=morpheus.Util.readLines(fileOrUrl);result.always(function(){d.resolve()});result.done(function(lines){_this.annotateCls(heatMap,dataset,fileName,isAnnotateColumns,lines)})}else if(morpheus.Util.endsWith(fileName,".gmt")){morpheus.ArrayBufferReader.getArrayBuffer(fileOrUrl,function(err,buf){d.resolve();if(err){throw new Error("Unable to read "+fileOrUrl)}var sets=(new morpheus.GmtReader).read(new morpheus.ArrayBufferReader(new Uint8Array(buf)));_this.promptSets(dataset,heatMap,isAnnotateColumns,sets,morpheus.Util.getBaseFileName(morpheus.Util.getFileName(fileOrUrl)))})}else{var result=morpheus.Util.readLines(fileOrUrl);result.done(function(lines){_this.prompt(lines,dataset,heatMap,isAnnotateColumns)}).always(function(){d.resolve()});return d}}},annotateCls:function(heatMap,dataset,fileName,isColumns,lines){if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var assignments=(new morpheus.ClsReader).read(lines);if(assignments.length!==dataset.getRowCount()){throw new Error("Number of samples in cls file does not match dataset.")}var vector=dataset.getRowMetadata().add(morpheus.Util.getBaseFileName(fileName));for(var i=0;i<assignments.length;i++){vector.setValue(i,assignments[i])}if(heatMap){heatMap.getProject().trigger("trackChanged",{vectors:[vector],display:["color"],columns:isColumns})}},annotateSets:function(dataset,isColumns,sets,datasetMetadataName,setSourceFileName){if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var vector=dataset.getRowMetadata().getByName(datasetMetadataName);var idToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector);var setVector=dataset.getRowMetadata().add(setSourceFileName);sets.forEach(function(set){var name=set.name;var members=set.ids;members.forEach(function(id){var indices=idToIndices.get(id);if(indices!==undefined){for(var i=0,nIndices=indices.length;i<nIndices;i++){var array=setVector.getValue(indices[i]);if(array===undefined){array=[]}array.push(name);setVector.setValue(indices[i],array)}}})});return setVector},annotate:function(lines,dataset,isColumns,sets,metadataName,fileColumnName,fileColumnNamesToInclude,transposed){if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset)}var vector=dataset.getRowMetadata().getByName(metadataName);if(!vector){throw new Error("vector "+metadataName+" not found.")}var fileColumnNamesToIncludeSet=null;if(fileColumnNamesToInclude){fileColumnNamesToIncludeSet=new morpheus.Set;fileColumnNamesToInclude.forEach(function(name){fileColumnNamesToIncludeSet.add(name)})}var vectors=[];var idToIndices=morpheus.VectorUtil.createValueToIndicesMap(vector);if(!lines){_.each(sets,function(set){var name=set.name;var members=set.ids;var v=dataset.getRowMetadata().add(name);vectors.push(v);_.each(members,function(id){var indices=idToIndices.get(id);if(indices!==undefined){for(var i=0,nIndices=indices.length;i<nIndices;i++){v.setValue(indices[i],name)}}})})}else{var tab=/\t/;if(!transposed){var header=lines[0].split(tab);var fileMatchOnColumnIndex=_.indexOf(header,fileColumnName);if(fileMatchOnColumnIndex===-1){throw new Error(fileColumnName+" not found in header:"+header)}var columnIndices=[];var nheaders=header.length;for(var j=0;j<nheaders;j++){var name=header[j];if(j===fileMatchOnColumnIndex){continue}if(fileColumnNamesToIncludeSet&&!fileColumnNamesToIncludeSet.has(name)){continue}var v=dataset.getRowMetadata().getByName(name);if(!v){v=dataset.getRowMetadata().add(name)}columnIndices.push(j);vectors.push(v)}var nheaders=columnIndices.length;for(var i=1,nrows=lines.length;i<nrows;i++){var line=lines[i].split(tab);var id=line[fileMatchOnColumnIndex];var indices=idToIndices.get(id);if(indices!==undefined){var nIndices=indices.length;for(var j=0;j<nheaders;j++){var token=line[columnIndices[j]];var v=vectors[j];for(var r=0;r<nIndices;r++){v.setValue(indices[r],token)}}}}}else{var splitLines=[];var matchOnLine;for(var i=0,nrows=lines.length;i<nrows;i++){var line=lines[i].split(tab);var name=line[0];if(fileColumnName===name){matchOnLine=line}else{if(fileColumnNamesToIncludeSet&&!fileColumnNamesToIncludeSet.has(name)){continue}splitLines.push(line);var v=dataset.getRowMetadata().getByName(name);if(!v){v=dataset.getRowMetadata().add(name)}vectors.push(v)}}if(matchOnLine==null){throw new Error(fileColumnName+" not found in header.")}for(var fileColumnIndex=1,ncols=matchOnLine.length;fileColumnIndex<ncols;fileColumnIndex++){var id=matchOnLine[fileColumnIndex];var indices=idToIndices.get(id);if(indices!==undefined){var nIndices=indices.length;for(var j=0;j<splitLines.length;j++){var token=splitLines[j][fileColumnIndex];var v=vectors[j];for(var r=0;r<nIndices;r++){v.setValue(indices[r],token)}}}}}}for(var i=0;i<vectors.length;i++){morpheus.VectorUtil.maybeConvertStringToNumber(vectors[i])}return vectors},promptSets:function(dataset,heatMap,isColumns,sets,setSourceFileName){var promptTool={};var _this=this;promptTool.execute=function(options){var metadataName=options.input.dataset_field_name;var vector=_this.annotateSets(dataset,isColumns,sets,metadataName,setSourceFileName);heatMap.getProject().trigger("trackChanged",{vectors:[vector],display:["text"],columns:isColumns})};promptTool.toString=function(){return"Select Fields To Match On"};promptTool.gui=function(){return[{name:"dataset_field_name",options:morpheus.MetadataUtil.getMetadataNames(isColumns?dataset.getColumnMetadata():dataset.getRowMetadata()),type:"select",value:"id",required:true}]};morpheus.HeatMap.showTool(promptTool,heatMap)},prompt:function(lines,dataset,heatMap,isColumns){var promptTool={};var _this=this;var header=lines!=null?lines[0].split("\t"):null;promptTool.execute=function(options){var metadataName=options.input.dataset_field_name;var fileColumnName=options.input.file_field_name;var vectors=_this.annotate(lines,dataset,isColumns,null,metadataName,fileColumnName);var nameToIndex=new morpheus.Map;var display=[];for(var i=0;i<vectors.length;i++){display.push(isColumns?"color":"text");nameToIndex.set(vectors[i].getName(),i)}if(lines.colors){var colorModel=isColumns?heatMap.getProject().getColumnColorModel():heatMap.getProject().getRowColorModel();lines.colors.forEach(function(item){var index=nameToIndex.get(item.header);var vector=vectors[index];display[index]="color";colorModel.setMappedValue(vector,item.value,item.color)})}heatMap.getProject().trigger("trackChanged",{vectors:vectors,display:display,columns:isColumns})};promptTool.toString=function(){return"Select Fields To Match On"};promptTool.gui=function(){var items=[{name:"dataset_field_name",options:morpheus.MetadataUtil.getMetadataNames(isColumns?dataset.getColumnMetadata():dataset.getRowMetadata()),type:"select",required:true}];if(lines){items.push({name:"file_field_name",type:"select",options:_.map(header,function(item){return{name:item,value:item}}),required:true})}return items};morpheus.HeatMap.showTool(promptTool,heatMap)}};morpheus.SaveDatasetTool=function(){};morpheus.SaveDatasetTool.prototype={toString:function(){return"Save Dataset"},init:function(project,form){form.find("file_name").prop("autofocus",true).focus();var seriesNames=[];var dataset=project.getFullDataset();for(var i=0,nseries=dataset.getSeriesCount();i<nseries;i++){seriesNames.push(dataset.getName(i))}form.setOptions("series",seriesNames.length>1?seriesNames:null);form.setVisible("series",seriesNames.length>1)},gui:function(){return[{name:"file_name",type:"text",help:'<a target="_blank" href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT 1.3</a>'+' or <a target="_blank" href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT 1.2</a> file name',required:true},{name:"file_format",type:"radio",options:[{name:"GCT version 1.2",value:"1.2"},{name:"GCT version 1.3",value:"1.3"}],value:"1.3"},{name:"series",type:"select",options:[],required:true},{name:"save_selection_only",type:"checkbox",required:true}]},execute:function(options){var project=options.project;var format=options.input.file_format;var fileName=options.input.file_name;if(fileName===""){fileName="dataset"}var series=options.input.series;var heatMap=options.heatMap;var dataset=options.input.save_selection_only?project.getSelectedDataset():project.getSortedFilteredDataset();var writer;if(format==="1.2"){writer=new morpheus.GctWriter12}else if(format==="1.3"){writer=new morpheus.GctWriter}if(series!=null){var seriesIndex=morpheus.DatasetUtil.getSeriesIndex(dataset,series);if(seriesIndex===-1){seriesIndex=0}dataset=seriesIndex===0?dataset:new morpheus.DatasetSeriesView(dataset,[seriesIndex])}var ext=writer.getExtension?writer.getExtension():"";if(ext!==""&&!morpheus.Util.endsWith(fileName.toLowerCase(),"."+ext)){fileName+="."+ext}writer.setNumberFormat(heatMap.getHeatMapElementComponent().getDrawValuesFormat());var blobs=[];var textArray=[];var proxy={push:function(text){textArray.push(text);if(textArray.length===1e4){var blob=new Blob([textArray.join("")],{type:"text/plain;charset=charset=utf-8"});textArray=[];blobs.push(blob)}},join:function(){if(textArray.length>0){var blob=new Blob([textArray.join("")],{type:"text/plain;charset=charset=utf-8"});blobs.push(blob);textArray=[]}var blob=new Blob(blobs,{type:"text/plain;charset=charset=utf-8"});saveAs(blob,fileName,true)}};writer.write(dataset,proxy)}};morpheus.SaveImageTool=function(){};morpheus.SaveImageTool.prototype={toString:function(){return"Save Image"},init:function(project,form){form.find("file_name").prop("autofocus",true).focus()},gui:function(){return[{name:"file_name",type:"text",required:true},{name:"format",type:"radio",options:["PDF","PNG","SVG"],value:"PNG",required:true}]},execute:function(options){var fileName=options.input.file_name;if(fileName===""){fileName="image"}var format=options.input.format.toLowerCase();if(!morpheus.Util.endsWith(fileName.toLowerCase(),"."+format)){fileName+="."+format}var heatMap=options.heatMap;heatMap.saveImage(fileName,format)}};morpheus.SaveSessionTool=function(){};morpheus.SaveSessionTool.prototype={toString:function(){return"Save Session"},init:function(project,form){form.find("file_name").prop("autofocus",true).focus()},gui:function(){return[{name:"file_name",type:"text",required:true}]},execute:function(options){var fileName=options.input.file_name;if(fileName===""){fileName="session.json"}if(!morpheus.Util.endsWith(fileName.toLowerCase(),".json")){fileName+=".json"}var heatMap=options.heatMap;var options={dataset:true};var json=heatMap.toJSON(options);var nativeArrayToArray=Array.from||function(typedArray){var normalArray=Array.prototype.slice.call(typedArray);normalArray.length===typedArray.length;normalArray.constructor===Array};var blob=new Blob([JSON.stringify(json,function(key,value){if(morpheus.Util.isArray(value)){return value instanceof Array?value:nativeArrayToArray(value)}return value})],{type:"application/json;charset=charset=utf-8"});saveAs(blob,fileName,true)}};morpheus.SimilarityMatrixTool=function(){};morpheus.SimilarityMatrixTool.Functions=[morpheus.Euclidean,morpheus.Jaccard,morpheus.Cosine,morpheus.KendallsCorrelation,morpheus.Pearson,morpheus.Spearman];morpheus.SimilarityMatrixTool.Functions.fromString=function(s){for(var i=0;i<morpheus.SimilarityMatrixTool.Functions.length;i++){if(morpheus.SimilarityMatrixTool.Functions[i].toString()===s){return morpheus.SimilarityMatrixTool.Functions[i]}}throw new Error(s+" not found")};morpheus.SimilarityMatrixTool.execute=function(dataset,input){var isColumnMatrix=input.compute_matrix_for=="Columns";var f=morpheus.SimilarityMatrixTool.Functions.fromString(input.metric);return morpheus.HCluster.computeDistanceMatrix(isColumnMatrix?new morpheus.TransposedDatasetView(dataset):dataset,f)};morpheus.SimilarityMatrixTool.prototype={toString:function(){return"Similarity Matrix"},init:function(project,form){},gui:function(){return[{name:"metric",options:morpheus.SimilarityMatrixTool.Functions,value:morpheus.SimilarityMatrixTool.Functions[4].toString(),type:"select"},{name:"compute_matrix_for",options:["Columns","Rows"],value:"Columns",type:"radio"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var isColumnMatrix=options.input.compute_matrix_for=="Columns";var f=morpheus.SimilarityMatrixTool.Functions.fromString(options.input.metric);var dataset=project.getSortedFilteredDataset();var blob=new Blob(["self.onmessage = function(e) {"+"importScripts(e.data.scripts);"+"self.postMessage(morpheus.SimilarityMatrixTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=window.URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:morpheus.Util.getScriptPath(),dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){var name=heatMap.getName();var matrix=e.data;var n=isColumnMatrix?dataset.getColumnCount():dataset.getRowCount();var d=new morpheus.Dataset({name:name,rows:n,columns:n});var isDistance=f.toString()===morpheus.Euclidean.toString()||f.toString()===morpheus.Jaccard.toString();for(var i=1;i<n;i++){for(var j=0;j<i;j++){var value=matrix[i][j];d.setValue(i,j,value);d.setValue(j,i,value)}}if(!isDistance){for(var i=0;i<n;i++){d.setValue(i,i,1)}}var metadata=isColumnMatrix?dataset.getColumnMetadata():dataset.getRowMetadata();d.rowMetadataModel=morpheus.MetadataUtil.shallowCopy(metadata);d.columnMetadataModel=morpheus.MetadataUtil.shallowCopy(metadata);var colorScheme;if(!isDistance){colorScheme={type:"fixed",map:[{value:-1,color:"blue"},{value:0,color:"white"},{value:1,color:"red"}]}}else{colorScheme={type:"fixed",map:[{value:0,color:"white"},{value:morpheus.DatasetUtil.max(d),color:"red"}]}}new morpheus.HeatMap({colorScheme:colorScheme,name:name,dataset:d,parent:heatMap,inheritFromParentOptions:{rows:!isColumnMatrix,columns:isColumnMatrix}});worker.terminate();window.URL.revokeObjectURL(url)};return worker}};morpheus.TransposeTool=function(){};morpheus.TransposeTool.prototype={toString:function(){return"Transpose"},execute:function(options){var project=options.project;var heatMap=options.heatMap;var dataset=new morpheus.TransposedDatasetView(project.getSortedFilteredDataset());var rowMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getRowMetadata());var columnMetadataModel=morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata());dataset.getRowMetadata=function(){return rowMetadataModel};dataset.getColumnMetadata=function(){return columnMetadataModel};var name=options.input.name||heatMap.getName();new morpheus.HeatMap({name:name,dataset:dataset,inheritFromParentOptions:{transpose:true},parent:heatMap})}};morpheus.TsneTool=function(){};morpheus.TsneTool.execute=function(dataset,input){var matrix=[];var rows=input.project=="Rows";if(!rows){dataset=new morpheus.TransposedDatasetView(dataset)}var N=dataset.getRowCount();var f=morpheus.HClusterTool.Functions.fromString(input.metric);if(f===morpheus.TsneTool.PRECOMPUTED_DIST){for(var i=0;i<N;i++){matrix.push([]);for(var j=i+1;j<N;j++){matrix[i][j]=dataset.getValue(i,j)}}}else if(f===morpheus.TsneTool.PRECOMPUTED_SIM){var max=morpheus.DatasetUtil.max(dataset);for(var i=0;i<N;i++){matrix.push([]);for(var j=i+1;j<N;j++){matrix[i][j]=max-dataset.getValue(i,j)}}}else{var list1=new morpheus.DatasetRowView(dataset);var list2=new morpheus.DatasetRowView(dataset);for(var i=0;i<N;i++){matrix.push([]);list1.setIndex(i);for(var j=i+1;j<N;j++){var d=f(list1,list2.setIndex(j));matrix[i][j]=d}}}var opt={};opt.epsilon=input.epsilon;opt.perplexity=input.perplexity;opt.dim=2;var tsne=new tsnejs.tSNE(opt);tsne.initDataDist(matrix);for(var k=0;k<1e3;k++){tsne.step()}var Y=tsne.getSolution();return{solution:Y}};morpheus.TsneTool.prototype={toString:function(){return"t-SNE"},init:function(project,form){},gui:function(){return[{name:"metric",options:morpheus.HClusterTool.Functions,value:morpheus.HClusterTool.Functions[3].toString(),type:"select"},{name:"project",options:["Columns","Rows"],value:"Columns",type:"select"},{name:"epsilon",value:"10",type:"text",help:"learning rate"},{name:"perplexity",value:"30",type:"text",help:"number of effective nearest neighbors"}]},execute:function(options){var project=options.project;var heatMap=options.heatMap;var rows=options.input.project=="Rows";var dataset=project.getSortedFilteredDataset();options.input.epsilon=parseInt(options.input.epsilon);options.input.perplexity=parseInt(options.input.perplexity);var blob=new Blob(["self.onmessage = function(e) {"+"e.data.scripts.forEach(function (s) { importScripts(s); });"+"self.postMessage(morpheus.TsneTool.execute(morpheus.Dataset.fromJSON(e.data.dataset), e.data.input));"+"}"]);var url=URL.createObjectURL(blob);var worker=new Worker(url);worker.postMessage({scripts:[morpheus.Util.getScriptPath()],dataset:morpheus.Dataset.toJSON(dataset,{columnFields:[],rowFields:[],seriesIndices:[0]}),input:options.input});worker.onmessage=function(e){if(rows){dataset=new morpheus.TransposedDatasetView(dataset)}var result=e.data.solution;var newDataset=new morpheus.Dataset({name:"t-SNE",rows:dataset.getColumnCount(),columns:2});for(var i=0;i<result.length;i++){newDataset.setValue(i,0,result[i][0]);newDataset.setValue(i,1,result[i][1])}var idVector=newDataset.getColumnMetadata().add("id");idVector.setValue(0,"P1");idVector.setValue(1,"P2");newDataset.setRowMetadata(morpheus.MetadataUtil.shallowCopy(dataset.getColumnMetadata()));var min=morpheus.DatasetUtil.min(newDataset);var max=morpheus.DatasetUtil.max(newDataset);new morpheus.HeatMap({inheritFromParentOptions:{transpose:!rows},name:"t-SNE",dataset:newDataset,parent:heatMap,columns:[{field:"id",display:"text"}],colorScheme:{type:"fixed",map:[{value:min,color:colorbrewer.Greens[3][0]},{value:max,color:colorbrewer.Greens[3][2]}]}});worker.terminate();window.URL.revokeObjectURL(url)};return worker}};morpheus.AbstractCanvas=function(offscreen){this.canvas=morpheus.CanvasUtil.createCanvas();this.lastClip=null;if(offscreen){this.offscreenCanvas=morpheus.CanvasUtil.createCanvas()}this.offset={x:0,y:0}};morpheus.AbstractCanvas.prototype={visible:true,invalid:true,scrollX:0,scrollY:0,prefWidth:undefined,prefHeight:undefined,getCanvas:function(){return this.canvas},scrollTop:function(pos){if(pos===undefined){return this.offset.y}this.offset.y=pos},appendTo:function($el){$(this.canvas).appendTo($el)},scrollLeft:function(pos){if(pos===undefined){return this.offset.x}this.offset.x=pos},dispose:function(){$(this.canvas).remove();this.offscreenCanvas=undefined},getPrefWidth:function(){return this.prefWidth},setInvalid:function(invalid){this.invalid=invalid},setBounds:function(bounds){var backingScale=morpheus.CanvasUtil.BACKING_SCALE;var canvases=[this.canvas];if(this.offscreenCanvas){canvases.push(this.offscreenCanvas)}if(bounds.height!=null){_.each(canvases,function(canvas){canvas.height=bounds.height*backingScale;canvas.style.height=bounds.height+"px"})}if(bounds.width!=null){_.each(canvases,function(canvas){canvas.width=bounds.width*backingScale;canvas.style.width=bounds.width+"px"})}if(bounds.left!=null){_.each(canvases,function(canvas){canvas.style.left=bounds.left+"px"})}if(bounds.top!=null){_.each(canvases,function(canvas){canvas.style.top=bounds.top+"px"})}},paint:function(clip){var canvas=this.canvas;var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();context.clearRect(0,0,width,height);if(this.prePaint){morpheus.CanvasUtil.resetTransform(context);context.translate(this.offset.x,this.offset.y);this.prePaint(clip,context)}morpheus.CanvasUtil.resetTransform(context);if(this.offscreenCanvas){if(this.invalid){var oc=this.offscreenCanvas.getContext("2d");morpheus.CanvasUtil.resetTransform(oc);context.translate(this.offset.x,this.offset.y);oc.clearRect(0,0,width,height);this.draw(clip,oc)}context.drawImage(this.offscreenCanvas,0,0,width,height)}else{this.draw(clip,context)}if(this.postPaint){morpheus.CanvasUtil.resetTransform(context);context.translate(this.offset.x,this.offset.y);this.postPaint(clip,context)}this.lastClip=clip;this.invalid=false},repaint:function(){if(!this.lastClip){this.lastClip={x:0,y:0,width:this.getUnscaledWidth(),height:this.getUnscaledHeight()}}this.paint(this.lastClip)},draw:function(clip,context){console.log("Not implemented")},getPrefHeight:function(){return this.prefHeight},setPrefWidth:function(prefWidth){this.prefWidth=prefWidth},setPrefHeight:function(prefHeight){this.prefHeight=prefHeight},isVisible:function(){return this.visible},setVisible:function(visible){if(this.visible!==visible){this.visible=visible;this.canvas.style.display=visible?"":"none"}},getUnscaledWidth:function(){return this.canvas.width/morpheus.CanvasUtil.BACKING_SCALE},getUnscaledHeight:function(){return this.canvas.height/morpheus.CanvasUtil.BACKING_SCALE},getWidth:function(){return this.canvas.width},getHeight:function(){return this.canvas.height}};morpheus.AbstractColorSupplier=function(){this.fractions=[0,.5,1];this.colors=["#0000ff","#ffffff","#ff0000"];this.names=null;this.min=0;this.max=1;this.missingColor="#c0c0c0";this.scalingMode=morpheus.HeatMapColorScheme.ScalingMode.RELATIVE;this.stepped=false;this.sizer=new morpheus.HeatMapSizer;this.conditions=new morpheus.HeatMapConditions;this.transformValues=0};morpheus.AbstractColorSupplier.Z_SCORE=1;morpheus.AbstractColorSupplier.ROBUST_Z_SCORE=2;morpheus.AbstractColorSupplier.toJSON=function(cs){var json={fractions:cs.fractions,colors:cs.colors,min:cs.min,max:cs.max,missingColor:cs.missingColor,scalingMode:cs.scalingMode,stepped:cs.stepped,transformValues:cs.transformValues};if(cs.names){json.names=cs.names}if(cs.conditions&&cs.conditions.array.length>0){json.conditions=cs.conditions.array}if(cs.sizer&&cs.sizer.seriesName!=null){json.size={seriesName:cs.sizer.seriesName,min:cs.sizer.min,max:cs.sizer.max}}return json};morpheus.AbstractColorSupplier.fromJSON=function(json){var cs=json.stepped?new morpheus.SteppedColorSupplier:new morpheus.GradientColorSupplier;if(json.scalingMode==null&&json.type!=null){json.scalingMode=json.type}if(json.scalingMode==="relative"||json.scalingMode===0){json.scalingMode=0}else if(json.scalingMode==="fixed"||json.scalingMode===1){json.scalingMode=1}else{json.scalingMode=0}cs.setScalingMode(json.scalingMode);if(json.min!=null){cs.setMin(json.min)}if(json.max!=null){cs.setMax(json.max)}if(json.missingColor!=null){cs.setMissingColor(json.missingColor)}if(morpheus.HeatMapColorScheme.ScalingMode.RELATIVE!==json.scalingMode){cs.setTransformValues(json.transformValues)}if(json.map){json.values=json.map.map(function(item){return item.value});json.colors=json.map.map(function(item){return item.color})}var fractions=json.fractions;if(json.values){fractions=[];var values=json.values;var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;for(var i=0;i<values.length;i++){var value=values[i];min=Math.min(min,value);max=Math.max(max,value)}var valueToFraction=d3.scale.linear().domain([min,max]).range([0,1]).clamp(true);for(var i=0;i<values.length;i++){fractions.push(valueToFraction(values[i]))}if(json.min==null){cs.setMin(min)}if(json.max==null){cs.setMax(max)}}if(json.colors!=null&&json.colors.length>0){cs.setFractions({colors:json.colors,fractions:fractions,names:json.names})}if(json.size){cs.getSizer().setSeriesName(json.size.seriesName);cs.getSizer().setMin(json.size.min);cs.getSizer().setMax(json.size.max)}if(json.conditions&&_.isArray(json.conditions)){json.conditions.forEach(function(condition){var gtf=function(){return true};var ltf=function(){return true};if(condition.seriesName==null){condition.seriesName=condition.series}if(condition.v1!=null&&!isNaN(condition.v1)){gtf=condition.v1Op==="gt"?function(val){return val>condition.v1}:function(val){return val>=condition.v1}}if(condition.v2!=null&&!isNaN(condition.v2)){ltf=condition.v2Op==="lt"?function(val){return val<condition.v2}:function(val){return val<=condition.v2}}condition.accept=function(val){return gtf(val)&&ltf(val)}});cs.conditions.array=json.conditions}return cs};morpheus.AbstractColorSupplier.prototype={getTransformValues:function(){return this.transformValues},setTransformValues:function(transformValues){this.transformValues=transformValues},getSizer:function(){return this.sizer},getConditions:function(){return this.conditions},createInstance:function(){throw"not implemented"},copy:function(){var c=this.createInstance();c.stepped=this.stepped;c.setFractions({fractions:this.fractions.slice(0),colors:this.colors.slice(0)});if(this.names!=null){c.names=this.names.slice(0)}if(this.sizer){c.sizer=this.sizer.copy()}if(this.conditions){c.conditions=this.conditions.copy()}c.scalingMode=this.scalingMode;c.min=this.min;c.max=this.max;c.missingColor=this.missingColor;if(this.scalingMode!==morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){c.transformValues=this.transformValues}return c},setMissingColor:function(missingColor){this.missingColor=missingColor},getMissingColor:function(){return this.missingColor},getScalingMode:function(){return this.scalingMode},setScalingMode:function(scalingMode){if(scalingMode!==this.scalingMode){if(scalingMode===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){this.min=0;this.max=1}this.scalingMode=scalingMode}},isStepped:function(){return false},getColor:function(row,column,value){throw"not implemented"},getColors:function(){return this.colors},getNames:function(){return this.names},getFractions:function(){return this.fractions},getMin:function(){return this.min},getMax:function(){return this.max},setMin:function(min){this.min=min},setMax:function(max){this.max=max},setFractions:function(options){var index=morpheus.Util.indexSort(options.fractions,true);this.fractions=morpheus.Util.reorderArray(options.fractions,index);this.colors=morpheus.Util.reorderArray(options.colors,index);this.names=options.names?morpheus.Util.reorderArray(options.names,index):null}};morpheus.AbstractComponent=function(){this.lastClip=null;var c=document.createElement("div");c.setAttribute("tabindex","0");c.style.outline=0;c.style.overflow="hidden";c.style.position="absolute";this.el=c;this.$el=$(c)};morpheus.AbstractComponent.prototype={visible:true,invalid:true,prefWidth:undefined,prefHeight:undefined,appendTo:function($el){$(this.el).appendTo($el)},dispose:function(){$(this.el).remove()},getPrefWidth:function(){return this.prefWidth},setInvalid:function(invalid){this.invalid=invalid},setBounds:function(bounds){if(bounds.left!=null){this.$el.css("left",bounds.left+"px")}if(bounds.top!=null){this.$el.css("top",bounds.top+"px")}},paint:function(clip){var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();this.draw(clip);this.lastClip=clip;this.invalid=false},repaint:function(){if(!this.lastClip){this.lastClip={x:0,y:0,width:this.getUnscaledWidth(),height:this.getUnscaledHeight()}}this.paint(this.lastClip)},draw:function(clip){},getPrefHeight:function(){return this.prefHeight},setPrefWidth:function(prefWidth){this.prefWidth=prefWidth},setPrefHeight:function(prefHeight){this.prefHeight=prefHeight},isVisible:function(){return this.visible},setVisible:function(visible){if(this.visible!==visible){this.visible=visible;this.el.style.display=visible?"":"none"}},getUnscaledWidth:function(){return this.$el.width()},getUnscaledHeight:function(){return this.$el.height()},getWidth:function(){return this.$el.width()},getHeight:function(){return this.$el.height()}};morpheus.AbstractDendrogram=function(heatMap,tree,positions,project,type){morpheus.AbstractCanvas.call(this,true);this._overviewHighlightColor="#d8b365";this._searchHighlightColor="#e41a1c";this._selectedNodeColor=type===morpheus.AbstractDendrogram.Type.COLUMN?"#377eb8":"#984ea3";this.tree=tree;this.type=type;this.squishEnabled=false;this.heatMap=heatMap;this.positions=positions;this.project=project;var $label=$("<span></span>");$label.addClass("label label-info");$label.css("position","absolute");this.$label=$label;var $squishedLabel=$("<span></span>");$squishedLabel.addClass("label label-default");$squishedLabel.css("position","absolute").css("top",18);this.$squishedLabel=$squishedLabel;this.$label=$label;this.cutHeight=this.tree.maxHeight;this.drawLeafNodes=true;this.lineWidth=.7;this.selectedNodeIds={};this.selectedRootNodeIdToNode={};this.nodeIdToHighlightedPathsToRoot={};var _this=this;this.defaultStroke="rgb(0,0,0)";this.mouseMoveNodes=null;var mouseMove=function(event){if(!morpheus.CanvasUtil.dragging){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.lastClip.x,_this.lastClip.y);if(_this.isDragHotSpot(position)){_this.canvas.style.cursor=_this.getResizeCursor()}else{var nodes;if(_this.getNodes){nodes=_this.getNodes(position)}else{var node=_this.getNode(position);if(node){nodes=[node]}}_this.mouseMoveNodes=nodes;if(nodes!=null){nodes.sort(function(a,b){return a.name<b.name});var tipOptions={event:event};tipOptions[type===morpheus.AbstractDendrogram.Type.COLUMN?"columnNodes":"rowNodes"]=nodes;_this.heatMap.setToolTip(-1,-1,tipOptions);_this.canvas.style.cursor="pointer"}else{_this.heatMap.setToolTip(-1,-1);_this.canvas.style.cursor="default"}}}};var mouseExit=function(e){if(!morpheus.CanvasUtil.dragging){_this.mouseMoveNodes=null;_this.canvas.style.cursor="default"}};if(type!==morpheus.AbstractDendrogram.Type.RADIAL){$(this.canvas).on("contextmenu",function(e){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();var position=morpheus.CanvasUtil.getMousePosWithScroll(e.target,e,_this.lastClip.x,_this.lastClip.y);var selectedNode=_this.getNode(position);morpheus.Popup.showPopup([{name:"Flip",disabled:selectedNode==null},{name:"Branch Color",disabled:selectedNode==null},{separator:true},{name:"Annotate..."},{name:"Save"},{separator:true},{name:"Enrichment..."},{separator:true},{name:"Squish Singleton Clusters",checked:_this.squishEnabled},{separator:true},{name:"Delete"}],{x:e.pageX,y:e.pageY},e.target,function(menuItem,item){if(item==="Save"){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"file_name",type:"text",required:true});formBuilder.append({name:"leaf_node_id_field",type:"bootstrap-select",required:true,options:morpheus.MetadataUtil.getMetadataNames(type===morpheus.AbstractDendrogram.Type.COLUMN?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata())});morpheus.FormBuilder.showOkCancel({title:"Save Dendrogram",content:formBuilder.$form,focus:document.activeElement,okCallback:function(){var fileName=formBuilder.getValue("file_name");if(fileName===""){fileName="dendrogram.txt"}var leafNodeIdField=formBuilder.getValue("leaf_node_id_field");var out=[];var vector=type===morpheus.AbstractDendrogram.Type.COLUMN?project.getFullDataset().getColumnMetadata().getByName(leafNodeIdField):project.getFullDataset().getRowMetadata().getByName(leafNodeIdField);var leafNodeToString=function(n){return vector.getValue(n.index)};morpheus.DendrogramUtil.writeNewick(tree.rootNode,out,leafNodeToString);var blob=new Blob([out.join("")],{type:"text/plain;charset=charset=utf-8"});saveAs(blob,fileName,true)}})}else if(item==="Flip"){if(selectedNode!=null){var isColumns=morpheus.AbstractDendrogram.Type.COLUMN===_this.type;var min=selectedNode.minIndex;var max=selectedNode.maxIndex;var leafNodes=tree.leafNodes;for(var i=min,index=max;i<=max;i++,index--){var n=leafNodes[i];n.index=index;n.maxIndex=index;n.minIndex=index}leafNodes.sort(function(a,b){return a.index<b.index?-1:1});var setIndex=function(n){if(n.children!=null&&n.children.length>0){for(var i=0;i<n.children.length;i++){setIndex(n.children[i])}var sum=0;for(var i=0;i<n.children.length;i++){sum+=n.children[i].index}n.index=sum/n.children.length;var maxIndex=-Number.MAX_VALUE;var minIndex=Number.MAX_VALUE;for(var i=0;i<n.children.length;i++){maxIndex=Math.max(maxIndex,n.children[i].maxIndex);minIndex=Math.min(minIndex,n.children[i].minIndex)}n.minIndex=minIndex;n.maxIndex=maxIndex}};setIndex(selectedNode);var currentOrder=[];var count=isColumns?heatMap.getProject().getSortedFilteredDataset().getColumnCount():heatMap.getProject().getSortedFilteredDataset().getRowCount();for(var i=0;i<count;i++){currentOrder.push(isColumns?project.convertViewColumnIndexToModel(i):project.convertViewRowIndexToModel(i))}for(var i=min,j=max;i<j;i++,j--){var tmp=currentOrder[j];currentOrder[j]=currentOrder[i];currentOrder[i]=tmp}var key=new morpheus.SpecifiedModelSortOrder(currentOrder,currentOrder.length,"dendrogram",isColumns);key.setPreservesDendrogram(true);key.setLockOrder(2);key.setUnlockable(false);if(isColumns){heatMap.getProject().setColumnSortKeys([key],true)}else{heatMap.getProject().setRowSortKeys([key],true)}heatMap.revalidate()}}else if(item==="Branch Color"){if(selectedNode!=null){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"color",type:"color",value:selectedNode.color,required:true,style:"max-width:50px;"});formBuilder.find("color").on("change",function(){var color=$(this).val();morpheus.DendrogramUtil.dfs(selectedNode,function(n){n.color=color;return true});_this.setSelectedNode(null)});morpheus.FormBuilder.showInModal({title:"Color",close:"Close",html:formBuilder.$form,focus:document.activeElement})}}else if(item==="Annotate..."){morpheus.HeatMap.showTool(new morpheus.AnnotateDendrogramTool(type===morpheus.AbstractDendrogram.Type.COLUMN),_this.heatMap)}else if(item==="Enrichment..."){morpheus.HeatMap.showTool(new morpheus.DendrogramEnrichmentTool(type===morpheus.AbstractDendrogram.Type.COLUMN),_this.heatMap)}else if(item==="Squish Singleton Clusters"){_this.squishEnabled=!_this.squishEnabled;if(!_this.squishEnabled){_this.positions.setSquishedIndices(null)}}else if(item==="Delete"){_this.resetCutHeight();_this.heatMap.setDendrogram(null,type===morpheus.AbstractDendrogram.Type.COLUMN)}});return false});$(this.canvas).on("mousemove",_.throttle(mouseMove,100)).on("mouseout",_.throttle(mouseExit,100)).on("mouseenter",_.throttle(mouseMove,100))}var dragStartScaledCutHeight=0;this.cutTreeHotSpot=false;if(type!==morpheus.AbstractDendrogram.Type.RADIAL){this.hammer=morpheus.Util.hammer(this.canvas,["pan","tap"]).on("tap",this.tap=function(event){if(!morpheus.CanvasUtil.dragging){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.lastClip.x,_this.lastClip.y);_this.cutTreeHotSpot=_this.isDragHotSpot(position);if(_this.cutTreeHotSpot){return}var node=_this.getNode(position);if(node!=null&&node.parent===undefined){node=null}var commandKey=morpheus.Util.IS_MAC?event.srcEvent.metaKey:event.srcEvent.ctrlKey;_this.setSelectedNode(node,event.srcEvent.shiftKey||commandKey)}}).on("panend",this.panend=function(event){morpheus.CanvasUtil.dragging=false;_this.canvas.style.cursor="default";_this.cutTreeHotSpot=true}).on("panstart",this.panstart=function(event){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.lastClip.x,_this.lastClip.y,true);_this.cutTreeHotSpot=_this.isDragHotSpot(position);if(_this.cutTreeHotSpot){morpheus.CanvasUtil.dragging=true;_this.canvas.style.cursor=_this.getResizeCursor();dragStartScaledCutHeight=_this.scale(_this.cutHeight)}}).on("panmove",this.panmove=function(event){if(_this.cutTreeHotSpot){var cutHeight;if(_this.type===morpheus.AbstractDendrogram.Type.COLUMN){var delta=event.deltaY;cutHeight=Math.max(0,Math.min(_this.tree.maxHeight,_this.scale.invert(dragStartScaledCutHeight+delta)))}else if(_this.type===morpheus.AbstractDendrogram.Type.ROW){var delta=event.deltaX;cutHeight=Math.max(0,Math.min(_this.tree.maxHeight,_this.scale.invert(dragStartScaledCutHeight+delta)))}else{var point=morpheus.CanvasUtil.getMousePos(event.target,event);point.x=_this.radius-point.x;point.y=_this.radius-point.y;var radius=Math.sqrt(point.x*point.x+point.y*point.y);if(radius<=4){cutHeight=_this.tree.maxHeight}else{cutHeight=Math.max(0,Math.min(_this.tree.maxHeight,_this.scale.invert(radius)))}}if(cutHeight>=_this.tree.maxHeight){_this.resetCutHeight()}else{_this.setCutHeight(cutHeight)}event.preventDefault()}})}};morpheus.AbstractDendrogram.Type={COLUMN:0,ROW:1,RADIAL:2};morpheus.AbstractDendrogram.prototype={setSelectedNode:function(node,add){var _this=this;var viewIndices;var selectionModel=this.type===morpheus.AbstractDendrogram.Type.COLUMN?this.project.getColumnSelectionModel():this.project.getRowSelectionModel();if(node==null){_this.selectedNodeIds={};_this.selectedRootNodeIdToNode={};viewIndices=new morpheus.Set}else{if(add){viewIndices=selectionModel.getViewIndices()}else{viewIndices=new morpheus.Set;_this.selectedNodeIds={};_this.selectedRootNodeIdToNode={}}if(node!=null){if(node.children===undefined){var contains=_this.nodeIdToHighlightedPathsToRoot[node.id];if(!add){_this.nodeIdToHighlightedPathsToRoot={}}if(contains){delete _this.nodeIdToHighlightedPathsToRoot[node.id]}else{_this.nodeIdToHighlightedPathsToRoot[node.id]=node}}else{_this.selectedRootNodeIdToNode[node.id]=node;morpheus.DendrogramUtil.dfs(node,function(d){_this.selectedNodeIds[d.id]=true;return true})}for(var i=node.minIndex;i<=node.maxIndex;i++){viewIndices.add(i)}}}_this.trigger("nodeSelectionChanged",_this.selectedRootNodeIdToNode);selectionModel.setViewIndices(viewIndices,true);_this.repaint()},getPathStroke:function(node){if(this.selectedNodeIds[node.id]){return this._selectedNodeColor}if(node.color!==undefined){return node.color}return this.defaultStroke},getNodeFill:function(node){if(this.selectedRootNodeIdToNode[node.id]){return this._selectedNodeColor}if(node.search){return this._searchHighlightColor}if(node.info!==undefined){return this._overviewHighlightColor}},resetCutHeight:function(){this.positions.setSquishedIndices(null);if(this.type===morpheus.AbstractDendrogram.Type.COLUMN){this.project.setGroupColumns([],true)}else{this.project.setGroupRows([],true)}this.$label.text("");this.$squishedLabel.text("");var dataset=this.project.getSortedFilteredDataset();var clusterIdVector=this.type===morpheus.AbstractDendrogram.Type.COLUMN?dataset.getColumnMetadata().getByName("dendrogram_cut"):dataset.getRowMetadata().getByName("dendrogram_cut");if(clusterIdVector){for(var i=0,size=clusterIdVector.size();i<size;i++){clusterIdVector.setValue(i,NaN)}}},setCutHeight:function(height){this.cutHeight=height;var squishedIndices={};var clusterNumber=0;var nsquished=0;var squishEnabled=this.squishEnabled;var roots=morpheus.DendrogramUtil.cutAtHeight(this.tree.rootNode,this.cutHeight);var dataset=this.project.getSortedFilteredDataset();var clusterIdVector=this.type===morpheus.AbstractDendrogram.Type.COLUMN?dataset.getColumnMetadata().add("dendrogram_cut"):dataset.getRowMetadata().add("dendrogram_cut");for(var i=0,nroots=roots.length;i<nroots;i++){var root=roots[i];var minChild=morpheus.DendrogramUtil.getDeepestChild(root,true);var maxChild=morpheus.DendrogramUtil.getDeepestChild(root,false);var clusterId;if(squishEnabled&&minChild.index===maxChild.index){squishedIndices[minChild.index]=true;clusterId=-2;nsquished++}else{clusterNumber++;clusterId=clusterNumber}for(var j=minChild.index;j<=maxChild.index;j++){clusterIdVector.setValue(j,clusterId)}}this.$label.text(clusterNumber+" cluster"+morpheus.Util.s(clusterNumber));if(nsquished>0){this.$squishedLabel.text(nsquished+" squished")}else{this.$squishedLabel.text("")}if(squishEnabled){this.positions.setSquishedIndices(squishedIndices)}if(this.heatMap.getTrackIndex(clusterIdVector.getName(),this.type===morpheus.AbstractDendrogram.Type.COLUMN)===-1){var settings={discrete:true,discreteAutoDetermined:true,display:["color"]};this.heatMap.addTrack(clusterIdVector.getName(),this.type===morpheus.AbstractDendrogram.Type.COLUMN,settings)}if(this.type===morpheus.AbstractDendrogram.Type.COLUMN){this.project.setGroupColumns([new morpheus.SortKey(clusterIdVector.getName(),morpheus.SortKey.SortOrder.UNSORTED)],true)}else{this.project.setGroupRows([new morpheus.SortKey(clusterIdVector.getName(),morpheus.SortKey.SortOrder.UNSORTED)],true)}},dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.$label.remove();this.$squishedLabel.remove();this.hammer.off("panend",this.panend).off("panstart",this.panstart).off("panmove",this.panmove).off("tap",this.tap);this.hammer.destroy();this.$label=null;this.$squishedLabel=null},isCut:function(){return this.cutHeight<this.tree.maxHeight},getMinIndex:function(){return 0},getMaxIndex:function(){return this.positions.getLength()-1},getNode:function(p){var _this=this;if(this.lastNode){var xy=_this.toPix(this.lastNode);if(Math.abs(xy[0]-p.x)<4&&Math.abs(xy[1]-p.y)<4){return this.lastNode}}this.lastNode=this._getNode(p);return this.lastNode},_getNode:function(p){var _this=this;var hit=null;try{morpheus.DendrogramUtil.dfs(this.tree.rootNode,function(node){var xy=_this.toPix(node);if(Math.abs(xy[0]-p.x)<4&&Math.abs(xy[1]-p.y)<4){hit=node;throw"break"}return hit===null})}catch(x){}return hit},getResizeCursor:function(){if(this.type===morpheus.AbstractDendrogram.Type.COLUMN){return"ns-resize"}else if(this.type===morpheus.AbstractDendrogram.Type.ROW){return"ew-resize"}return"nesw-resize"},isDragHotSpot:function(p){return false},preDraw:function(context,clip){},postDraw:function(context,clip){},prePaint:function(clip,context){this.scale=this.createScale();var min=this.getMinIndex(clip);var max=this.getMaxIndex(clip);if(min!==this.lastMinIndex||max!==this.lastMinIndex){this.lastMinIndex=min;this.lastMaxIndex=max}this.invalid=true},draw:function(clip,context){context.translate(-clip.x,-clip.y);context.strokeStyle="black";context.fillStyle="black";this.scale=this.createScale();var min=this.lastMinIndex;var max=this.lastMaxIndex;context.lineWidth=this.lineWidth;this.preDraw(context,clip);context.strokeStyle=this.defaultStroke;context.fillStyle="rgba(166,206,227,0.5)";this.drawDFS(context,this.tree.rootNode,min,max,0);context.strokeStyle="black";context.fillStyle="black";this.postDraw(context,clip)},drawCutSlider:function(){throw new Error},postPaint:function(clip,context){context.strokeStyle="black";this.paintMouseOver(clip,context);this.drawCutSlider(clip,context)},getNodeRadius:function(node){return 4},drawNode:function(context,node){},drawDFS:function(context,node,minIndex,maxIndex){if(this.type!==morpheus.AbstractDendrogram.Type.RADIAL){if(node.maxIndex<minIndex||node.minIndex>maxIndex){return}}var nodeFill=this.getNodeFill(node);if(nodeFill!==undefined){context.fillStyle=nodeFill;this.drawNode(context,node)}context.strokeStyle=this.getPathStroke(node);var children=node.children;if(children!==undefined){this.drawNodePath(context,node,minIndex,maxIndex);for(var i=0,nchildren=children.length;i<nchildren;i++){this.drawDFS(context,children[i],minIndex,maxIndex)}}}};morpheus.Util.extend(morpheus.AbstractDendrogram,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.AbstractDendrogram,morpheus.Events);morpheus.ActionManager=function(){this.actionNameToAction=new morpheus.Map;this.actions=[];this.add({ellipsis:true,name:"Sort/Group",cb:function(options){new morpheus.SortDialog(options.heatMap.getProject())},icon:"fa fa-sort-alpha-asc"});var $filterModal=null;this.add({name:"Filter",ellipsis:true,cb:function(options){if($filterModal==null){var filterModal=[];var filterLabelId=_.uniqueId("morpheus");filterModal.push('<div class="modal" tabindex="1" role="dialog" aria-labelledby="'+filterLabelId+'">');filterModal.push('<div class="modal-dialog" role="document">');filterModal.push('<div class="modal-content">');filterModal.push('<div class="modal-header">');filterModal.push('<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>');filterModal.push('<h4 class="modal-title" id="'+filterLabelId+'">Filter</h4>');filterModal.push("</div>");filterModal.push('<div class="modal-body"></div>');filterModal.push('<div class="modal-footer"><button type="button" class="btn btn-default" data-dismiss="modal">Close</button></div>');filterModal.push("</div>");filterModal.push("</div>");filterModal.push("</div>");$filterModal=$(filterModal.join(""));$filterModal.on("mousewheel",function(e){e.stopPropagation()});var $filter=$('<div style="padding-bottom:30px;"></div>');$filter.appendTo($filterModal.find(".modal-body"));var filterHtml=[];filterHtml.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="rows" checked>Rows</label></div> ');filterHtml.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="columns">Columns</label></div>');var $filterChooser=$(filterHtml.join(""));$filterChooser.appendTo($filter);var columnFilterUI=new morpheus.FilterUI(options.heatMap.getProject(),true);var rowFilterUI=new morpheus.FilterUI(options.heatMap.getProject(),false);rowFilterUI.$div.appendTo($filter);columnFilterUI.$div.appendTo($filter);columnFilterUI.$div.css("display","none");var $filterRadio=$filterChooser.find("[name=rowsOrColumns]");$filterRadio.on("change",function(e){var val=$filterRadio.filter(":checked").val();if(val==="columns"){columnFilterUI.$div.show();rowFilterUI.$div.hide()}else{columnFilterUI.$div.hide();rowFilterUI.$div.show()}e.preventDefault()});$filterModal.appendTo(options.heatMap.$content);$filterModal.on("hidden.bs.modal",function(){options.heatMap.focus()})}$filterModal.modal("show")},icon:"fa fa-filter"});this.add({name:"Options",ellipsis:true,cb:function(options){options.heatMap.showOptions()},icon:"fa fa-cog"});this.add({which:[191],commandKey:true,global:true,name:"Toggle Search",cb:function(options){options.heatMap.getToolbar().toggleSearch()}});this.add({name:"Copy Image",icon:"fa fa-clipboard",cb:function(options){var bounds=options.heatMap.getTotalSize();var height=bounds.height;var width=bounds.width;var canvas=$("<canvas></canvas>")[0];var backingScale=morpheus.CanvasUtil.BACKING_SCALE;canvas.height=backingScale*height;canvas.style.height=height+"px";canvas.width=backingScale*width;canvas.style.width=width+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);options.heatMap.snapshot(context);var url=canvas.toDataURL();morpheus.Util.setClipboardData([{format:"text/html",data:'<img src="'+url+'">'}],true)}});this.add({name:"Close Tab",cb:function(options){options.heatMap.getTabManager().remove(options.heatMap.tabId)}});this.add({name:"Rename Tab",ellipsis:true,cb:function(options){options.heatMap.getTabManager().rename(options.heatMap.tabId)}});this.add({which:[88],commandKey:true,name:"New Heat Map",accept:function(options){return!options.isInputField||window.getSelection().toString()===""},cb:function(options){morpheus.HeatMap.showTool(new morpheus.NewHeatMapTool,options.heatMap)}});this.add({which:[67],commandKey:true,name:"Copy"});this.add({which:[86],commandKey:true,name:"Paste Dataset"});this.add({global:true,name:"Open",ellipsis:true,cb:function(options){morpheus.HeatMap.showTool(new morpheus.OpenFileTool,options.heatMap)},which:[79],commandKey:true,icon:"fa fa-folder-open-o"});this.add({ellipsis:true,name:"Save Image",gui:function(){return new morpheus.SaveImageTool},cb:function(options){morpheus.HeatMap.showTool(this.gui(),options.heatMap)},which:[83],commandKey:true,global:true,icon:"fa fa-file-image-o"});this.add({ellipsis:true,name:"Save Dataset",gui:function(){return new morpheus.SaveDatasetTool},cb:function(options){morpheus.HeatMap.showTool(this.gui(),options.heatMap)},icon:"fa fa-floppy-o"});this.add({ellipsis:true,name:"Save Session",gui:function(){return new morpheus.SaveSessionTool},cb:function(options){morpheus.HeatMap.showTool(this.gui(),options.heatMap)},icon:"fa fa-anchor"});if(typeof echarts!=="undefined"){this.add({name:"Chart",cb:function(options){new morpheus.ChartTool({project:options.heatMap.getProject(),heatmap:options.heatMap,getVisibleTrackNames:_.bind(options.heatMap.getVisibleTrackNames,options.heatMap)})},icon:"fa fa-line-chart"})}this.add({name:"Zoom In",cb:function(options){options.heatMap.zoom(true)},which:[107,61,187]});this.add({name:"Zoom Out",cb:function(options){options.heatMap.zoom(false)},which:[173,189,109]});this.add({name:"Fit To Window",cb:function(options){options.heatMap.fitToWindow({fitRows:true,fitColumns:true,repaint:true})},which:[48],commandKey:true,icon:"fa fa-compress"});this.add({name:"Fit Columns To Window",cb:function(options){options.heatMap.fitToWindow({fitRows:false,fitColumns:true,repaint:true})}});this.add({name:"Fit Rows To Window",cb:function(options){options.heatMap.fitToWindow({fitRows:true,fitColumns:false,repaint:true})}});this.add({name:"100%",cb:function(options){options.heatMap.resetZoom()},button:"100%"});this.add({which:[35],name:"Go To End",cb:function(options){options.heatMap.scrollLeft(options.heatMap.heatmap.getPreferredSize().width);options.heatMap.scrollTop(options.heatMap.heatmap.getPreferredSize().height)}});this.add({which:[36],name:"Go To Start",cb:function(options){options.heatMap.scrollLeft(0);options.heatMap.scrollTop(0)}});this.add({which:[34],commandKey:true,name:"Go To Bottom",cb:function(options){options.heatMap.scrollTop(options.heatMap.heatmap.getPreferredSize().height)}});this.add({which:[34],commandKey:false,name:"Scroll Page Down",cb:function(options){var pos=options.heatMap.scrollTop();options.heatMap.scrollTop(pos+options.heatMap.heatmap.getUnscaledHeight()-2)}});this.add({which:[33],commandKey:true,name:"Go To Top",cb:function(options){options.heatMap.scrollTop(0)}});this.add({which:[33],commandKey:false,name:"Scroll Page Up",cb:function(options){var pos=options.heatMap.scrollTop();options.heatMap.scrollTop(pos-options.heatMap.heatmap.getUnscaledHeight()+2)}});this.add({which:[38],commandKey:true,name:"Zoom Out Rows",cb:function(options){options.heatMap.zoom(false,{columns:false,rows:true})}});this.add({which:[38],commandKey:false,name:"Scroll Up",cb:function(options){options.heatMap.scrollTop(options.heatMap.scrollTop()-8)}});this.add({which:[40],commandKey:true,name:"Zoom In Rows",cb:function(options){options.heatMap.zoom(true,{columns:false,rows:true})}});this.add({which:[40],commandKey:false,name:"Scroll Down",cb:function(options){options.heatMap.scrollTop(options.heatMap.scrollTop()+8)}});this.add({which:[37],commandKey:true,name:"Zoom Out Columns",cb:function(options){options.heatMap.zoom(false,{columns:true,rows:false})}});this.add({which:[37],commandKey:false,name:"Scroll Left",cb:function(options){options.heatMap.scrollLeft(options.heatMap.scrollLeft()-8)}});this.add({which:[39],commandKey:true,name:"Zoom In Columns",cb:function(options){options.heatMap.zoom(true,{columns:true,rows:false})}});this.add({which:[39],commandKey:false,name:"Scroll Right",cb:function(options){options.heatMap.scrollLeft(options.heatMap.scrollLeft()+8)}});this.add({name:"Tutorial",cb:function(){window.open("https://software.broadinstitute.org/morpheus/tutorial.html")}});this.add({icon:"fa fa-code",name:"Source Code",cb:function(){window.open("https://github.com/cmap/morpheus.js")}});var $findModal;var $search;this.add({which:[65],ellipsis:true,shiftKey:true,commandKey:true,name:"Search Menus",cb:function(options){if($findModal==null){var findModal=[];var id=_.uniqueId("morpheus");findModal.push('<div class="modal" tabindex="1" role="dialog" aria-labelledby="'+id+'">');findModal.push('<div class="modal-dialog" role="document">');findModal.push('<div class="modal-content">');findModal.push('<div class="modal-header">');findModal.push('<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>');findModal.push('<h4 class="modal-title" id="'+id+'">Enter action</h4>');findModal.push("</div>");findModal.push('<div class="modal-body ui-front"><input class="form-control input-sm"></div>');findModal.push("</div>");findModal.push("</div>");findModal.push("</div>");$findModal=$(findModal.join(""));$findModal.appendTo(options.heatMap.$content);var allActions=options.heatMap.getActionManager().getActions();$search=$findModal.find("input");$search.on("keyup",function(e){if(e.which===13){var text=$search.val().trim();if(text!==""){var action=_this.getAction(text);if(action){$findModal.modal("hide");_this.execute(text,{event:e})}}}});morpheus.Util.autosuggest({$el:$search,multi:false,suggestWhenEmpty:false,filter:function(tokens,response){var token=tokens[0].trim();var matches=[];var replaceRegex=new RegExp("("+morpheus.Util.escapeRegex(token)+")","i");for(var i=0;i<allActions.length;i++){if(allActions[i].cb){var name=allActions[i].name;if(replaceRegex.test(name)){matches.push({clear:true,value:name,label:'<span style="margin-left: 10px">'+name.replace(replaceRegex,"<b>$1</b>")+"</span>"})}}}response(matches)},select:function(){setTimeout(function(){var text=$search.val().trim();if(text!==""){var action=_this.getAction(text);if(action){$findModal.modal("hide");_this.execute(text)}}},20)}});$findModal.on("hidden.bs.modal",function(){options.heatMap.focus()})}$findModal.modal("show");$search.focus()}});this.add({name:"Keyboard Shortcuts",cb:function(options){new morpheus.HeatMapKeyListener(options.heatMap).showKeyMapReference()}});this.add({name:"Configuration",cb:function(){window.open("https://software.broadinstitute.org/morpheus/configuration.html")}});this.add({name:"Contact",icon:"fa fa-envelope-o",cb:function(options){morpheus.FormBuilder.showInModal({title:"Contact",html:"Please email us at morpheus@broadinstitute.org",focus:options.heatMap.getFocusEl()})}});this.add({which:[65],commandKey:true,name:"Select All",accept:function(options){var active=options.heatMap.getActiveComponent();return active==="rowTrack"||active==="columnTrack"},cb:function(options){var active=options.heatMap.getActiveComponent();var selectionModel=active==="rowTrack"?options.heatMap.getProject().getRowSelectionModel():options.heatMap.getProject().getColumnSelectionModel();var count=active==="rowTrack"?options.heatMap.getProject().getSortedFilteredDataset().getRowCount():options.heatMap.getProject().getSortedFilteredDataset().getColumnCount();var indices=new morpheus.Set;for(var i=0;i<count;i++){indices.add(i)}selectionModel.setViewIndices(indices,true)}});var invertAction=function(options,isColumns){var model=isColumns?options.heatMap.getProject().getColumnSelectionModel():options.heatMap.getProject().getRowSelectionModel();var viewIndices=model.getViewIndices();var inverse=new morpheus.Set;var n=n=isColumns?options.heatMap.getProject().getSortedFilteredDataset().getColumnCount():options.heatMap.getProject().getSortedFilteredDataset().getRowCount();for(var i=0;i<n;i++){if(!viewIndices.has(i)){inverse.add(i)}}model.setViewIndices(inverse,true)};this.add({name:"Invert Selected Rows",cb:function(options){invertAction(options,false)}});this.add({name:"Invert Selected Columns",cb:function(options){invertAction(options,true)}});var clearAction=function(options,isColumns){var model=isColumns?options.heatMap.getProject().getColumnSelectionModel():options.heatMap.getProject().getRowSelectionModel();model.setViewIndices(new morpheus.Set,true)};this.add({name:"Clear Selected Rows",cb:function(options){clearAction(options,false)}});this.add({name:"Clear Selected Columns",cb:function(options){clearAction(options,true)}});var moveToTop=function(options,isColumns){var project=options.heatMap.getProject();var selectionModel=!isColumns?project.getRowSelectionModel():project.getColumnSelectionModel();var viewIndices=selectionModel.getViewIndices().values();if(viewIndices.length===0){return}viewIndices.sort(function(a,b){return a===b?0:a<b?-1:1});var converter=isColumns?project.convertViewColumnIndexToModel:project.convertViewRowIndexToModel;converter=_.bind(converter,project);var modelIndices=[];for(var i=0,n=viewIndices.length;i<n;i++){modelIndices.push(converter(viewIndices[i]))}var sortKey=new morpheus.MatchesOnTopSortKey(project,modelIndices,"selection on top",isColumns);sortKey.setLockOrder(1);sortKey.setUnlockable(false);if(isColumns){project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getColumnSortKeys().filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.toString()===sortKey.toString())})),true)}else{project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getRowSortKeys().filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.toString()===sortKey.toString())})),true)}};this.add({name:"Move Selected Rows To Top",cb:function(options){moveToTop(options,false)}});this.add({name:"Move Selected Columns To Top",cb:function(options){moveToTop(options,true)}});var selectAll=function(options,isColumns){var project=options.heatMap.getProject();var selectionModel=!isColumns?project.getRowSelectionModel():project.getColumnSelectionModel();var count=!isColumns?project.getSortedFilteredDataset().getRowCount():project.getSortedFilteredDataset().getColumnCount();var indices=new morpheus.Set;for(var i=0;i<count;i++){indices.add(i)}selectionModel.setViewIndices(indices,true)};this.add({name:"Select All Rows",cb:function(options){selectAll(options,false)}});this.add({name:"Select All Columns",cb:function(options){selectAll(options,true)}});var copySelection=function(options,isColumns){var project=options.heatMap.getProject();var dataset=project.getSortedFilteredDataset();var activeTrackName=options.heatMap.getSelectedTrackName(isColumns);var v;if(activeTrackName==null){v=isColumns?dataset.getColumnMetadata().get(0):dataset.getRowMetadata().get(0)}else{v=isColumns?dataset.getColumnMetadata().getByName(activeTrackName):dataset.getRowMetadata().getByName(activeTrackName)}var selectionModel=isColumns?project.getColumnSelectionModel():project.getRowSelectionModel();var text=[];var toStringFunction=morpheus.VectorTrack.vectorToString(v);selectionModel.getViewIndices().forEach(function(index){text.push(toStringFunction(v.getValue(index)))});morpheus.Util.setClipboardData([{format:"text/plain",data:text.join("\n")}])};this.add({name:"Copy Selected Rows",cb:function(options){copySelection(options,false)}});this.add({name:"Copy Selected Columns",cb:function(options){copySelection(options,true)}});var annotateSelection=function(options,isColumns){var project=options.heatMap.getProject();var selectionModel=isColumns?project.getColumnSelectionModel():project.getRowSelectionModel();if(selectionModel.count()===0){morpheus.FormBuilder.showMessageModal({title:"Annotate Selection",html:"No "+(isColumns?"columns":"rows")+" selected.",focus:options.heatMap.getFocusEl()});return}var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"annotation_name",type:"text",required:true});formBuilder.append({name:"annotation_value",type:"text",required:true});morpheus.FormBuilder.showOkCancel({title:"Annotate",content:formBuilder.$form,focus:options.heatMap.getFocusEl(),okCallback:function(){var value=formBuilder.getValue("annotation_value");var annotationName=formBuilder.getValue("annotation_name");var dataset=project.getSortedFilteredDataset();var fullDataset=project.getFullDataset();if(isColumns){dataset=morpheus.DatasetUtil.transposedView(dataset);fullDataset=morpheus.DatasetUtil.transposedView(fullDataset)}var existingVector=fullDataset.getRowMetadata().getByName(annotationName);var v=dataset.getRowMetadata().add(annotationName);selectionModel.getViewIndices().forEach(function(index){v.setValue(index,value)});morpheus.VectorUtil.maybeConvertStringToNumber(v);project.trigger("trackChanged",{vectors:[v],display:existingVector!=null?[]:[morpheus.VectorTrack.RENDER.TEXT],columns:isColumns})}})};this.add({ellipsis:true,name:"Annotate Selected Rows",cb:function(options){annotateSelection(options,false)}});this.add({ellipsis:true,name:"Annotate Selected Columns",cb:function(options){annotateSelection(options,true)}});this.add({name:"Copy Selected Dataset",cb:function(options){var project=options.heatMap.getProject();var dataset=project.getSelectedDataset({emptyToAll:false});var columnMetadata=dataset.getColumnMetadata();var rowMetadata=dataset.getRowMetadata();var visibleColumnFields=options.heatMap.getVisibleTrackNames(true);var columnFieldIndices=[];_.each(visibleColumnFields,function(name){var index=morpheus.MetadataUtil.indexOf(columnMetadata,name);if(index!==-1){columnFieldIndices.push(index)}});columnMetadata=new morpheus.MetadataModelColumnView(columnMetadata,columnFieldIndices);var rowMetadata=dataset.getRowMetadata();var visibleRowFields=options.heatMap.getVisibleTrackNames(false);var rowFieldIndices=[];_.each(visibleRowFields,function(name){var index=morpheus.MetadataUtil.indexOf(rowMetadata,name);if(index!==-1){rowFieldIndices.push(index)}});rowMetadata=new morpheus.MetadataModelColumnView(rowMetadata,rowFieldIndices);var text=(new morpheus.GctWriter).write(dataset);morpheus.Util.setClipboardData([{format:"text/plain",data:text}])}});var _this=this;[new morpheus.HClusterTool,new morpheus.KMeansTool,new morpheus.MarkerSelection,new morpheus.NearestNeighbors,new morpheus.AdjustDataTool,new morpheus.CollapseDatasetTool,new morpheus.CreateAnnotation,new morpheus.SimilarityMatrixTool,new morpheus.TransposeTool,new morpheus.TsneTool,new morpheus.DevAPI].forEach(function(tool){_this.add({ellipsis:true,name:tool.toString(),gui:function(){return tool},cb:function(options){morpheus.HeatMap.showTool(tool,options.heatMap)}})});this.add({name:"Edit Fonts",ellipse:true,cb:function(options){var trackInfo=options.heatMap.getLastSelectedTrackInfo();var project=options.heatMap.getProject();var model=trackInfo.isColumns?project.getColumnFontModel():project.getRowFontModel();var chooser=new morpheus.FontChooser({fontModel:model,track:options.heatMap.getTrack(trackInfo.name,trackInfo.isColumns),heatMap:options.heatMap});morpheus.FormBuilder.showInModal({title:"Edit Fonts",html:chooser.$div,close:"Close",focus:options.heatMap.getFocusEl()})}})};morpheus.ActionManager.prototype={getActions:function(){return this.actions},getAction:function(name){return this.actionNameToAction.get(name)},execute:function(name,args){var action=this.getAction(name);if(args==null){args={}}args.heatMap=this.heatMap;action.cb(args);morpheus.Util.trackEvent({eventCategory:"Tool",eventAction:name})},add:function(action){this.actions.push(action);this.actionNameToAction.set(action.name,action)}};morpheus.CanvasUtil=function(){};morpheus.CanvasUtil.dragging=false;morpheus.CanvasUtil.FONT_NAME='"Helvetica Neue",Helvetica,Arial,sans-serif';morpheus.CanvasUtil.FONT_COLOR="rgb(0, 0, 0)";morpheus.CanvasUtil.getFontFamily=function(context){return typeof C2S!=="undefined"&&context instanceof C2S||typeof canvas2pdf!=="undefined"&&context instanceof canvas2pdf.PdfContext?"Helvetica":morpheus.CanvasUtil.FONT_NAME};morpheus.CanvasUtil.getPreferredSize=function(c){var size=c.getPreferredSize();var prefWidth=c.getPrefWidth();var prefHeight=c.getPrefHeight();if(prefWidth!==undefined){size.widthSet=true;size.width=prefWidth}if(prefHeight!==undefined){size.heightSet=true;size.height=prefHeight}return size};morpheus.CanvasUtil.BACKING_SCALE=1;if(typeof window!=="undefined"&&"devicePixelRatio"in window){if(window.devicePixelRatio>1){morpheus.CanvasUtil.BACKING_SCALE=window.devicePixelRatio}}morpheus.CanvasUtil.setBounds=function(canvas,bounds){var backingScale=morpheus.CanvasUtil.BACKING_SCALE;if(bounds.height!=null){canvas.height=bounds.height*backingScale;canvas.style.height=bounds.height+"px"}if(bounds.width!=null){canvas.width=bounds.width*backingScale;canvas.style.width=bounds.width+"px"}if(bounds.left!=null){canvas.style.left=bounds.left+"px"}if(bounds.top!=null){canvas.style.top=bounds.top+"px"}};morpheus.CanvasUtil.drawShape=function(context,shape,x,y,size2,isFill){if(size2<0){return}context.beginPath();if(shape==="circle-minus"){context.arc(x,y,size2,0,2*Math.PI,false);context.moveTo(x-size2,y);context.lineTo(x+size2,y)}else if(shape==="circle"){context.arc(x,y,size2,0,2*Math.PI,false)}else if(shape==="square"){context.rect(x-size2,y-size2,size2*2,size2*2)}else if(shape==="plus"){context.moveTo(x,y-size2);context.lineTo(x,y+size2);context.moveTo(x-size2,y);context.lineTo(x+size2,y)}else if(shape==="x"){context.moveTo(x-size2,y-size2);context.lineTo(x+size2,y+size2);context.moveTo(x+size2,y-size2);context.lineTo(x-size2,y+size2)}else if(shape==="asterisk"){context.moveTo(x-size2,y-size2);context.lineTo(x+size2,y+size2);context.moveTo(x+size2,y-size2);context.lineTo(x-size2,y+size2);context.moveTo(x,y-size2);context.lineTo(x,y+size2)}else if(shape==="diamond"){context.moveTo(x,y-size2);context.lineTo(x+size2,y);context.lineTo(x,y+size2);context.lineTo(x-size2,y);context.lineTo(x,y-size2)}else if(shape==="triangle-up"){context.moveTo(x,y-size2);context.lineTo(x+size2,y+size2);context.lineTo(x-size2,y+size2);context.lineTo(x,y-size2)}else if(shape==="triangle-down"){context.moveTo(x,y+size2);context.lineTo(x-size2,y-size2);context.lineTo(x+size2,y-size2);context.lineTo(x,y+size2)}else if(shape==="triangle-left"){context.moveTo(x-size2,y);context.lineTo(x+size2,y-size2);context.lineTo(x+size2,y+size2);context.lineTo(x-size2,y)}else if(shape==="triangle-right"){context.moveTo(x+size2,y);context.lineTo(x-size2,y+size2);context.lineTo(x-size2,y-size2);context.lineTo(x+size2,y)}isFill?context.fill():context.stroke()};morpheus.CanvasUtil.drawLine=function(context,x1,y1,x2,y2){context.beginPath();context.moveTo(x1,y1);context.lineTo(x2,y2);context.stroke()};morpheus.CanvasUtil.resetTransform=function(context){context.setTransform(1,0,0,1,0,0);if(morpheus.CanvasUtil.BACKING_SCALE!==1){context.scale(morpheus.CanvasUtil.BACKING_SCALE,morpheus.CanvasUtil.BACKING_SCALE)}};morpheus.CanvasUtil.bezierCurveTo=function(context,start,end){var m1=(start[1]+end[1])/2;context.beginPath();context.moveTo(start[0],start[1]);context.bezierCurveTo(start[0],m1,end[0],m1,end[0],end[1]);context.stroke()};morpheus.CanvasUtil.createCanvas=function(){var $c=$("<canvas></canvas>");$c.attr("tabindex","0");$c.css({cursor:"default",outline:0,overflow:"hidden",position:"absolute","z-index":1});return $c[0]};morpheus.CanvasUtil.getHeaderStringWidth=function(context,s){context.font="14px "+morpheus.CanvasUtil.getFontFamily(context);return context.measureText(s).width+18};morpheus.CanvasUtil.forceSubPixelRendering=function(context){context.getImageData(0,0,1,1)};morpheus.CanvasUtil.getVectorStringWidth=function(context,vector,positions,end){if(positions.getSize()<6){return 0}var fontSize=Math.min(morpheus.VectorTrack.MAX_FONT_SIZE,positions.getSize()-2);if(fontSize<=0){return 0}context.font=fontSize+"px "+morpheus.CanvasUtil.getFontFamily(context);var toString=morpheus.VectorTrack.vectorToString(vector);var maxWidth=0;var n=end<=0?vector.size():Math.min(end,vector.size());for(var i=0;i<n;i++){var value=vector.getValue(i);if(value!=null&&value!=""){value=toString(value)}else{continue}var width=context.measureText(value).width;if(width>maxWidth){maxWidth=width}}return maxWidth===0?maxWidth:maxWidth+2};morpheus.CanvasUtil.clipString=function(context,string,availTextWidth){var textWidth=context.measureText(string).width;if(textWidth<=availTextWidth){return string}var clipString="...";availTextWidth-=context.measureText(clipString).width;if(availTextWidth<=0){return clipString}var width=0;for(var nChars=0,stringLength=string.length;nChars<stringLength;nChars++){width+=context.measureText(string[nChars]).width;if(width>availTextWidth){string=string.substring(0,nChars);break}}return string+clipString};morpheus.CanvasUtil.toSVG=function(drawable,file){var totalSize={width:drawable.getWidth(),height:drawable.getHeight()};var context=new C2S(totalSize.width,totalSize.height);context.save();drawable.draw({x:0,y:0,width:totalSize.width,height:totalSize.height},context);context.restore();var svg=context.getSerializedSvg();var blob=new Blob([svg],{type:"text/plain;charset=utf-8"});saveAs(blob,file)};morpheus.CanvasUtil.getMousePos=function(element,event,useDelta){return morpheus.CanvasUtil.getMousePosWithScroll(element,event,0,0,useDelta)};morpheus.CanvasUtil.getClientXY=function(event,useDelta){var clientX;var clientY;if(event.pointers){if(event.pointers.length>0){clientX=event.pointers[0].clientX-(useDelta?event.deltaX:0);clientY=event.pointers[0].clientY-(useDelta?event.deltaY:0)}else{clientX=event.srcEvent.clientX-(useDelta?event.deltaX:0);clientY=event.srcEvent.clientY-(useDelta?event.deltaY:0)}}else{clientX=event.clientX;clientY=event.clientY}return{x:clientX,y:clientY}};morpheus.CanvasUtil.getMousePosWithScroll=function(element,event,scrollX,scrollY,useDelta){return morpheus.CanvasUtil._getMousePosWithScroll(element,scrollX,scrollY,morpheus.CanvasUtil.getClientXY(event,useDelta))};morpheus.CanvasUtil._getMousePosWithScroll=function(element,scrollX,scrollY,clientXY){var rect=element.getBoundingClientRect();return{x:clientXY.x-rect.left+scrollX,y:clientXY.y-rect.top+scrollY}};morpheus.CheckBoxList=function(options){var _this=this;var set=options.set||new morpheus.Set;options=$.extend(true,{},{height:"150px",showHeader:false,select:false,search:true,checkBoxSelectionOnTop:false,rowHeader:function(item){var header=[];header.push('<span><input name="toggle" type="checkbox" '+(set.has(_this.getter(item))?" checked":"")+"/> ");header.push("</span>");return header.join("")}},options);options=morpheus.Table.createOptions(options);if(options.columns.length===1){options.maxWidth=583}var idColumn=options.columns[0];for(var i=0;i<options.columns.length;i++){if(options.columns[i].idColumn){idColumn=options.columns[i];break}}this.getter=idColumn.getter;var html=[];var table=new morpheus.Table(options);if(options.columns.length===1){options.$el.find(".slick-table-header").find("[name=right]").remove()}this.table=table;var html=[];html.push('<div style="display:inline;">');html.push('<div style="display:inline;" class="dropdown">');html.push('<button class="btn btn-default btn-xs dropdown-toggle" type="button"'+' data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">');html.push('<i data-name="checkbox" class="fa fa-square-o"'+' aria-hidden="true"></i>');html.push(' <span class="fa fa-caret-down"></span>');html.push("</button>");html.push('<ul style="font-size:12px;" class="dropdown-menu">');html.push('<li><a name="selectAll" href="#">Select All</a></li>');html.push('<li><a name="selectNone" href="#">Select None</a></li>');html.push('<li><a name="invertSel" href="#">Invert Selection</a></li>');html.push("</ul>");html.push("</div>");html.push('<span data-name="available" style="font-size:12px;padding-left:6px;"></span>');html.push("</div>");var $checkBoxEl=$(html.join(""));table.$header.find("[name=left]").html($checkBoxEl);var $selection=$checkBoxEl.find("[data-name=available]");var $selectAll=$checkBoxEl.find("[name=selectAll]");var $selectNone=$checkBoxEl.find("[name=selectNone]");var $cb=$checkBoxEl.find("[data-name=checkbox]");var updateLabel=function(){var label=[];label.push("selected ");label.push(morpheus.Util.intFormat(set.size()));label.push(" of ");label.push(morpheus.Util.intFormat(table.getAllItemCount()));if(table.getFilteredItemCount()!==table.getAllItemCount()){label.push(", ");label.push(morpheus.Util.intFormat(table.getFilteredItemCount()));label.push(table.getFilteredItemCount()===1?" match":" matches")}$selection.html(label.join(""))};table.grid.on("filter",function(e){updateLabel()});$cb.on("click",function(e){if($cb.hasClass("fa-square-o")){var items=table.getItems();for(var i=0;i<items.length;i++){set.add(_this.getter(items[i]))}}else{var items=table.getItems();for(var i=0;i<items.length;i++){set.remove(_this.getter(items[i]))}}table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();e.stopPropagation()});$selectAll.on("click",function(e){var items=table.getItems();for(var i=0,nitems=items.length;i<nitems;i++){set.add(_this.getter(items[i]))}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();_this.table.redraw()});$checkBoxEl.find("[name=invertSel]").on("click",function(e){var items=table.getItems();for(var i=0,nitems=items.length;i<nitems;i++){var val=_this.getter(items[i]);if(set.has(val)){set.remove(val)}else{set.add(val)}}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();_this.table.redraw()});$selectNone.on("click",function(e){var items=table.getItems();for(var i=0,nitems=items.length;i<nitems;i++){set.remove(_this.getter(items[i]))}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set});e.preventDefault();_this.table.redraw()});this.set=set;this.table=table;updateLabel();var priorCount=0;this.table.on("checkBoxSelectionChanged",function(){if(set.size()===0){$cb.attr("class","fa fa-square-o")}else{var items=table.getItems();var count=0;var found=false;var notFound=false;for(var i=0;i<items.length;i++){if(set.has(_this.getter(items[i]))){count++;found=true;if(notFound){break}}else{notFound=true;if(found){break}}}if(count===0){$cb.attr("class","fa fa-square-o")}else if(count===items.length){$cb.attr("class","fa fa-check-square-o")}else{$cb.attr("class","fa fa-minus-square-o")}}updateLabel();_this.table.redraw()});table.on("click",function(e){var $target=$(e.target);var item=table.getItems()[e.row];var value=_this.getter(item);if($target.is(".morpheus-hover-show")){set.clear();set.add(value);_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set})}else if(!options.select||$target.is("[type=checkbox]")&&$target.attr("name")==="toggle"){if(set.has(value)){set.remove(value)}else{set.add(value)}_this.table.trigger("checkBoxSelectionChanged",{source:_this,set:set})}})};morpheus.CheckBoxList.prototype={searchWithPredicates:function(predicates){this.table.searchWithPredicates(predicates)},autocomplete:function(tokens,cb){this.table.autocomplete(tokens,cb)},setHeight:function(height){this.table.setHeight(height)},resize:function(){this.table.resize()},setSearchVisible:function(visible){this.table.setSearchVisible(visible)},getSelectedRows:function(){return this.table.getSelectedRows()},getSelectedItems:function(){return this.table.getSelectedItems()},setSelectedRows:function(rows){this.table.setSelectedRows(rows)},getItems:function(items){return this.table.getItems()},getAllItemCount:function(){return this.table.getAllItemCount()},getFilteredItemCount:function(){return this.table.getFilteredItemCount()},setFilter:function(f){this.table.setFilter(f)},redraw:function(){this.table.redraw()},getSelection:function(){return this.set},clearSelection:function(values){this.set.clear();this.table.redraw()},setValue:function(values){this.setSelectedValues(values)},setSelectedValues:function(values){this.set.clear();if(morpheus.Util.isArray(values)){for(var i=0;i<values.length;i++){this.set.add(values[i])}}else{this.set.add(values)}this.table.redraw()},val:function(){return this.set.values()},on:function(evtStr,handler){this.table.on(evtStr,handler);return this},off:function(evtStr,handler){this.table.off(evtStr,handler)},setItems:function(items){var newItems=new morpheus.Set;var getter=this.getter;for(var i=0;i<items.length;i++){newItems.add(getter(items[i]))}var selection=this.set;selection.forEach(function(val){if(!newItems.has(val)){selection.remove(val)}});this.table.setItems(items);this.table.trigger("checkBoxSelectionChanged",{source:this,set:selection})}};morpheus.ColorSchemeChooser=function(options){var colorModel=options.colorModel;var track=options.track;var heatMap=options.heatMap;colorModel.getMappedValue(track.getVector(track.settings.colorByField),track.getVector(track.settings.colorByField).getValue(0));var formBuilder=new morpheus.FormBuilder;if(track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)){formBuilder.append({value:track.settings.colorByField!=null,type:"checkbox",name:"use_another_annotation_to_determine_color"});var annotationNames=morpheus.MetadataUtil.getMetadataNames(track.isColumns?heatMap.getProject().getFullDataset().getColumnMetadata():heatMap.getProject().getFullDataset().getRowMetadata());annotationNames.splice(annotationNames.indexOf(track.getName()),1);formBuilder.append({name:"annotation_name",type:"bootstrap-select",options:annotationNames,search:annotationNames.length>10,value:track.settings.colorByField})}formBuilder.append({name:"discrete",type:"checkbox",value:track.getVector(track.settings.colorByField).getProperties().get(morpheus.VectorKeys.DISCRETE)});var dataType=morpheus.VectorUtil.getDataType(track.getVector(track.settings.colorByField));var isNumber=dataType==="number"||dataType==="[number]";formBuilder.setVisible("discrete",isNumber);formBuilder.setVisible("annotation_name",track.settings.colorByField!=null);var $chooser=$("<div></div>");$chooser.appendTo(formBuilder.$form);var updateChooser=function(){var colorSchemeChooser;var v=track.getVector(track.settings.colorByField);formBuilder.setValue("discrete",v.getProperties().get(morpheus.VectorKeys.DISCRETE));if(v.getProperties().get(morpheus.VectorKeys.DISCRETE)){colorModel.getMappedValue(v,v.getValue(0));colorSchemeChooser=new morpheus.DiscreteColorSchemeChooser({colorScheme:{scale:colorModel.getDiscreteColorScheme(track.getVector(track.settings.colorByField))}});colorSchemeChooser.on("change",function(event){colorModel.setMappedValue(track.getVector(track.settings.colorByField),event.value,event.color);track.setInvalid(true);track.repaint()})}else{colorModel.getContinuousMappedValue(v,v.getValue(0));colorSchemeChooser=new morpheus.HeatMapColorSchemeChooser({showRelative:false});colorSchemeChooser.setColorScheme(colorModel.getContinuousColorScheme(v));colorSchemeChooser.on("change",function(event){track.setInvalid(true);track.repaint()})}$chooser.html(colorSchemeChooser.$div);track.setInvalid();track.repaint()};formBuilder.find("use_another_annotation_to_determine_color").on("change",function(){var checked=$(this).prop("checked");formBuilder.setValue("annotation_name",null);formBuilder.setVisible("annotation_name",checked);if(!checked){track.settings.colorByField=null;updateChooser()}else{$chooser.empty()}formBuilder.setVisible("discrete",false)});formBuilder.find("annotation_name").on("change",function(){var annotationName=$(this).val();colorModel.getMappedValue(track.getVector(annotationName),track.getVector(annotationName).getValue(0));track.settings.colorByField=annotationName;var dataType=morpheus.VectorUtil.getDataType(track.getVector(track.settings.colorByField));var isNumber=dataType==="number"||dataType==="[number]";formBuilder.setVisible("discrete",isNumber);updateChooser();track.setInvalid(true);track.repaint()});formBuilder.find("discrete").on("change",function(){track.getVector(track.settings.colorByField).getProperties().set(morpheus.VectorKeys.DISCRETE,$(this).prop("checked"));updateChooser();track.setInvalid(true);track.repaint()});updateChooser();this.$div=formBuilder.$form};morpheus.ColumnDendrogram=function(heatMap,tree,positions,project){morpheus.AbstractDendrogram.call(this,heatMap,tree,positions,project,morpheus.AbstractDendrogram.Type.COLUMN)};morpheus.ColumnDendrogram.prototype={drawNode:function(context,node){var radius=this.getNodeRadius(node);var pix=this.toPix(node);context.beginPath();context.arc(pix[0],pix[1],4,Math.PI*2,false);context.fill()},isDragHotSpot:function(p){return Math.abs(this.scale(this.cutHeight)-p.y)<=2},drawCutSlider:function(clip,context){if(context.setLineDash){context.setLineDash([5])}context.strokeStyle="black";var ny=this.scale(this.cutHeight);context.beginPath();context.moveTo(clip.x,ny);context.lineTo(this.getUnscaledWidth(),ny);context.stroke();if(context.setLineDash){context.setLineDash([])}},createScale:function(){return d3.scale.linear().domain([this.tree.maxHeight,0]).range([0,this.getUnscaledHeight()])},paintMouseOver:function(clip,context){if(this.project.getHoverColumnIndex()!==-1){morpheus.CanvasUtil.resetTransform(context);context.translate(-clip.x,0);this.drawColumnBorder(context,this.positions,this.project.getHoverColumnIndex(),this.getUnscaledWidth())}},drawColumnBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(pix+size,0);context.lineTo(pix+size,gridSize);context.stroke();context.beginPath();context.moveTo(pix,0);context.lineTo(pix,gridSize);context.stroke()},getMaxIndex:function(clip){return morpheus.Positions.getRight(clip,this.positions)},getMinIndex:function(clip){return morpheus.Positions.getLeft(clip,this.positions)},getPreferredSize:function(context){return{width:Math.ceil(this.positions.getPosition(this.positions.getLength()-1)+this.positions.getItemSize(this.positions.getLength()-1)),height:100}},toPix:function(node){var min=this.positions.getPosition(node.minIndex)+this.positions.getItemSize(node.minIndex)/2;var max=this.positions.getPosition(node.maxIndex)+this.positions.getItemSize(node.maxIndex)/2;return[(min+max)/2,this.scale(node.height)]},drawPathFromNodeToParent:function(context,node){var pix=this.toPix(node);var parentPix=this.toPix(node.parent);context.beginPath();context.moveTo(pix[0],pix[1]);context.lineTo(pix[0],parentPix[1]);context.lineTo(parentPix[0],parentPix[1]);context.stroke()},drawNodePath:function(context,node,minIndex,maxIndex){var children=node.children;var left=children[0];var right=children[1];var ny=this.scale(node.height);var rx=this.toPix(right)[0];var ry=this.scale(right.height);var lx=this.toPix(left)[0];var ly=this.scale(left.height);var x,y;if(!this.drawLeafNodes){var leftIsLeaf=left.children!==undefined;var rightIsLeaf=right.children!==undefined;if(leftIsLeaf){ly=ny+4}if(rightIsLeaf){ry=ny+4}x=[rx,rx,lx,lx];y=[ry,ny,ny,ly]}else{x=[rx,rx,lx,lx];y=[ry,ny,ny,ly]}context.beginPath();context.moveTo(x[0],y[0]);for(var i=1,length=x.length;i<length;i++){context.lineTo(x[i],y[i])}context.stroke()}};morpheus.Util.extend(morpheus.ColumnDendrogram,morpheus.AbstractDendrogram);morpheus.ConditionalRenderingUI=function(heatmap){var _this=this;this.heatmap=heatmap;var $div=$('<div class="container-fluid" style="min-width:180px;"></div>');$div.on("click","[data-name=add]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index();var condition={seriesName:null,color:"rgb(0,0,0)",shape:null,inheritColor:true,accept:function(val){return false}};heatmap.heatmap.getColorScheme().getConditions().insert(index,condition);$row.after(_this.add(condition));e.preventDefault()});$div.on("click","[data-name=delete]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index()-1;heatmap.heatmap.getColorScheme().getConditions().remove(index);heatmap.revalidate();$row.remove();e.preventDefault()});var html=[];html.push('<div class="morpheus-entry">');html.push('<div class="row">');html.push('<div style="padding-bottom:20px;" class="col-xs-8"><a class="btn btn-default btn-xs"'+' role="button"'+' data-name="add" href="#">Add Condition</a></div>');html.push("</div>");html.push("</div>");$div.append(html.join(""));this.$div=$div;heatmap.heatmap.getColorScheme().getConditions().getConditions().forEach(function(c){_this.add(c).appendTo($div)})};morpheus.ConditionalRenderingUI.prototype={add:function(condition){var _this=this;var html=[];html.push('<div style="border-top:1px solid LightGrey;padding-bottom:6px;padding-top:6px;"'+' class="morpheus-entry">');html.push('<form class="form-horizontal">');html.push('<div class="form-group">');html.push('<label class="col-xs-2">Series</label>');html.push('<div class="col-xs-6">');html.push('<select class="form-control morpheus-form-control-inline" name="cond_series">');html.push(morpheus.Util.createOptions(morpheus.DatasetUtil.getSeriesNames(this.heatmap.getProject().getFullDataset())));html.push("</select>");html.push("</div>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-2">Condition</label>');html.push('<div class="col-xs-6">');html.push('<select class="form-control morpheus-form-control-inline" name="lower"><option value="gte">&gt;=</option><option value="gt">&gt;</option></select>');html.push('<input class="form-control morpheus-form-control-inline" name="v1" size="5" type="text">');html.push('<span style="margin-right:1em;">and</span>');html.push('<select class="form-control morpheus-form-control-inline" name="upper"><option value="lte">&lt;=</option><option value="lt">&lt;</option></select>');html.push('<input class="form-control morpheus-form-control-inline" name="v2" size="5" type="text">');html.push("</div>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-2">Shape</label>');var shapeField=new morpheus.ShapeField({shapes:morpheus.VectorShapeModel.FILLED_SHAPES,showNone:false});html.push('<div class="col-xs-4">');html.push('<div style="display:inline;" data-name="shapeHolder"></div>');html.push("</div>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-offset-2 col-xs-4"><input name="inherit_color"'+' type="checkbox" checked> Inherit'+" color</label>");html.push("</div>");html.push('<div class="form-group">');html.push('<label class="col-xs-2">Color</label>');html.push('<div class="col-xs-4">');html.push('<input class="form-control" type="color" name="color" style="display:inline;'+' width:6em;" disabled>');html.push("</div>");html.push("</div>");html.push('<div class="row"><div class="col-xs-11">');html.push('<a class="btn btn-default btn-xs" role="button" data-name="delete"'+' href="#">Delete Condition</a>');html.push("</div></div>");html.push("</div>");var $el=$(html.join(""));console.log($el.find("form").length);$el.find("form").on("submit",function(e){e.preventDefault()});shapeField.$el.appendTo($el.find("[data-name=shapeHolder]"));var $color=$el.find("[name=color]");var $series=$el.find("[name=cond_series]");var $v1=$el.find("[name=v1]");var $v2=$el.find("[name=v2]");var $v1Op=$el.find("[name=lower]");var $v2Op=$el.find("[name=upper]");var $inherit_color=$el.find("[name=inherit_color]");$color.prop("disabled",condition.inheritColor);$color.val(condition.color);$series.val(condition.seriesName);shapeField.setShapeValue(condition.shape);if(condition.v1!=null&&!isNaN(condition.v1)){$v1.val(condition.v1)}if(condition.v2!=null&&!isNaN(condition.v2)){$v2.val(condition.v2)}$v1Op.val(condition.v1Op);$v2Op.val(condition.v2Op);function updateAccept(){var v1=parseFloat($($v1).val());var v2=parseFloat($($v2).val());var v1Op=$v1Op.val();var v2Op=$v2Op.val();condition.v1=v1;condition.v2=v2;condition.v1Op=v1Op;condition.v2Op=v2Op;var gtf=function(){return true};var ltf=function(){return true};if(!isNaN(v1)){gtf=v1Op==="gt"?function(val){return val>v1}:function(val){return val>=v1}}if(!isNaN(v2)){ltf=v2Op==="lt"?function(val){return val<v2}:function(val){return val<=v2}}condition.accept=function(val){return gtf(val)&&ltf(val)};_this.heatmap.revalidate()}$v1Op.on("change",function(e){updateAccept()});$v2Op.on("change",function(e){updateAccept()});$v1.on("keyup",_.debounce(function(e){updateAccept()},100));$v2.on("keyup",_.debounce(function(e){updateAccept()},100));$inherit_color.on("click",function(e){condition.inheritColor=$(this).prop("checked");$color.prop("disabled",condition.inheritColor);_this.heatmap.revalidate()});$color.on("change",function(e){condition.color=$(this).val();_this.heatmap.revalidate()});shapeField.on("change",function(e){condition.shape=e.shape;_this.heatmap.revalidate()});$series.on("change",function(e){condition.seriesName=$(this).val();_this.heatmap.revalidate()});condition.seriesName=$series.val();return $el}};morpheus.DendrogramUtil={};morpheus.DendrogramUtil.setIndices=function(root,counter){counter=counter||0;var setIndex=function(node){var children=node.children;var maxIndex=children[0].maxIndex;var minIndex=children[0].minIndex;var sum=children[0].index;for(var i=1,length=children.length;i<length;i++){var child=children[i];sum+=child.index;minIndex=Math.min(minIndex,child.minIndex);maxIndex=Math.max(maxIndex,child.maxIndex)}node.minIndex=minIndex;node.maxIndex=maxIndex;node.index=sum/children.length;node.children.sort(function(a,b){return a.index===b.index?0:a.index<b.index?-1:1})};var visit=function(node,callback){var children=node.children;var n;if(children&&(n=children.length)){var i=-1;while(++i<n){visit(children[i],callback)}}callback(node)};visit(root,function(n){if(n.children===undefined){n.minIndex=counter;n.maxIndex=counter;n.index=counter;counter++}else{setIndex(n)}return true})};morpheus.DendrogramUtil.convertEdgeLengthsToHeights=function(rootNode){var maxHeight=0;function setHeights(node,height){var newHeight=height;if(node.length!==undefined){newHeight+=node.length}node.height=newHeight;maxHeight=Math.max(maxHeight,node.height);if(node.children!=null){node.children.forEach(function(child){setHeights(child,newHeight)})}}setHeights(rootNode,0);var counter=0;morpheus.DendrogramUtil.dfs(rootNode,function(node){node.id=counter;counter++;node.height=maxHeight-node.height;return true});return{maxHeight:maxHeight,n:counter}};morpheus.DendrogramUtil.writeNewick=function(node,out,leafNodeIdFunction){if(node.children!=null&&node.children.length>0){out.push("(");for(var i=0;i<node.children.length;i++){if(i>0){out.push(",")}morpheus.DendrogramUtil.writeNewick(node.children[i],out,leafNodeIdFunction)}out.push(")")}out.push(node.index!=null?leafNodeIdFunction(node):"");out.push(":");var parentHeight=node.parent?node.parent.height:node.height;out.push(parentHeight-node.height)};morpheus.DendrogramUtil.parseNewick=function(text){var rootNode=Newick.parse(text);var counter=0;var leafNodes=[];function visit(node){var children=node.children;if(children!==undefined){var left=children[0];var right=children[1];left.parent=node;right.parent=node;visit(left);visit(right)}else{node.minIndex=counter;node.maxIndex=counter;node.index=counter;leafNodes.push(node);counter++}}visit(rootNode);var maxHeight=morpheus.DendrogramUtil.convertEdgeLengthsToHeights(rootNode).maxHeight;morpheus.DendrogramUtil.setNodeDepths(rootNode);morpheus.DendrogramUtil.setIndices(rootNode);return{maxHeight:rootNode.height,rootNode:rootNode,leafNodes:leafNodes,nLeafNodes:leafNodes.length}};morpheus.DendrogramUtil.cutAtHeight=function(rootNode,h){var roots=[];morpheus.DendrogramUtil.dfs(rootNode,function(node){if(node.height<h){roots.push(node);return false}return true});roots.sort(function(a,b){return a.index<b.index?-1:a.index==b.index?0:1});return roots};morpheus.DendrogramUtil.getDeepestChild=function(node,isMin){while(true){if(node.children===undefined){return node}var index;if(isMin){index=node.children[0].index<node.children[node.children.length-1].index?0:node.children.length-1}else{index=node.children[0].index>node.children[node.children.length-1].index?0:node.children.length-1}node=node.children[index]}};morpheus.DendrogramUtil.dfs=function(node,callback,childrenAccessor){if(childrenAccessor===undefined){childrenAccessor=function(n){return n.children}}if(callback(node)){var children=childrenAccessor(node);var n;if(children&&(n=children.length)){var i=-1;while(++i<n){morpheus.DendrogramUtil.dfs(children[i],callback,childrenAccessor)}}}};morpheus.DendrogramUtil.copyTree=function(tree){var counter=0;function recurse(node){var children=node.children;if(children!==undefined){var newChildren=[];for(var i=0,n=children.length;i<n;i++){var copy=$.extend({},children[i]);copy.parent=node;newChildren.push(copy)}node.children=newChildren;for(var i=0,n=newChildren.length;i<n;i++){recurse(newChildren[i])}}else{node.index=counter;node.minIndex=counter;node.maxIndex=counter;counter++}}var rootNode=$.extend({},tree.rootNode);rootNode.parent=undefined;recurse(rootNode);return{nLeafNodes:tree.nLeafNodes,maxDepth:tree.maxDepth,rootNode:rootNode}};morpheus.DendrogramUtil.collapseAtDepth=function(rootNode,maxDepth){morpheus.DendrogramUtil.dfs(rootNode,function(d){if(d.collapsedChildren){d.children=d.collapsedChildren;d.collapsedChildren=undefined}return true});morpheus.DendrogramUtil.dfs(rootNode,function(d){var depth=d.depth;if(depth>maxDepth){d.collapsedChildren=d.children;d.children=undefined;return false}return true})};morpheus.DendrogramUtil.setNodeDepths=function(rootNode){var max=0;function recurse(node,depth){var children=node.children;node.depth=depth;max=Math.max(depth,max);if(children!==undefined){var i=-1;var j=depth+1;var n=children.length;while(++i<n){var d=recurse(children[i],j)}}return node}recurse(rootNode,0);return max};morpheus.DendrogramUtil.sortDendrogram=function(root,vectorToSortBy,project,summaryFunction){summaryFunction=summaryFunction||function(array){var min=Number.MAX_VALUE;for(var i=0;i<array.length;i++){min=Math.min(min,array[i].weight)}return min};var setWeights=function(node){if(node.children!==undefined){var children=node.children;for(var i=0;i<children.length;i++){setWeights(children[i])}node.weight=summaryFunction(children)}else{node.weight=vectorToSortBy.getValue(node.index)}};setWeights(root);var nodeIdToModelIndex={};var leafNodes=morpheus.DendrogramUtil.getLeafNodes(root);_.each(leafNodes,function(node){nodeIdToModelIndex[node.id]=project.convertViewColumnIndexToModel(node.index)});morpheus.DendrogramUtil.dfs(root,function(node){if(node.children){node.children.sort(function(a,b){return a.weight===b.weight?0:a.weight<b.weight?-1:1})}return true});morpheus.DendrogramUtil.setIndices(root);var sortOrder=[];_.each(leafNodes,function(node){var oldModelIndex=nodeIdToModelIndex[node.id];var newIndex=node.index;sortOrder[newIndex]=oldModelIndex});return sortOrder};morpheus.DendrogramUtil.leastCommonAncestor=function(leafNodes){function getPathToRoot(node){var path=new morpheus.Map;while(node!=null){path.set(node.id,node);node=node.parent}return path}var path=getPathToRoot(leafNodes[0]);for(var i=1;i<leafNodes.length;i++){var path2=getPathToRoot(leafNodes[i]);path.forEach(function(node,id){if(!path2.has(id)){path.remove(id)}})}var max=-Number.MAX_VALUE;var maxNode;path.forEach(function(n,id){if(n.depth>max){max=n.depth;maxNode=n}});return maxNode};morpheus.DendrogramUtil.search=function(options){var searchText=options.text;var rootNode=options.rootNode;var tokens=morpheus.Util.getAutocompleteTokens(searchText);var predicates;var nmatches=0;var matchAllPredicates=options.matchAllPredicates===true;if(tokens==null||tokens.length==0){morpheus.DendrogramUtil.dfs(rootNode,function(node){node.search=false;return true});nmatches=-1}else{predicates=morpheus.Util.createSearchPredicates({tokens:tokens,defaultMatchMode:options.defaultMatchMode});var npredicates=predicates.length;morpheus.DendrogramUtil.dfs(rootNode,function(node){var matches=false;if(node.info){searchLabel:if(!matchAllPredicates){for(var p=0;p<npredicates;p++){var predicate=predicates[p];var filterColumnName=predicate.getField();if(filterColumnName!=null){var vals=node.info[filterColumnName];for(var i=0,nvals=vals.length;i<nvals;i++){if(predicate.accept(vals[i])){matches=true;break searchLabel}}}else{for(var name in node.info){var vals=node.info[name];for(var i=0,nvals=vals.length;i<nvals;i++){if(predicate.accept(vals[i])){matches=true;break searchLabel}}}}}}else{matches=true;for(var p=0;p<npredicates;p++){var predicate=predicates[p];var filterColumnName=predicate.getField();if(filterColumnName!=null){var vals=node.info[filterColumnName];for(var i=0,nvals=vals.length;i<nvals;i++){if(!predicate.accept(vals[i])){matches=false;break searchLabel}}}else{for(var name in node.info){var vals=node.info[name];for(var i=0,nvals=vals.length;i<nvals;i++){if(!predicate.accept(vals[i])){matches=false;break searchLabel}}}}}}}node.search=matches;if(matches){nmatches++}return true})}return nmatches};morpheus.DendrogramUtil.squishNonSearchedNodes=function(heatMap,isColumns){if(isColumns){heatMap.getHeatMapElementComponent().getColumnPositions().setSize(13)}else{heatMap.getHeatMapElementComponent().getRowPositions().setSize(13)}var expandedLeafNodes={};var dendrogram=isColumns?heatMap.columnDendrogram:heatMap.rowDendrogram;morpheus.DendrogramUtil.dfs(dendrogram.tree.rootNode,function(node){for(var i=node.minIndex;i<=node.maxIndex;i++){if(node.search){expandedLeafNodes[i]=true}}return true});var clusterIds=[];var previous=expandedLeafNodes[0];var squishedIndices={};if(!previous){squishedIndices[0]=true}var clusterNumber=0;clusterIds.push(clusterNumber);for(var i=1,nleaves=dendrogram.tree.leafNodes.length;i<nleaves;i++){var expanded=expandedLeafNodes[i];if(expanded!==previous){clusterNumber++;previous=expanded}if(!expanded){squishedIndices[i]=true}clusterIds.push(clusterNumber)}if(isColumns){heatMap.getHeatMapElementComponent().getColumnPositions().setSquishedIndices(squishedIndices);heatMap.getProject().setGroupColumns([new morpheus.SpecifiedGroupByKey(clusterIds)],false)}else{heatMap.getHeatMapElementComponent().getRowPositions().setSquishedIndices(squishedIndices);heatMap.getProject().setGroupRows([new morpheus.SpecifiedGroupByKey(clusterIds)],false)}};morpheus.DendrogramUtil.getLeafNodes=function(rootNode){var leafNodes=[];morpheus.DendrogramUtil.dfs(rootNode,function(node){if(node.children===undefined){leafNodes.push(node)}return true});return leafNodes};morpheus.DiscreteColorSchemeChooser=function(options){var formBuilder=new morpheus.FormBuilder;var map=options.colorScheme.scale;formBuilder.append({name:"selected_value",type:"bootstrap-select",options:map.keys()});var $select=formBuilder.find("selected_value");formBuilder.append({style:"max-width:50px;",name:"selected_color",type:"color"});var selectedVal=$select.val();var _this=this;var $color=formBuilder.find("selected_color");$color.val(map.get(selectedVal));$color.on("change",function(e){var color=$(this).val();map.set(selectedVal,color);_this.trigger("change",{value:selectedVal,color:color})});$select.on("change",function(){selectedVal=$select.val();var c=map.get(selectedVal);$color.val(c)});this.$div=formBuilder.$form};morpheus.DiscreteColorSchemeChooser.prototype={};morpheus.Util.extend(morpheus.DiscreteColorSchemeChooser,morpheus.Events);morpheus.DiscreteColorSupplier=function(){this.colorMap=new morpheus.Map;this.hiddenValue=0;this.hiddenValues=new morpheus.Set;morpheus.AbstractColorSupplier.call(this);this.scalingMode=morpheus.HeatMapColorScheme.ScalingMode.FIXED};morpheus.DiscreteColorSupplier.prototype={createInstance:function(){return new morpheus.DiscreteColorSupplier},setColorMap:function(array){this.colorMap=new morpheus.Map;this.colors=[];this.fractions=[];this.names=[];this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;for(var i=0;i<array.length;i++){this.colorMap.set(array[i].value,array[i].color);this.fractions.push(array[i].value);this.names.push(array[i].name);this.colors.push(array[i].color);this.min=Math.min(this.min,array[i].value);this.max=Math.max(this.max,array[i].value)}},copy:function(){var c=this.createInstance();c.names=this.names.slice(0);c.colorMap=new morpheus.Map;this.colorMap.forEach(function(color,value){c.colorMap.set(value,color)});c.colors=this.colors.slice(0);c.fractions=this.fractions.slice(0);this.hiddenValues.forEach(function(val){c.hiddenValues.add(val)});c.missingColor=this.missingColor;return c},isStepped:function(){return true},getColor:function(row,column,value){if(this.hiddenValues.has(value)){value=this.hiddenValue}if(isNaN(value)){return this.missingColor}return this.colorMap.get(value)}};morpheus.Util.extend(morpheus.DiscreteColorSupplier,morpheus.AbstractColorSupplier);morpheus.Divider=function(vertical){morpheus.AbstractCanvas.call(this,false);this.vertical=vertical;var that=this;var canvas=this.canvas;canvas.style.cursor=vertical?"ew-resize":"ns-resize";if(vertical){this.setBounds({height:15,width:4})}else{this.setBounds({height:4,width:15})}this.hammer=morpheus.Util.hammer(canvas,["pan"]).on("panstart",this.panstart=function(event){that.trigger("resizeStart");morpheus.CanvasUtil.dragging=true}).on("panmove",this.panmove=function(event){if(that.vertical){that.trigger("resize",{delta:event.deltaX})}else{that.trigger("resize",{delta:event.deltaY})}}).on("panend",this.panend=function(event){morpheus.CanvasUtil.dragging=false;that.trigger("resizeEnd")});this.paint()};morpheus.Divider.prototype={dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.hammer.off("panstart",this.panstart).off("panmove",this.panmove).off("panend",this.panend);this.hammer.destroy()},getPreferredSize:function(){return{width:3,height:this.getUnscaledHeight()}},draw:function(clip,context){var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();context.clearRect(0,0,width,height);context.strokeStyle="#ddd";if(!this.vertical){context.beginPath();context.moveTo(0,1.5);context.lineTo(width,1.5);context.stroke()}else{context.beginPath();context.moveTo(0,0);context.lineTo(0,height);context.stroke()}}};morpheus.Util.extend(morpheus.Divider,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.Divider,morpheus.Events);morpheus.DualList=function(leftOptions,rightOptions){var html=[];html.push('<div class="container-fluid">');html.push('<div class="row">');html.push('<div class="col-xs-4"><label>Available Fields</label></div>');html.push('<div class="col-xs-2"></div>');html.push('<div class="col-xs-4"><label>Selected Fields</label></div>');html.push("</div>");html.push('<div class="row">');html.push('<div class="col-xs-4"><select class="form-control" name="left" multiple></select></div>');html.push('<div class="col-xs-2"><div class="btn-group-vertical" role="group">'+'<button name="add" type="button" class="btn btn-xs btn-default">Add</button>'+'<button name="remove" type="button" class="btn btn-xs btn-default">Remove</button>'+'<button name="up" type="button" class="btn btn-xs btn-default">Move Up</button>'+'<button name="down" type="button" class="btn btn-xs btn-default">Move Down</button>'+"</div></div>");html.push('<div class="col-xs-4"><select class="form-control" name="right" multiple></select></div>');html.push("</div>");html.push("</div>");this.$el=$(html.join(""));var _this=this;this.$el.find("[name=add]").on("click",function(){_this.addSelected()});this.$el.find("[name=remove]").on("click",function(){_this.removeSelected()});this.$el.find("[name=up]").on("click",function(){_this.moveUp()});this.$el.find("[name=down]").on("click",function(){_this.moveDown()});this.left=this.$el.find("[name=left]")[0];this.right=this.$el.find("[name=right]")[0];for(var i=0;i<leftOptions.length;i++){this.left.options[i]=leftOptions[i]}for(var i=0;i<rightOptions.length;i++){this.right.options[i]=rightOptions[i]}};morpheus.DualList.prototype={addSelected:function(){var left=this.left;var right=this.right;for(var i=0;i<left.options.length;i++){if(left.options[i].selected){var opt=left.options[i];right.options[right.options.length]=new Option(opt.innerHTML,opt.value);left.options[i]=null;i--}}},addAll:function(){var left=this.left;var right=this.right;for(var i=0;i<left.options.length;i++){var opt=left.options[i];right.options[right.options.length]=new Option(opt.innerHTML,opt.value)}left.options.length=0},removeSelected:function(){var left=this.left;var right=this.right;for(var i=0;i<right.options.length;i++){if(right.options[i].selected){var opt=right.options[i];left.options[left.options.length]=new Option(opt.innerHTML,opt.value);right.options[i]=null;i--}}},getOptions:function(isLeft){var sel=isLeft?this.left:this.right;var options=[];for(var i=0;i<sel.options.length;i++){options.push(sel.options[i].value)}return options},removeAll:function(){var left=this.left;var right=this.right;for(var i=0;i<right.options.length;i++){var opt=right.options[i];left.options[left.options.length]=new Option(opt.innerHTML,opt.value)}right.options.length=0},moveUp:function(){var right=this.right;var selectedOptions=right.selectedOptions;var indices=[];for(var i=0;i<selectedOptions.length;i++){indices.push(selectedOptions[i].index)}var index=morpheus.Util.indexSort(indices,false);for(var i=0;i<selectedOptions.length;i++){var sel=selectedOptions[index[i]].index;var optHTML=right.options[sel].innerHTML;var optVal=right.options[sel].value;var opt1HTML=right.options[sel-1].innerHTML;var opt1Val=right.options[sel-1].value;right.options[sel]=new Option(opt1HTML,opt1Val);right.options[sel-1]=new Option(optHTML,optVal);right.options.selectedIndex=sel-1}},moveDown:function(){var right=this.right;var selectedOptions=right.selectedOptions;var indices=[];for(var i=0;i<selectedOptions.length;i++){indices.push(selectedOptions[i].index)}var index=morpheus.Util.indexSort(indices,false);for(var i=0;i<selectedOptions.length;i++){var sel=selectedOptions[index[i]].index;var optHTML=right.options[sel].innerHTML;var optVal=right.options[sel].value;var opt1HTML=right.options[sel+1].innerHTML;var opt1Val=right.options[sel+1].value;right.options[sel]=new Option(opt1HTML,opt1Val);right.options[sel+1]=new Option(optHTML,optVal);right.options.selectedIndex=sel+1}}};morpheus.FilePicker=function(options){var html=[];html.push("<div>");var myComputer=_.uniqueId("morpheus");var url=_.uniqueId("morpheus");var googleId=_.uniqueId("morpheus");var dropbox=_.uniqueId("morpheus");var preloaded=_.uniqueId("morpheus");html.push('<ul style="margin-bottom:10px;" class="nav nav-pills morpheus">');html.push('<li role="presentation" class="active"><a href="#'+myComputer+'"'+' aria-controls="'+myComputer+'" role="tab" data-toggle="tab"><i class="fa fa-desktop"></i>'+" My Computer</a></li>");html.push('<li role="presentation"><a href="#'+url+'"'+' aria-controls="'+url+'" role="tab" data-toggle="tav"><i class="fa fa-link"></i>'+" URL</a></li>");if(typeof gapi!=="undefined"){html.push('<li role="presentation"><a href="#'+googleId+'"'+' aria-controls="'+googleId+'" role="tab" data-toggle="tab"><i class="fa'+' fa-google"></i>'+" Google</a></li>")}if(typeof Dropbox!=="undefined"){html.push('<li role="presentation"><a href="#'+dropbox+'"'+' aria-controls="'+dropbox+'" role="tab" data-toggle="tab"><i class="fa fa-dropbox"></i>'+" Dropbox</a></li>")}var $sampleDatasetsEl=$('<div class="morpheus-preloaded"></div>');if(navigator.onLine){html.push('<li role="presentation"><a href="#'+preloaded+'"'+' aria-controls="'+preloaded+'" role="tab" data-toggle="tab"><i class="fa fa-database"></i>'+" Preloaded Datasets</a></li>");new morpheus.SampleDatasets({$el:$sampleDatasetsEl,show:true,callback:function(heatMapOptions){options.optionsCallback(heatMapOptions)}})}html.push("</ul>");html.push('<div class="tab-content"'+' style="text-align:center;cursor:pointer;height:300px;">');html.push('<div role="tabpanel" class="tab-pane active" id="'+myComputer+'">');html.push('<div data-name="drop" class="morpheus-file-drop morpheus-landing-panel">');html.push('<button class="btn btn-default"><span class="fa-stack"><i'+' class="fa fa-file-o'+' fa-stack-2x"></i> <i class="fa fa-plus fa-stack-1x"></i></span> Select File</button>'+' <div style="padding-top:10px;">or Copy and Paste Clipboard Data, <span'+' class="morpheus-drag-text">Drag and'+" Drop</span></div>");html.push('<input name="hiddenFile" style="display:none;" type="file">');html.push("</div>");html.push("</div>");html.push('<div role="tabpanel" class="tab-pane" id="'+url+'">');html.push('<div class="morpheus-landing-panel">');html.push('<input name="url" placeholder="Enter a URL" class="form-control"'+' style="display:inline;max-width:400px;'+' type="text"><button name="openUrl" class="btn btn-default"'+' type="button">Go</button>');html.push("</div>");html.push("</div>");if(typeof Dropbox!=="undefined"){html.push('<div role="tabpanel" class="tab-pane" id="'+dropbox+'">');html.push('<div class="morpheus-landing-panel">');html.push('<button name="dropbox" class="btn btn-default">Browse Dropbox</button>');html.push("</div>");html.push("</div>")}if(typeof gapi!=="undefined"){html.push('<div role="tabpanel" class="tab-pane" id="'+googleId+'">');html.push('<div class="morpheus-landing-panel">');html.push('<button name="google" class="btn btn-default">Browse Google Drive</button>');html.push("</div>");html.push("</div>")}if(navigator.onLine){html.push('<div role="tabpanel" class="tab-pane" id="'+preloaded+'">');html.push('<div class="morpheus-landing-panel">');html.push("</div>");html.push("</div>")}html.push("</div>");html.push("</div>");var $el=$(html.join(""));$sampleDatasetsEl.appendTo($el.find("#"+preloaded+" > .morpheus-landing-panel"));this.$el=$el;var $file=$el.find("[name=hiddenFile]");var $myComputer=$el.find("[id="+myComputer+"]");this.$el.find(".nav").on("click","li > a",function(e){e.preventDefault();$(this).tab("show")});var $url=$el.find("[name=url]");$url.on("keyup",function(evt){if(evt.which===13){var text=$.trim($(this).val());if(text!==""){options.fileCallback(text)}}});$el.find("[name=openUrl]").on("click",function(evt){var text=$.trim($url.val());if(text!==""){options.fileCallback(text)}});var $dropbox=$el.find("[name=dropbox]");$dropbox.on("click",function(e){Dropbox.choose({success:function(results){var val=results[0].link;options.fileCallback(val)},linkType:"direct",multiselect:false})});var $google=$el.find("[name=google]");$google.on("click",function(){var developerKey="AIzaSyBCRqn5xgdUsJZcC6oJnIInQubaaL3aYvI";var clientId="936482190815-85k6k06b98ihv272n0b7f7fm33v5mmfa.apps.googleusercontent.com";var scope=["https://www.googleapis.com/auth/drive"];var oauthToken;var pickerApiLoaded=false;var oauthToken;function onApiLoad(){gapi.load("auth",{callback:onAuthApiLoad});gapi.load("picker",{callback:onPickerApiLoad})}function onAuthApiLoad(){window.gapi.auth.authorize({client_id:clientId,scope:scope,immediate:false},handleAuthResult)}function onPickerApiLoad(){pickerApiLoaded=true;createPicker()}function handleAuthResult(authResult){if(authResult&&!authResult.error){oauthToken=authResult.access_token;createPicker()}}function createPicker(){if(pickerApiLoaded&&oauthToken){var picker=(new google.picker.PickerBuilder).addView(google.picker.ViewId.DOCS).setOAuthToken(oauthToken).setDeveloperKey(developerKey).setCallback(pickerCallback).build();picker.setVisible(true);$(".picker-dialog-bg").css("z-index",1052);$(".picker-dialog").css("z-index",1053)}}function pickerCallback(data){if(data.action==google.picker.Action.PICKED){var file=data.docs[0];var fileName=file.name;var accessToken=gapi.auth.getToken().access_token;var xhr=new XMLHttpRequest;var url=new String("https://www.googleapis.com/drive/v3/files/"+file.id+"?alt=media");url.name=fileName;url.headers={Authorization:"Bearer "+accessToken};options.fileCallback(url)}}onApiLoad()});$file.on("change",function(evt){var files=evt.target.files;for(var i=0;i<files.length;i++){options.fileCallback(files[i])}});$(window).on("paste.morpheus",this.paste=function(e){if($myComputer.is(":visible")){var text=e.originalEvent.clipboardData.getData("text/plain");if(text!=null&&text.length>0){e.preventDefault();e.stopPropagation();var url;if(text.indexOf("http")===0){url=text}else{var blob=new Blob([text]);url=new String(window.URL.createObjectURL(blob));url.name="clipboard"}options.fileCallback(url)}}});var $drop=$el.find("[data-name=drop]");var _this=this;$el.on("remove",function(){$(window).off(_this.paste).off(_this.dragover).off(_this.dragenter).off(_this.dragleave).off(_this.drop)});var clicking=false;$drop.on("click",function(e){if(!clicking){clicking=true;$file.click();clicking=false}});$(window).on("dragover",this.dragover=function(e){if($myComputer.is(":visible")){$drop.addClass("drag");e.preventDefault();e.stopPropagation()}}).on("dragenter",this.dragenter=function(e){if($myComputer.is(":visible")){$drop.addClass("drag");e.preventDefault();e.stopPropagation()}}).on("dragleave",this.dragleave=function(e){if($myComputer.is(":visible")){$drop.removeClass("drag");e.preventDefault();e.stopPropagation()}}).on("drop",this.drop=function(e){if($myComputer.is(":visible")){$drop.removeClass("drag");if(e.originalEvent.dataTransfer){if(e.originalEvent.dataTransfer.files.length){e.preventDefault();e.stopPropagation();var files=e.originalEvent.dataTransfer.files;for(var i=0;i<files.length;i++){options.fileCallback(files[i])}}else{var url=e.originalEvent.dataTransfer.getData("URL");options.fileCallback(url);e.preventDefault();e.stopPropagation()}}}})};morpheus.FilterUI=function(project,isColumns){var _this=this;this.project=project;this.isColumns=isColumns;var $div=$('<div style="min-width:180px;"></div>');this.$div=$div;$div.append(this.addBase());var $filterMode=$div.find("[name=filterMode]");$filterMode.on("change",function(e){var isAndFilter=$filterMode.prop("checked");(isColumns?project.getColumnFilter():project.getRowFilter()).setAnd(isAndFilter);isColumns?_this.project.setColumnFilter(_this.project.getColumnFilter(),true):_this.project.setRowFilter(_this.project.getRowFilter(),true);e.preventDefault()});$div.on("click","[data-name=add]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index();var newFilter=new morpheus.AlwaysTrueFilter;(isColumns?project.getColumnFilter():project.getRowFilter()).insert(index,newFilter);$row.after(_this.add(newFilter));e.preventDefault()});$div.on("click","[data-name=delete]",function(e){var $this=$(this);var $row=$this.closest(".morpheus-entry");var index=$row.index()-1;(isColumns?project.getColumnFilter():project.getRowFilter()).remove(index);$row.remove();isColumns?_this.project.setColumnFilter(_this.project.getColumnFilter(),true):_this.project.setRowFilter(_this.project.getRowFilter(),true);e.preventDefault()});$div.on("submit","form",function(e){var $this=$(this);e.preventDefault()});$div.on("change","[name=by]",function(e){var $this=$(this);var fieldName=$this.val();var $row=$this.closest(".morpheus-entry");var index=$row.index()-1;if(fieldName==""){$row.find("[data-name=ui]").empty()}else{_this.createFilter({fieldName:fieldName,$div:$this})}isColumns?_this.project.setColumnFilter(_this.project.getColumnFilter(),true):_this.project.setRowFilter(_this.project.getRowFilter(),true)});var combinedFilter=isColumns?project.getColumnFilter():project.getRowFilter();var filters=combinedFilter.getFilters?combinedFilter.getFilters():[];for(var i=0;i<filters.length;i++){this.createFilter({filter:filters[i]})}if(combinedFilter.on){combinedFilter.on("add",function(e){_this.createFilter({filter:e.filter})});combinedFilter.on("remove",function(e){var $row=$div.find(".morpheus-entry")[1+e.index].remove()});combinedFilter.on("and",function(e){$filterMode.prop("checked",e.source.isAnd())})}};morpheus.FilterUI.rangeFilter=function(project,name,isColumns,$ui,filter){$ui.empty();var html=[];html.push("<label>Range of values</label><br />");html.push('<label>>= </label> <input style="max-width:200px;" class="form-control input-sm" name="min" type="text" />');html.push('<label> and <= </label> <input style="max-width:200px;" class="form-control input-sm" name="max" type="text" />');html.push('<br /><a data-name="switch" href="#">Switch to top filter</a>');var $form=$(html.join(""));$form.appendTo($ui);$ui.find("[data-name=switch]").on("click",function(e){e.preventDefault();var newFilter=morpheus.FilterUI.topFilter(project,name,isColumns,$ui);var index=-1;var filters=isColumns?project.getColumnFilter().getFilters():project.getRowFilter().getFilters();for(var i=0;i<filters.length;i++){if(filters[i]===filter){index=i;break}}if(index===-1){throw new Error("Filter not found.")}(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,newFilter);isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)});var $min=$ui.find("[name=min]");var $max=$ui.find("[name=max]");if(!filter){filter=new morpheus.RangeFilter(-Number.MAX_VALUE,Number.MAX_VALUE,name,isColumns)}else{$min.val(filter.min);$max.val(filter.max)}$min.on("keyup",_.debounce(function(e){filter.setMin(parseFloat($.trim($(this).val())));isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)},500));$max.on("keyup",_.debounce(function(e){filter.setMax(parseFloat($.trim($(this).val())));isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)},500));return filter};morpheus.FilterUI.topFilter=function(project,name,isColumns,$ui,filter){$ui.empty();var html=[];html.push("<label>Top</label><br />");html.push('<select style="width:auto;" class="form-control input-sm" name="direction"><option value="Top">Top</option><option value="Bottom">Bottom</option><option value="TopBottom">Top/Bottom</option></select>');html.push(' <label>N </label> <input style="max-width:200px;" class="form-control input-sm" name="n" type="text" />');html.push('<br /><a data-name="switch" href="#">Switch to range filter</a>');var $form=$(html.join(""));$form.appendTo($ui);var $n=$ui.find("[name=n]");var $direction=$ui.find("[name=direction]");$ui.find("[data-name=switch]").on("click",function(e){e.preventDefault();var newFilter=morpheus.FilterUI.rangeFilter(project,name,isColumns,$ui);var index=-1;var filters=isColumns?project.getColumnFilter().getFilters():project.getRowFilter().getFilters();for(var i=0;i<filters.length;i++){if(filters[i]===filter){index=i;break}}if(index===-1){throw new Error("Filter not found.")}(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,newFilter);isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)});if(!filter){filter=new morpheus.TopNFilter(NaN,morpheus.TopNFilter.TOP,name,isColumns)}else{var dirVal;if(filter.direction===morpheus.TopNFilter.TOP){dirVal="Top"}else if(filter.direction===morpheus.TopNFilter.BOTTOM){dirVal="Bottom"}else{dirVal="TopBottom"}$direction.val(dirVal);$n.val(filter.n)}$direction.on("change",function(){var dir=$(this).val();var dirVal;if(dir==="Top"){dirVal=morpheus.TopNFilter.TOP}else if(dir==="Bottom"){dirVal=morpheus.TopNFilter.BOTTOM}else{dirVal=morpheus.TopNFilter.TOP_BOTTOM}filter.setDirection(dirVal);isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)});$n.on("keyup",_.debounce(function(e){filter.setN(parseInt($.trim($(this).val())));isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)},500));return filter};morpheus.FilterUI.prototype={createFilter:function(options){var index=-1;var $div=options.$div;var isColumns=this.isColumns;var filter=options.filter;var project=this.project;var fieldName=filter?filter.name:options.fieldName;var $ui;if(!$div){var $add=$(this.add(filter));$add.appendTo(this.$div);$ui=$add.find("[data-name=ui]")}else{var $row=$div.closest(".morpheus-entry");index=$row.index()-1;$ui=$row.find("[data-name=ui]")}$ui.empty();var vector=(isColumns?this.project.getFullDataset().getColumnMetadata():this.project.getFullDataset().getRowMetadata()).getByName(fieldName);if(filter instanceof morpheus.RangeFilter){morpheus.FilterUI.rangeFilter(project,fieldName,isColumns,$ui,filter)}else if(filter instanceof morpheus.TopNFilter){morpheus.FilterUI.topFilter(project,fieldName,isColumns,$ui,filter)}else if(filter==null&&morpheus.VectorUtil.isNumber(vector)&&morpheus.VectorUtil.containsMoreThanNValues(vector,9)){filter=morpheus.FilterUI.rangeFilter(project,fieldName,isColumns,$ui,filter)}else{var set=morpheus.VectorUtil.getSet(vector);var array=set.values();array.sort(morpheus.SortKey.ASCENDING_COMPARATOR);if(!filter){filter=new morpheus.VectorFilter(new morpheus.Set,set.size(),fieldName,isColumns)}else{filter.maxSetSize=array.length}var checkBoxList=new morpheus.CheckBoxList({responsive:false,$el:$ui,items:array,set:filter.set});checkBoxList.on("checkBoxSelectionChanged",function(){isColumns?project.setColumnFilter(project.getColumnFilter(),true):project.setRowFilter(project.getRowFilter(),true)})}if(index!==-1){if(fieldName!==""){(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,filter)}else{(isColumns?project.getColumnFilter():project.getRowFilter()).set(index,new morpheus.AlwaysTrueFilter)}}return filter},addBase:function(){var html=[];html.push('<div style="padding-bottom:2px;border-bottom:1px solid #eee" class="morpheus-entry">');html.push('<div class="row">');html.push('<div class="col-xs-12">'+'<div class="checkbox"><label><input type="checkbox" name="filterMode">Pass all filters</label></div> '+"</div>");html.push("</div>");html.push('<div class="row">');html.push('<div class="col-xs-8"><a class="btn btn-default btn-xs" role="button"'+' data-name="add" href="#">Add</a></div>');html.push("</div>");html.push("</div>");return html.join("")},add:function(filter){var project=this.project;var isColumns=this.isColumns;var fields=morpheus.MetadataUtil.getMetadataNames(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata());var html=[];html.push('<div class="morpheus-entry">');html.push('<div class="form-group">');html.push("<label>Field</label>");html.push('<select style="max-width:160px;overflow-x:hidden;" name="by" class="form-control input-sm">');html.push('<option value=""></option>');var filterField=filter?filter.toString():null;_.each(fields,function(field){html.push('<option value="'+field+'"');if(field===filterField){html.push(" selected")}html.push(">");html.push(field);html.push("</option>")});html.push("</select>");html.push("</div>");html.push('<div class="row">');html.push('<div data-name="ui" class="col-xs-12"></div>');html.push("</div>");html.push('<div style="padding-bottom:6px; border-bottom:1px solid #eee" class="row">');html.push('<div class="col-xs-11">');html.push('<a class="btn btn-default btn-xs" role="button" data-name="delete"'+' href="#">Remove</a>');html.push("</div>");html.push("</div>");html.push("</div>");return html.join("")}};morpheus.FontChooser=function(options){var _this=this;var fontModel=options.fontModel;var track=options.track;var heatMap=options.heatMap;fontModel.getMappedValue(track.getVector(track.settings.fontField),track.getVector(track.settings.fontField).getValue(0));var formBuilder=new morpheus.FormBuilder;formBuilder.append({value:track.settings.fontField!=null,type:"checkbox",name:"use_another_annotation_to_determine_font"});var annotationNames=morpheus.MetadataUtil.getMetadataNames(track.isColumns?heatMap.getProject().getFullDataset().getColumnMetadata():heatMap.getProject().getFullDataset().getRowMetadata());annotationNames.splice(annotationNames.indexOf(track.getName()),1);formBuilder.append({name:"annotation_name",type:"bootstrap-select",options:annotationNames,search:annotationNames.length>10,value:track.settings.fontField});formBuilder.setVisible("annotation_name",track.settings.fontField!=null);formBuilder.append({name:"selected_value",type:"bootstrap-select",search:true,options:fontModel.getMap(track.settings.fontField!=null?track.settings.fontField:track.getName()).keys()});var $selectedValue=formBuilder.find("selected_value");formBuilder.append({name:"selected_font",type:"bootstrap-select",options:[{name:"normal",value:400},{name:"bold",value:700},{name:"bolder",value:900}]});var repaint=function(){track.setInvalid(true);track.repaint()};formBuilder.find("use_another_annotation_to_determine_font").on("change",function(){var checked=$(this).prop("checked");formBuilder.setValue("annotation_name",null);formBuilder.setValue("selected_value",null);formBuilder.setVisible("annotation_name",checked);if(!checked){track.settings.fontField=null}repaint()});formBuilder.find("annotation_name").on("change",function(){var annotationName=$(this).val();fontModel.getMappedValue(track.getVector(annotationName),track.getVector(annotationName).getValue(0));track.settings.fontField=annotationName;formBuilder.setOptions("selected_value",fontModel.getMap(track.settings.fontField!=null?track.settings.fontField:track.getName()).keys());formBuilder.setValue("selected_value",null);repaint()});var $selectedFont=formBuilder.find("selected_font");$selectedFont.on("change",function(e){fontModel.setMappedValue(track.getVector(track.settings.fontField),$selectedValue.val(),{weight:$(this).val()});repaint()});var updateMappedValue=function(){var selectedVal=$selectedValue.val();var mappedValue=fontModel.getMappedValue(track.getVector(track.settings.fontField),selectedVal);formBuilder.setValue("selected_font",mappedValue.weight)};$selectedValue.on("change",function(){updateMappedValue()});updateMappedValue();this.$div=formBuilder.$form};morpheus.Util.extend(morpheus.FontChooser,morpheus.Events);morpheus.FormBuilder=function(options){var _this=this;this.prefix=_.uniqueId("form");this.$form=$("<form></form>");this.$form.attr("role","form").attr("id",this.prefix);this.formStyle=options==null||options.formStyle==null?"horizontal":options.formStyle;this.$form.addClass("morpheus");if(this.formStyle==="horizontal"){this.titleClass="col-xs-12 control-label";this.labelClass="col-xs-4 control-label";this.$form.addClass("form-horizontal")}else if(this.formStyle==="vertical"){this.labelClass="control-label";this.titleClass="control-label"}else if(this.formStyle==="inline"){this.titleClass="";this.labelClass="";this.$form.addClass("form-inline")}this.$form.on("submit",function(e){e.preventDefault()});this.$form.on("dragover",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){$(e.originalEvent.srcElement).parent().css("border","1px solid black");e.preventDefault();e.stopPropagation()}}).on("dragenter",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){$(e.originalEvent.srcElement).parent().css("border","1px solid black");e.preventDefault();e.stopPropagation()}}).on("dragleave",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){$(e.originalEvent.srcElement).parent().css("border","");e.preventDefault();e.stopPropagation()}}).on("drop",function(e){var node=$(e.originalEvent.srcElement).parent().parent().prev();if(node.is("select")&&node.hasClass("file-input")){var isMultiple=node.data("multiple");$(e.originalEvent.srcElement).parent().css("border","");var name=node.attr("name");name=name.substring(0,name.length-"_picker".length);if(e.originalEvent.dataTransfer){if(e.originalEvent.dataTransfer.files.length){e.preventDefault();e.stopPropagation();var files=e.originalEvent.dataTransfer.files;_this.setValue(name,isMultiple?files:files[0]);_this.trigger("change",{name:name,value:files[0]})}else{var url=e.originalEvent.dataTransfer.getData("URL");e.preventDefault();e.stopPropagation();_this.setValue(name,isMultiple?[url]:url);_this.trigger("change",{name:name,value:url})}}}})};morpheus.FormBuilder.showProgressBar=function(options){var content=[];content.push('<div class="container-fluid">');content.push('<div class="row">');content.push('<div class="col-xs-8">');content.push('<div class="progress progress-striped active"><div class="progress-bar" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width: 100%"></div></div>');content.push("</div>");content.push('<div class="col-xs-2">');content.push('<input class="btn btn-default" type="button" name="stop" value="Cancel">');content.push("</div>");content.push("</div>");if(options.subtitle){content.push('<div class="row"><div class="col-xs-8">');content.push('<p class="text-muted">');content.push(options.subtitle);content.push("</p>");content.push("</div></div>")}content.push("</div>");var $content=$(content.join(""));$content.find("[name=stop]").on("click",function(e){options.stop();e.preventDefault()});return morpheus.FormBuilder.showInDraggableDiv({title:options.title,$content:$content})};morpheus.FormBuilder.showInDraggableDiv=function(options){var width=options.width||"300px";var html=[];html.push('<div style="z-index: 1050; top: 100px; position:absolute; padding-left:10px; padding-right:10px; width:'+width+' ; background:white; box-shadow: 0 5px 15px rgba(0,0,0,0.5); border: 1px solid rgba(0,0,0,0.2); border-radius: 6px;">');if(options.title!=null){html.push('<h4 style="cursor:move; border-bottom: 1px solid #e5e5e5;" name="header">'+options.title+"</h4>")}html.push('<div name="content"></div>');html.push("</div>");var $div=$(html.join(""));var $content=$div.find("[name=content]");$div.find("[name=header]").on("dblclick",function(){if($content.css("display")==="none"){$content.css("display","")}else{$content.css("display","none")}});options.$content.appendTo($content);$div.css("left",$(window).width()/2-$content.outerWidth()/2);$div.draggable({containment:"document"});$div.appendTo(options.appendTo!=null?options.appendTo:$(document.body));return $div};morpheus.FormBuilder.showMessageModal=function(options){var $div=morpheus.FormBuilder._showInModal({modalClass:options.modalClass,title:options.title,html:options.html,footer:'<button type="button" class="btn btn-default"'+' data-dismiss="modal">OK</button>',backdrop:options.backdrop,size:options.size,focus:options.focus,appendTo:options.appendTo});$div.find("button").focus();return $div};morpheus.FormBuilder._showInModal=function(options){var html=[];options=$.extend({},{size:"",close:true,modalClass:""},options);html.push('<div tabindex="-1" class="modal'+(options.modalClass?" "+options.modalClass:"")+'" role="dialog"'+' aria-hidden="false"');if(options.z){html.push(' style="z-index: '+options.z+' !important;"')}html.push(">");html.push('<div class="modal-dialog '+options.size+'">');html.push('<div class="modal-content">');html.push(' <div class="modal-header">');if(options.close){html.push('  <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>')}if(options.title!=null){html.push('<h4 class="modal-title">'+options.title+"</h4>")}html.push("</div>");html.push('<div class="modal-body">');html.push("</div>");if(options.footer){html.push('<div class="modal-footer">');html.push(options.footer)}html.push("</div>");html.push("</div>");html.push("</div>");html.push("</div>");var $div=$(html.join(""));$div.on("mousewheel",function(e){e.stopPropagation()});$div.find(".modal-body").html(options.html);$div.prependTo(options.appendTo!=null?options.appendTo:$(document.body));$div.modal({keyboard:true,backdrop:options.backdrop===true?true:false}).on("hidden.bs.modal",function(e){$div.remove();if(options.onClose){options.onClose()}if(options.focus){$(options.focus).focus()}});return $div};morpheus.FormBuilder.showInModal=function(options){return morpheus.FormBuilder._showInModal({modalClass:options.modalClass,title:options.title,html:options.html,footer:options.close?'<button type="button" class="btn btn-default" data-dismiss="modal">'+options.close+"</button>":null,onClose:options.onClose,appendTo:options.appendTo,backdrop:options.backdrop,size:options.size,focus:options.focus})};morpheus.FormBuilder.showOkCancel=function(options){options=$.extend({},{ok:true,cancel:true},options);var footer=[];if(options.ok){footer.push('<button name="ok" type="button" class="btn btn-default">OK</button>')}if(options.apply){footer.push('<button name="apply" type="button" class="btn btn-default">Apply</button>')}if(options.cancel){footer.push('<button name="cancel" type="button" data-dismiss="modal" class="btn btn-default">Cancel</button>')}var $div=morpheus.FormBuilder._showInModal({title:options.title,html:options.content,footer:footer.join(""),size:options.size,close:options.close,onClose:options.onClose,focus:options.focus,appendTo:options.appendTo});var $ok=$div.find("[name=ok]");$ok.on("click",function(e){if(options.okCallback){options.okCallback()}$div.modal("hide")});$div.find("[name=cancel]").on("click",function(e){if(options.cancelCallback){options.cancelCallback()}$div.modal("hide")});if(options.okFocus){$ok.focus()}if(options.draggable){$div.draggable({handle:".modal-header",containment:"document"})}return $div};morpheus.FormBuilder.hasChanged=function(object,keyToUIElement){var keys=_.keys(keyToUIElement);for(var i=0;i<keys.length;i++){var key=keys[i];var value=object[key];var $element=keyToUIElement[key];if(value!==morpheus.FormBuilder.getValue($element)){return true}}return false};morpheus.FormBuilder.getValue=function($element){var list=$element.data("morpheus.checkbox-list");if(list!=null){return list.val()}if($element.attr("type")==="radio"){return $element.filter(":checked").val()}if($element.data("type")==="file"){return $element.data("files")}return $element.attr("type")==="checkbox"?$element.prop("checked"):$element.val()};morpheus.FormBuilder.prototype={appendContent:function($content){this.$form.append($content)},addSeparator:function(){var html=[];html.push('<div class="form-group">');if(this.formStyle==="horizontal"){html.push('<div class="col-xs-12">')}html.push("<hr />");if(this.formStyle==="horizontal"){html.push("</div>")}html.push("</div>");this.$form.append(html.join(""))},_append:function(html,field,isFieldStart){var _this=this;var required=field.required;var name=field.name;var type=field.type;if(type=="separator"){if(this.formStyle==="horizontal"){html.push('<div class="col-xs-12">')}else{html.push('<div class="form-group">')}html.push("<hr />");html.push("</div>");return}var title=field.title;var disabled=field.disabled;var help=field.help;var value=field.value;var showLabel=field.showLabel;var style=field.style||"";var col="";var labelColumn="";if(this.formStyle==="horizontal"){col=field.col||"col-xs-8"}if(showLabel===undefined){showLabel="checkbox"!==type&&"button"!==type&&"radio"!==type;showLabel=showLabel||field.options!==undefined}var id=_this.prefix+"_"+name;if(title===undefined){title=name.replace(/_/g," ");title=title[0].toUpperCase()+title.substring(1)}var endingDiv=false;if(showLabel){html.push('<label for="'+id+'" class="'+this.labelClass+'">');html.push(title);html.push("</label>");if(isFieldStart&&this.formStyle!=="inline"){html.push('<div class="'+col+'">');endingDiv=true}}else if(isFieldStart&&this.formStyle==="horizontal"){html.push('<div class="col-xs-offset-4 '+col+'">');endingDiv=true}if("radio"===type){if(field.options){_.each(field.options,function(choice){var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;var selected=value===optionValue;html.push('<div class="radio"><label>');html.push('<input style="'+style+'" value="'+optionValue+'" name="'+field.name+'" type="radio"');if(selected){html.push(" checked")}html.push("> ");if(choice.icon){html.push('<span class="'+choice.icon+'"></span> ')}optionText=optionText[0].toUpperCase()+optionText.substring(1);html.push(optionText);html.push("</label></div>")})}else{html.push('<div class="radio"><label>');html.push('<input style="'+style+'" value="'+value+'" name="'+name+'" id="'+id+'" type="radio"');if(field.checked){html.push(" checked")}html.push("> ");html.push(value[0].toUpperCase()+value.substring(1));html.push("</label></div>")}}else if("checkbox"===type){html.push('<div class="checkbox"><label>');html.push('<input style="'+style+'" name="'+name+'" id="'+id+'" type="checkbox"');if(value){html.push(" checked")}if(disabled){html.push(" disabled")}html.push("> ");html.push(title);html.push("</label></div>")}else if("checkbox-list"===type){html.push('<div name="'+name+'" class="checkbox-list"><div>')}else if("select"==type||type=="bootstrap-select"){if(type=="bootstrap-select"){html.push('<select style="'+style+'" data-live-search="'+(field.search?true:false)+'" data-selected-text-format="count" name="'+name+'" id="'+id+'" data-actions-box="'+(field.selectAll?true:false)+'" class="selectpicker'+(this.formStyle!=="inline"?" form-control":"")+'"')}else{html.push('<select style="'+style+'" name="'+name+'" id="'+id+'" class="form-control"')}if(disabled){html.push(" disabled")}if(field.multiple){html.push(" multiple")}html.push(">");_.each(field.options,function(choice){if(choice&&choice.divider){html.push('<option data-divider="true"></option>')}else{html.push('<option value="');var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;html.push(optionValue);html.push('"');var selected=false;if(_.isObject(value)){selected=value[optionValue]}else if(_.isArray(value)){selected=value.indexOf(optionValue)!==-1}else{selected=value==optionValue}if(selected){html.push(" selected")}html.push(">");html.push(optionText);html.push("</option>")}});html.push("</select>");if(field.type=="bootstrap-select"&&field.toggle){html.push('<p class="help-block"><a data-name="'+name+'_all" href="#">All</a>&nbsp;|&nbsp;<a data-name="'+name+'_none" href="#">None</a></p>');_this.$form.on("click","[data-name="+name+"_all]",function(evt){evt.preventDefault();var $select=_this.$form.find("[name="+name+"]");$select.selectpicker("val",$.map($select.find("option"),function(o){return $(o).val()}));$select.trigger("change")});_this.$form.on("click","[data-name="+name+"_none]",function(evt){evt.preventDefault();var $select=_this.$form.find("[name="+name+"]");$select.selectpicker("val",[]);$select.trigger("change")})}}else if("textarea"==type){html.push('<textarea style="'+style+'" id="'+id+'" class="form-control" name="'+name+'"');if(required){html.push(" required")}if(field.placeholder){html.push(' placeholder="'+field.placeholder+'"')}if(disabled){html.push(" disabled")}html.push(">");if(value!=null){html.push(value)}html.push("</textarea>")}else if("button"==type){html.push('<button style="'+style+'" id="'+id+'" name="'+name+'" type="button" class="btn btn-default btn-sm">');if(field.icon){html.push('<span class="'+field.icon+'"></span> ')}html.push(value?value:title);html.push("</button>")}else if("custom"===type){html.push(value)}else if("file"===type){var isMultiple=field.multiple==null?false:field.multiple;html.push('<select data-multiple="'+isMultiple+'" data-type="file" title="'+(field.placeholder||(isMultiple?"Choose one or more files...":"Choose a file..."))+'" name="'+name+'_picker" data-width="35%" class="file-input selectpicker form-control">');var options=[];if(field.options){options=options.concat(field.options)}options.push("My Computer");options.push("URL");if(field.text!=null){options.push(field.text)}_.each(options,function(choice,index){var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;html.push('<option value="');html.push(optionValue);html.push('"');if(isChoiceObject&&choice.disabled){html.push(" disabled")}if(optionValue==="Dropbox"){html.push(' data-icon="fa fa-dropbox"')}else if(optionValue==="My Computer"){html.push(' data-icon="fa fa-desktop"')}else if(optionValue==="URL"){html.push(' data-icon="fa fa-external-link"')}html.push(">");html.push(optionText);html.push("</option>")});html.push("</select>");html.push("<div>");html.push('<input placeholder="'+(isMultiple?"Enter one or more URLs":"Enter a URL")+'" class="form-control" style="width:50%; display:none;" type="text" name="'+name+'_url">');if(field.text){html.push('<input class="form-control" style="width:50%; display:none;" type="text" name="'+name+'_text">')}html.push("</div>");html.push('<input style="display:none;" type="file" name="'+name+'_file"'+(isMultiple?" multiple":"")+">");_this.$form.on("change","[name="+name+"_picker]",function(evt){var $this=$(this);var val=$this.val();var showUrlInput=val==="URL";var showTextInput=val===field.text;if("Dropbox"===val){var options={success:function(results){var val=!isMultiple?results[0].link:results.map(function(result){return result.link});_this.setValue(name,val);_this.trigger("change",{name:name,value:val})},linkType:"direct",multiselect:isMultiple};Dropbox.choose(options);_this.$form.find("[name="+name+"_picker]").selectpicker("val","")}else if("My Computer"===val){_this.$form.find("[name="+name+"_file]").click();_this.$form.find("[name="+name+"_picker]").selectpicker("val","")}_this.$form.find("[name="+name+"_url]").css("display",showUrlInput?"":"none");_this.$form.find("[name="+name+"_text]").css("display",showTextInput?"":"none")});_this.$form.on("keyup","[name="+name+"_url]",function(evt){var text=$.trim($(this).val());if(isMultiple){text=text.split(",").filter(function(t){t=$.trim(t);return t!==""})}_this.setValue(name,text);if(evt.which===13){_this.trigger("change",{name:name,value:text})}});_this.$form.on("keyup","[name="+name+"_text]",function(evt){var text=$.trim($(this).val());_this.setValue(name,text);if(evt.which===13){_this.trigger("change",{name:name,value:text})}});_this.$form.on("change","[name="+name+"_file]",function(evt){var files=evt.target.files;_this.setValue(name,isMultiple?files:files[0]);_this.trigger("change",{name:name,value:isMultiple?files:files[0]})})}else{type=type==null?"text":type;if(type==="div"){html.push('<div name="'+name+'" id="'+id+'"')}else{html.push('<input style="'+style+'" type="'+type+'" class="form-control" name="'+name+'" id="'+id+'"')}if(value!=null){html.push(' value="'+value+'"')}if(field.placeholder){html.push(' placeholder="'+field.placeholder+'"')}if(field.min!=null){html.push(' min="'+field.min+'"')}if(field.max!=null){html.push(' max="'+field.max+'"')}if(field.step){html.push(' step="'+field.step+'"')}if(required){html.push(" required")}if(disabled){html.push(" disabled")}if(field.autocomplete!=null){html.push(' autocomplete="'+field.autocomplete+'"')}html.push(">");if(type==="div"){html.push("</div>")}}if(help!==undefined){html.push('<span data-name="'+name+'_help" class="help-block">');html.push(help);html.push("</span>")}return endingDiv},append:function(fields){var html=[];var _this=this;var isArray=morpheus.Util.isArray(fields);if(!isArray){fields=[fields]}html.push('<div class="form-group">');var endingDiv=false;_.each(fields,function(field,index){endingDiv||_this._append(html,field,index===0)});html.push("</div>");if(endingDiv){html.push("</div>")}var $div=$(html.join(""));this.$form.append($div);var checkBoxLists=$div.find(".checkbox-list");if(checkBoxLists.length>0){var checkBoxIndex=0;_.each(fields,function(field){if(field.type==="checkbox-list"){var list=new morpheus.CheckBoxList({responsive:false,$el:$(checkBoxLists[checkBoxIndex]),items:field.options});$(checkBoxLists[checkBoxIndex]).data("morpheus.checkbox-list",list);checkBoxIndex++}})}$div.find(".selectpicker").selectpicker({iconBase:"fa",tickIcon:"fa-check",style:"btn-default btn-sm"})},clear:function(){this.$form.empty()},getValue:function(name){var $v=this.$form.find("[name="+name+"]");if($v.length===0){$v=this.$form.find("[name="+name+"_picker]")}return morpheus.FormBuilder.getValue($v)},setOptions:function(name,options,selectFirst){var $select=this.$form.find("[name="+name+"]");var checkBoxList=$select.data("morpheus.checkbox-list");if(checkBoxList){checkBoxList.setItems(options)}else{var html=[];var selection=$select.val();_.each(options,function(choice){var isChoiceObject=_.isObject(choice)&&choice.value!==undefined;if(choice&&choice.divider){html.push('<option data-divider="true"></option>')}else{html.push('<option value="');var optionValue=isChoiceObject?choice.value:choice;var optionText=isChoiceObject?choice.name:choice;html.push(optionValue);html.push('"');html.push(">");html.push(optionText);html.push("</option>")}});$select.html(html.join(""));$select.val(selection);if(selectFirst&&$select.val()==null){if($select[0].options.length>0){$select.val($select[0].options[0].value)}}if($select.hasClass("selectpicker")){$select.selectpicker("refresh");$select.selectpicker("render")}}},find:function(name){return this.$form.find("[name="+name+"]")},setHelpText:function(name,value){var v=this.$form.find("[data-name="+name+"_help]");v.html(value)},setValue:function(name,value){var v=this.$form.find("[name="+name+"]");if(v.length===0){v=this.$form.find("[name="+name+"_picker]");if(v.data("type")==="file"){v.val(value);v.selectpicker("render");v.data("files",value);return}}var type=v.attr("type");var list=v.data("morpheus.checkbox-list");if(list){list.setValue(value)}else{if(type==="radio"){v.filter("[value="+value+"]").prop("checked",true)}else if(type==="checkbox"){v.prop("checked",value)}else{v.val(value)}if(v.hasClass("selectpicker")){v.selectpicker("render")}}},setVisible:function(name,visible){var $div=this.$form.find("[name="+name+"]").parents(".form-group");if(visible){$div.show()}else{$div.hide()}},remove:function(name){var $div=this.$form.find("[name="+name+"]").parents(".form-group");$div.remove()},setEnabled:function(name,enabled){var $div=this.$form.find("[name="+name+"]");$div.attr("disabled",!enabled);if(!enabled){$div.parents(".form-group").find("label").addClass("text-muted")}else{$div.parents(".form-group").find("label").removeClass("text-muted")}}};morpheus.Util.extend(morpheus.FormBuilder,morpheus.Events);morpheus.GradientColorSupplier=function(){morpheus.AbstractColorSupplier.call(this);this._updateScale()};morpheus.GradientColorSupplier.prototype={createInstance:function(){return new morpheus.GradientColorSupplier},getColor:function(row,column,value){if(isNaN(value)){return this.missingColor}var min=this.min;var max=this.max;var colors=this.colors;if(value<=min){return colors[0]}else if(value>=max){return colors[colors.length-1]}var fraction=morpheus.SteppedColorSupplier.linearScale(value,min,max,0,100)/100;return this.colorScale(fraction)},setFractions:function(options){morpheus.AbstractColorSupplier.prototype.setFractions.call(this,options);this._updateScale()},_updateScale:function(){this.colorScale=d3.scale.linear().domain(this.fractions).range(this.colors).clamp(true)}};morpheus.Util.extend(morpheus.GradientColorSupplier,morpheus.AbstractColorSupplier);morpheus.Grid=function(options){this.options=options;var _this=this;var grid;this.items=options.items;this.modelToView=null;this.viewOrder=null;function getItemColumnValue(item,column){return column.getter(item)}this.filter=new morpheus.CombinedGridFilter;var model={getLength:function(){return _this.viewOrder!=null?_this.viewOrder.length:_this.items.length},getItem:function(index){return _this.items[_this.viewOrder!=null?_this.viewOrder[index]:index]}};this.$el=options.$el;var gridOptions=$.extend({},{select:true,headerRowHeight:0,showHeaderRow:false,multiColumnSort:true,multiSelect:false,topPanelHeight:0,enableColumnReorder:false,enableTextSelectionOnCells:true,forceFitColumns:true,dataItemColumnValueExtractor:getItemColumnValue,defaultFormatter:function(row,cell,value,columnDef,dataContext){if(_.isNumber(value)){return morpheus.Util.nf(value)}else if(morpheus.Util.isArray(value)){var s=[];for(var i=0,length=value.length;i<length;i++){if(i>0){s.push(", ")}var val=value[i];s.push(value[i])}return s.join("")}else{return value}}},options.gridOptions||{});grid=new Slick.Grid(options.$el,model,options.columns,gridOptions);this.grid=grid;grid.registerPlugin(new morpheus.AutoTooltips2);grid.onCellChange.subscribe(function(e,args){_this.trigger("edit",args)});if(gridOptions.select){grid.setSelectionModel(new Slick.RowSelectionModel({selectActiveRow:true,multiSelect:gridOptions.multiSelect}));grid.getSelectionModel().onSelectedRangesChanged.subscribe(function(e){var nitems=grid.getDataLength();_this.trigger("selectionChanged",{selectedRows:grid.getSelectedRows().filter(function(row){return row>=0&&row<=nitems})})})}grid.onSort.subscribe(function(e,args){_this.sortCols=args.sortCols;_this._updateMappings();grid.invalidate()});options.$el.on("click",function(e){var cell=grid.getCellFromEvent(e);if(cell){_this.trigger("click",{row:cell.row,target:e.target})}});options.$el.on("dblclick",function(e){var cell=grid.getCellFromEvent(e);if(cell){_this.trigger("dblclick",{row:cell.row,target:e.target})}});if(options.sort){var gridSortColumns=[];var gridColumns=grid.getColumns();var sortCols=[];options.sort.forEach(function(c){var column=null;for(var i=0;i<gridColumns.length;i++){if(gridColumns[i].name===c.name){column=gridColumns[i];break}}if(column!=null){gridSortColumns.push({columnId:column.id,sortAsc:c.sortAsc})}else{console.log(c.name+" not found.")}});this.setSortColumns(gridSortColumns)}this.grid.invalidate()};morpheus.Grid.prototype={columnsAutosized:false,setSortColumns:function(gridSortColumns){this.grid.setSortColumns(gridSortColumns);this.sortCols=[];for(var i=0;i<gridSortColumns.length;i++){var column=this.grid.getColumns()[this.grid.getColumnIndex(gridSortColumns[i].columnId)];if(column==null){throw"Unable to find column "+gridSortColumns[i]}this.sortCols.push({sortCol:column,sortAsc:gridSortColumns[i].sortAsc})}this._updateMappings();this.grid.invalidate()},setColumns:function(columns){this.grid.setColumns(columns);this.grid.resizeCanvas();this.grid.invalidate()},getColumns:function(){return this.grid.getColumns()},getSelectedRows:function(){var nitems=this.grid.getDataLength();return this.grid.getSelectedRows().filter(function(row){return row>=0&&row<=nitems})},getSelectedItems:function(){var rows=this.grid.getSelectedRows();var selection=[];for(var i=0,nrows=rows.length;i<nrows;i++){selection.push(this.items[this.convertViewIndexToModel(rows[i])])}return selection},getSelectedItem:function(){var rows=this.grid.getSelectedRows();if(rows.length===1){return this.items[this.convertViewIndexToModel(rows[0])]}return null},getItems:function(){var items=[];for(var i=0,length=this.getFilteredItemCount();i<length;i++){items.push(this.items[this.convertViewIndexToModel(i)])}return items},getAllItemCount:function(){return this.items.length},getAllItems:function(){return this.items},getFilteredItemCount:function(){return this.viewOrder?this.viewOrder.length:this.items.length},redraw:function(){this.grid.invalidate()},redrawRows:function(rows){this.grid.invalidateRows(rows);this.grid.render()},setItems:function(items){this.items=items;if(this.grid.getSelectionModel()){this.grid.setSelectedRows([])}this.setFilter(this.filter);this.maybeAutoResizeColumns()},maybeAutoResizeColumns:function(){if(!this.columnsAutosized){this.autosizeColumns()}},convertModelIndexToView:function(modelIndex){if(this.modelToView!==null){var index=this.modelToView.get(modelIndex);return index!==undefined?index:-1}return modelIndex},convertViewIndexToModel:function(viewIndex){return this.viewOrder!=null?viewIndex<this.viewOrder.length&&viewIndex>=0?this.viewOrder[viewIndex]:-1:viewIndex},_updateMappings:function(){var selectedViewIndices=this.grid.getSelectionModel()!=null?this.grid.getSelectedRows():null;var selectedModelIndices=[];if(selectedViewIndices){for(var i=0,length=selectedViewIndices.length;i<length;i++){selectedModelIndices.push(this.convertViewIndexToModel(selectedViewIndices[i]))}}this.viewOrder=null;if(this.filter!=null){this.filter.init();if(!this.filter.isEmpty()){this.viewOrder=[];for(var i=0,length=this.items.length;i<length;i++){if(this.filter.accept(this.items[i])){this.viewOrder.push(i)}}}}var cols=this.sortCols;if(cols&&cols.length>0){if(this.viewOrder==null){this.viewOrder=[];for(var i=0,length=this.items.length;i<length;i++){this.viewOrder.push(i)}}var ncols=cols.length;var items=this.items;this.viewOrder.sort(function(index1,index2){for(var i=0;i<ncols;i++){var getter=cols[i].sortCol.getter;var comparator=cols[i].sortAsc?morpheus.SortKey.ASCENDING_COMPARATOR:morpheus.SortKey.DESCENDING_COMPARATOR;var value1=getter(items[index1]);var value2=getter(items[index2]);var result=comparator(value1,value2);if(result!==0){return result}}return 0})}if(this.viewOrder!=null){this.modelToView=new morpheus.Map;for(var i=0,length=this.viewOrder.length;i<length;i++){this.modelToView.set(this.viewOrder[i],i)}}else{this.modelToView=null}if(this.grid.getSelectionModel()!=null){var newSelectedViewIndices=[];for(var i=0,length=selectedModelIndices.length;i<length;i++){var index=this.convertModelIndexToView(selectedModelIndices[i]);if(index!==undefined){newSelectedViewIndices.push(index)}}this.grid.setSelectedRows(newSelectedViewIndices)}},setSelectedRows:function(rows){this.grid.setSelectedRows(rows)},setFilter:function(filter){this.filter=filter;this._updateMappings();this.grid.invalidate();this.trigger("filter")},getFilter:function(){return this.filter},autosizeColumns:function(){var columns=this.grid.getColumns();var items=this.getItems();if(!items||items.length===0||!columns||columns.length===0){return}var gridWidth=this.options.$el.width()-30;if(gridWidth<=0){return}this.columnsAutosized=true;if(columns.length>-1){var div=document.createElement("div");document.body.appendChild(div);var $d=$(div);$d.css({position:"absolute",left:-1e3,top:-1e3});var $row=$('<div class="slick-table">'+'<div class="ui-state-default slick-header-column slick-header-sortable ui-sortable-handle"></div>'+'<div class="ui-widget-content slick-row"><div class="slick-cell selected"></div></div>'+"</div>");var $cell=$row.find(".slick-cell");var $header=$row.find(".slick-header-column");$row.appendTo($d);var maxWidth=Math.min(parseInt(gridWidth/2),400);var getColumnWidth=function(column){var w=$header.html(column.name).outerWidth()+13;if(column.prototypeValue){$cell.html(column.prototypeValue);w=Math.max($cell.outerWidth(),w)}else{for(var i=0,nrows=Math.min(items.length,10);i<nrows;i++){var html=column.formatter(i,null,column.getter(items[i]),column,items[i]);var $html=$(html);$html.find(".slick-cell-wrapper").attr("class","");$cell.html($html);w=Math.max($cell.outerWidth(),w)}}column.width=parseInt(Math.min(maxWidth,w))};var totalWidth=0;for(var i=0;i<columns.length;i++){getColumnWidth(columns[i]);totalWidth+=columns[i].width}if(totalWidth<gridWidth){}else if(totalWidth>gridWidth){}$d.remove();this.grid.resizeCanvas()}}};morpheus.Util.extend(morpheus.Grid,morpheus.Events);morpheus.AutoTooltips2=function(options){var _grid;var _self=this;var tip;function init(grid){_grid=grid;$(_grid.getCanvasNode()).on("mouseover",".slick-row",showToolTip);$(_grid.getCanvasNode()).on("mouseout",".slick-row",hideToolTip);$(_grid.getCanvasNode()).on("mouseup",hideAll)}function destroy(){$(_grid.getCanvasNode()).off("mouseover",showToolTip);$(_grid.getCanvasNode()).off("mouseout",hideToolTip);$(_grid.getCanvasNode()).off("mouseup",hideAll)}function hideToolTip(e){var cell=_grid.getCellFromEvent(e);if(cell){var $node=$(_grid.getCellNode(cell.row,cell.cell));if($node.data("bs.tooltip")){$node.tooltip("hide")}}}function hideAll(){$(_grid.getCanvasNode()).find("[data-original-title]").attr("data-original-title","").tooltip("hide")}function hideHeaderToolTip(e){var $node=$(e.target);if($node.data("bs.tooltip")){$node.tooltip("hide")}}function showHeaderToolTip(e){var show=false;var $node=$(e.target);if($node[0].scrollWidth>$node[0].offsetWidth){show=true;var $name=$node.find(".slick-column-name");if(!$node.data("bs.tooltip")){$node.tooltip({placement:"auto",html:true,container:"body",trigger:"manual"})}$node.attr("data-original-title",$name.text());if(show){$node.tooltip("show")}else{$node.tooltip("hide")}}}function showToolTip(e){var cell=_grid.getCellFromEvent(e);if(cell){var $node=$(_grid.getCellNode(cell.row,cell.cell));var text="";var c=_grid.getColumns()[cell.cell];var show=false;var $checkNode=$node.find(".slick-cell-wrapper");if(c.alwaysShowTooltip||$checkNode[0].scrollWidth>$checkNode[0].offsetWidth){var item=_grid.getDataItem(cell.row);text=c.tooltip(item,c.getter(item));show=true}$node.attr("data-original-title",text);var hasTip=$node.data("bs.tooltip");if(!hasTip){$node.tooltip({placement:"auto",html:true,container:"body",trigger:"manual"})}if(show){$node.tooltip("show")}else if(hasTip){$node.tooltip("hide")}}}function handleHeaderMouseEnter(e,args){var column=args.column,$node=$(e.target).closest(".slick-header-column");if(!column.toolTip){$node.attr("title",$node.innerWidth()<$node[0].scrollWidth?column.name:"")}}$.extend(this,{init:init,destroy:destroy})};morpheus.CombinedGridFilter=function(){this.filters=[]};morpheus.CombinedGridFilter.prototype={add:function(filter){this.filters.push(filter)},getFilters:function(){return this.filters},get:function(index){return this.filters[index]},set:function(index,f){this.filters[index]=f},init:function(){for(var i=0;i<this.filters.length;i++){this.filters[i].init()}this.activeFilters=this.filters.filter(function(f){return!f.isEmpty()});this.nActiveFilters=this.activeFilters.length},accept:function(item){for(var i=0;i<this.nActiveFilters;i++){if(!this.activeFilters[i].accept(item)){return false}}return true},isEmpty:function(){return this.activeFilters.length===0}};morpheus.HeatMapColorSchemeChooser=function(options){var _this=this;this.$div=$("<div></div>");this.currentValue=null;this.legend=new morpheus.LegendWithStops;this.colorScheme=options.colorScheme||new morpheus.HeatMapColorScheme(new morpheus.Project(new morpheus.Dataset({rows:0,columns:0})));this.legend.on("added",function(e){var fractions=_this.colorScheme.getFractions();fractions.push(e.fraction);var colors=_this.colorScheme.getColors();colors.push("black");_this.colorScheme.setFractions({fractions:fractions,colors:colors});var newIndex=_this.getFractionIndex(e.fraction,"black");_this.setSelectedIndex(newIndex);_this.fireChanged()}).on("selectedIndex",function(e){_this.setSelectedIndex(e.selectedIndex)}).on("delete",function(index){_this.deleteSelectedStop()}).on("moved",function(e){var fraction=e.fraction;var fractions=_this.colorScheme.getFractions();fractions[_this.legend.selectedIndex]=fraction;var color=_this.colorScheme.getColors()[_this.legend.selectedIndex];_this.colorScheme.setFractions({fractions:fractions,colors:_this.colorScheme.getColors()});_this.legend.selectedIndex=_this.getFractionIndex(e.fraction,color);var fractionToValue=d3.scale.linear().domain([0,1]).range([_this.colorScheme.getMin(),_this.colorScheme.getMax()]).clamp(true);_this.formBuilder.setValue("selected_value",fractionToValue(fractions[_this.legend.selectedIndex]));_this.fireChanged()});var $row=$("<div></div>");$row.css("height","50px").css("width","300px").css("margin-left","auto").css("margin-right","auto");$row.appendTo(this.$div);$(this.legend.canvas).appendTo($row);var formBuilder=new morpheus.FormBuilder;var items=[];items=items.concat({name:"selected_color",type:"color",style:"max-width: 50px;"},{name:"selected_value",type:"text",style:"max-width: 100px;"},[{name:"delete",type:"button",value:"Delete Selected Color Stop"},{name:"add",type:"button",value:"Add Color Stop"}],{name:"minimum",type:"text",style:"max-width: 100px;"},{name:"maximum",type:"text",style:"max-width: 100px;"});if(options.showRelative){items=items.concat({name:"relative_color_scheme",type:"checkbox",help:"A relative color scheme uses the minimum and maximum values in each row"+" to convert values to colors"});items=items.concat({name:"transform_values",type:"select",value:0,options:[{name:"None",value:0},{name:"Subtract row mean, divide by row standard deviation",value:morpheus.AbstractColorSupplier.Z_SCORE},{name:"Subtract row median, divide by row median absolute deviation",value:morpheus.AbstractColorSupplier.ROBUST_Z_SCORE}]})}items=items.concat({name:"missing_color",type:"color",style:"max-width: 50px;"});items.push({name:"stepped_colors",type:"checkbox",value:false,help:"Intervals include left end point and exclude right end point, except for the highest interval"});_.each(items,function(item){formBuilder.append(item)});this.getFractionIndex=function(fraction,color){var fractions=_this.colorScheme.getFractions();var colors=_this.colorScheme.getColors();for(var i=0,len=fractions.length;i<len;i++){if(fractions[i]===fraction&&colors[i]===color){return i}}return-1};this.$div.append(formBuilder.$form);formBuilder.$form.find("[name^=selected],[name=delete]").prop("disabled",true);formBuilder.$form.find("[name=add]").on("click",function(e){var fractions=_this.colorScheme.getFractions();var val=.5;while(val>=0&&_.indexOf(fractions,val)!==-1){val-=.1}val=Math.max(0,val);fractions.push(val);var colors=_this.colorScheme.getColors();colors.push("black");_this.colorScheme.setFractions({fractions:fractions,colors:colors});var newIndex=_this.getFractionIndex(e.fraction,"black");_this.setSelectedIndex(newIndex);_this.fireChanged()});formBuilder.$form.find("[name=delete]").on("click",function(e){_this.deleteSelectedStop()});formBuilder.$form.find("[name=transform_values]").on("change",function(e){_this.colorScheme.setTransformValues(parseInt(formBuilder.getValue("transform_values")));_this.fireChanged()});formBuilder.$form.on("keyup","[name=selected_value]",_.debounce(function(e){var val=parseFloat($(this).val());if(!isNaN(val)){_this.setSelectedValue(val);_this.fireChanged()}},100));formBuilder.$form.on("change","[name=selected_color]",function(e){var colors=_this.colorScheme.getColors();colors[_this.legend.selectedIndex]=$(this).val();_this.colorScheme.setFractions({fractions:_this.colorScheme.getFractions(),colors:colors});_this.fireChanged()});formBuilder.$form.on("change","[name=missing_color]",function(e){var color=$(this).val();_this.colorScheme.setMissingColor(color);_this.fireChanged(false)});formBuilder.$form.on("change","[name=stepped_colors]",function(e){_this.colorScheme.setStepped($(this).prop("checked"));_this.fireChanged()});formBuilder.$form.on("keyup","[name=minimum]",_.debounce(function(e){var val=parseFloat($(this).val());if(!isNaN(val)){_this.colorScheme.setMin(val);_this.setSelectedIndex(_this.legend.selectedIndex);_this.fireChanged(false)}},100));formBuilder.$form.on("keyup","[name=maximum]",_.debounce(function(e){var val=parseFloat($(this).val());if(!isNaN(val)){_this.colorScheme.setMax(val);_this.setSelectedIndex(_this.legend.selectedIndex);_this.fireChanged(false)}},100));formBuilder.$form.on("change","[name=relative_color_scheme]",_.throttle(function(e){_this.legend.selectedIndex=-1;var scalingMode=$(this).prop("checked")?morpheus.HeatMapColorScheme.ScalingMode.RELATIVE:morpheus.HeatMapColorScheme.ScalingMode.FIXED;_this.colorScheme.setScalingMode(scalingMode);_this.setColorScheme(_this.colorScheme);_this.fireChanged()},100));this.formBuilder=formBuilder};morpheus.HeatMapColorSchemeChooser.prototype={deleteSelectedStop:function(){var fractions=this.colorScheme.getFractions();fractions.splice(this.legend.selectedIndex,1);var colors=this.colorScheme.getColors();colors.splice(this.legend.selectedIndex,1);this.colorScheme.setFractions({fractions:fractions,colors:colors});this.formBuilder.$form.find("[name^=selected],[name=delete]").prop("disabled",true);this.legend.setSelectedIndex(-1);this.fireChanged()},setSelectedValue:function(val){var valueToFraction=d3.scale.linear().domain([this.colorScheme.getMin(),this.colorScheme.getMax()]).range([0,1]).clamp(true);var fractions=this.colorScheme.getFractions();var fraction=valueToFraction(val);fractions[this.legend.selectedIndex]=fraction;var color=this.colorScheme.getColors()[this.legend.selectedIndex];this.colorScheme.setFractions({fractions:fractions,colors:this.colorScheme.getColors()});this.legend.selectedIndex=this.getFractionIndex(fraction,color)},setSelectedIndex:function(index){var fractions=this.colorScheme.getFractions();if(index>=fractions.length){index=-1}this.legend.setSelectedIndex(index);var formBuilder=this.formBuilder;formBuilder.$form.find("[name^=selected],[name=delete]").prop("disabled",this.legend.selectedIndex===-1);if(this.legend.selectedIndex!==-1){var fractionToValue=d3.scale.linear().domain([0,1]).range([this.colorScheme.getMin(),this.colorScheme.getMax()]).clamp(true);formBuilder.setValue("selected_value",fractionToValue(fractions[this.legend.selectedIndex]));var context=this.legend.canvas.getContext("2d");var colors=this.colorScheme.getColors();context.fillStyle=colors[this.legend.selectedIndex];formBuilder.setValue("selected_color",context.fillStyle)}else{formBuilder.setValue("selected_value","")}this.draw()},setMinMax:function(){if(this.colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){this.colorScheme.setMin(0);this.colorScheme.setMax(1)}},dispose:function(){this.off("change");this.legend.destroy();this.formBuilder.$form.off("keyup","input");this.formBuilder.$form.off("change","[name=relative_color_scheme]")},restoreCurrentValue:function(){if(this.colorScheme.setCurrentValue){this.colorScheme.setCurrentValue(this.currentValue)}},setCurrentValue:function(value){this.currentValue=value;if(this.colorScheme&&this.colorScheme.setCurrentValue){this.colorScheme.setCurrentValue(this.currentValue)}this.setColorScheme(this.colorScheme)},setColorScheme:function(colorScheme){this.colorScheme=colorScheme;this.setMinMax();if(colorScheme.setCurrentValue){colorScheme.setCurrentValue(this.currentValue)}this.formBuilder.setValue("relative_color_scheme",colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE?true:false);this.formBuilder.setValue("transform_values",colorScheme.getTransformValues());this.formBuilder.setEnabled("transform_values",colorScheme.getScalingMode()!==morpheus.HeatMapColorScheme.ScalingMode.RELATIVE);this.formBuilder.$form.find("[name=minimum],[name=maximum]").prop("disabled",colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE);this.formBuilder.setValue("minimum",this.colorScheme.getMin());this.formBuilder.setValue("maximum",this.colorScheme.getMax());this.formBuilder.setValue("stepped_colors",this.colorScheme.isStepped());this.formBuilder.setValue("missing_color",this.colorScheme.getMissingColor());this.draw()},getFractionToStopPix:function(){return d3.scale.linear().clamp(true).domain([0,1]).range([this.legend.border,this.legend.getUnscaledWidth()-this.legend.border])},fireChanged:function(noreset){this.trigger("change");if(noreset!==false){this.setColorScheme(this.colorScheme)}},draw:function(){var colorScheme=this.colorScheme;if(colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){colorScheme.setMin(0);colorScheme.setMax(1)}var fractions=colorScheme.getFractions();var colors=colorScheme.getColors();var fractionToStopPix=this.getFractionToStopPix();this.legend.draw(fractions,colors,colorScheme.isStepped(),fractionToStopPix)}};morpheus.Util.extend(morpheus.HeatMapColorSchemeChooser,morpheus.Events);morpheus.HeatMapColorSchemeLegend=function(heatMap,$keyContent){var colorScheme=heatMap.heatmap.getColorScheme();var colorByValues=colorScheme.getColorByValues();var totalHeight;$keyContent.empty();var ntracks=colorByValues.length;colorByValues.forEach(function(value){if(value!=null||ntracks===1){if(value!="null"){var $label=$('<div style="overflow:hidden;text-overflow:'+' ellipsis;width:250px;max-width:250px;">'+value+"</div>");$keyContent.append($label);totalHeight+=$label.height()}var trackLegend=new morpheus.ColorSupplierLegend(colorScheme,value);$(trackLegend.canvas).css("position","");trackLegend.repaint();trackLegend.on("selectionChanged",function(){heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()});$keyContent.append($(trackLegend.canvas));totalHeight+=trackLegend.getUnscaledHeight()}});if(heatMap.options.$key){$keyContent.append(heatMap.options.$key);totalHeight+=heatMap.options.$key.height()}var $edit=$('<div style="padding-left:4px; display:inline;"><a data-name="options"'+' href="#">Edit</a></div>');$edit.find("[data-name=options]").on("click",function(e){e.preventDefault();heatMap.showOptions();morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"options"})});totalHeight+=$edit.height();$keyContent.append($edit);$keyContent.css({"text-overflow":"ellipsis",overflow:"hidden",width:250+"px",height:totalHeight+"px"})};morpheus.HeatMapColorSchemeLegend.drawColorScheme=function(context,colorScheme,width,printing,hideText,legendHeight){if(!legendHeight){legendHeight=12}context.font="11px "+morpheus.CanvasUtil.getFontFamily(context);var names=colorScheme.getNames();var hasNames=names!=null;if(hasNames){morpheus.HeatMapColorSchemeLegend.drawColorSchemeVertically(context,colorScheme,colorScheme.getHiddenValues(),printing)}else{morpheus.HeatMapColorSchemeLegend.draw(context,colorScheme.getFractions(),colorScheme.getColors(),width,legendHeight,colorScheme.isStepped());context.strokeStyle="LightGrey";context.strokeRect(0,0,width,legendHeight);if(hideText){return}var map=d3.scale.linear().domain([0,1]).range([0,width]).clamp(true);var fractionToValue=d3.scale.linear().domain([0,1]).range([colorScheme.getMin(),colorScheme.getMax()]).clamp(true);context.textAlign="center";context.textBaseline="top";context.fillStyle="black";if(colorScheme.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){context.fillText("row min",0,14);context.fillText("row max",width,legendHeight+2)}else{var fractions=colorScheme.getFractions();var lastTextPixEnd=-1;var halfway=parseInt(fractions.length/2);for(var i=0;i<halfway;i++){var pix=map(fractions[i]);var text="";if(hasNames){text=names[i]!=""?names[i]+" ("+fractionToValue(fractions[i])+")":names[i]}else{text=morpheus.Util.nf(fractionToValue(fractions[i]))}var textWidth=context.measureText(text).width;if(pix>lastTextPixEnd){context.fillText(text,pix,legendHeight+2)}lastTextPixEnd=pix+textWidth/2}var lastTextPixStart=1e4;for(var i=fractions.length-1;i>=halfway;i--){var pix=map(fractions[i]);var text="";if(hasNames){text=names[i]!=""?names[i]+" ("+fractionToValue(fractions[i])+")":names[i]}else{text=morpheus.Util.nf(fractionToValue(fractions[i]))}var textWidth=context.measureText(text).width;var textPixEnd=pix+textWidth/2;if(textPixEnd<lastTextPixStart){context.fillText(text,pix,legendHeight+2);lastTextPixStart=pix-textWidth/2}}}}};morpheus.HeatMapColorSchemeLegend.drawColorSchemeVertically=function(context,colorScheme,hiddenValues,printing){var fractionToValue=d3.scale.linear().domain([0,1]).range([colorScheme.getMin(),colorScheme.getMax()]).clamp(true);context.textAlign="left";context.textBaseline="top";context.fillStyle="black";var fractions=colorScheme.getFractions();var colors=colorScheme.getColors();var names=colorScheme.getNames();context.strokeStyle="LightGrey";var xpix=0;var ypix=0;context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);for(var i=0;i<colors.length;i++){var name=names[i];if(name!=null){context.fillStyle=colors[i];context.fillRect(xpix,ypix,12,12);context.strokeRect(xpix,ypix,12,12);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;if(hiddenValues&&!printing){var value=fractionToValue(fractions[i]);context.font="12px FontAwesome";if(!hiddenValues.has(value)){context.fillText("",-14,ypix)}context.font="12px "+morpheus.CanvasUtil.getFontFamily(context)}context.fillText(name,xpix+16,ypix)}ypix+=14}};morpheus.HeatMapColorSchemeLegend.draw=function(context,fractions,colors,width,height,stepped){if(!stepped){var gradient=context.createLinearGradient(0,0,width,height);for(var i=0,length=fractions.length;i<length;i++){gradient.addColorStop(fractions[i],colors[i])}context.fillStyle=gradient;context.fillRect(0,0,width,height)}else{var map=d3.scale.linear().domain([0,1]).range([0,width]).clamp(true);for(var i=0,length=fractions.length;i<length;i++){context.fillStyle=colors[i];var x1=map(fractions[i]);var x2=i===length-1?width:map(fractions[i+1]);context.fillRect(Math.min(x1,x2),0,Math.abs(x2-x1),height)}}};morpheus.ColorSupplierLegend=function(colorScheme,value){morpheus.AbstractCanvas.call(this,false);var _this=this;this.value=value;this.colorScheme=colorScheme;colorScheme.setCurrentValue(value);var hiddenValues=colorScheme.getHiddenValues();var names=colorScheme.getNames();var hasNames=names!=null;var legendHeight=hasNames?names.length*14:30;var bounds={width:250,height:legendHeight};this.hasNames=hasNames;this.setBounds(bounds);if(hasNames&&hiddenValues){$(this.canvas).on("click",function(e){e.preventDefault();e.stopPropagation();var clickedRow=Math.floor((e.clientY-_this.canvas.getBoundingClientRect().top)/14);var fractionToValue=d3.scale.linear().domain([0,1]).range([colorScheme.getMin(),colorScheme.getMax()]).clamp(true);var fractions=colorScheme.getFractions();var value=fractionToValue(fractions[clickedRow]);if(!hiddenValues.has(value)){hiddenValues.add(value)}else{hiddenValues.remove(value)}_this.trigger("selectionChanged");_this.repaint()})}};morpheus.ColorSupplierLegend.prototype={draw:function(clip,context){var colorScheme=this.colorScheme;colorScheme.setCurrentValue(this.value);context.translate(this.hasNames?14:(this.getUnscaledWidth()-200)/2,0);morpheus.HeatMapColorSchemeLegend.drawColorScheme(context,colorScheme,200)}};morpheus.Util.extend(morpheus.ColorSupplierLegend,morpheus.Events);morpheus.Util.extend(morpheus.ColorSupplierLegend,morpheus.AbstractCanvas);morpheus.HeatMapColorScheme=function(project,scheme){this.project=project;var _this=this;this.separateColorSchemeForRowMetadataField=null;this.rowValueToColorSupplier={};this.value=null;if(scheme){if(scheme.valueToColorScheme){this.fromJSON(scheme)}else{this.rowValueToColorSupplier[null]=this.fromJSON(scheme);this.currentColorSupplier=this.rowValueToColorSupplier[this.value]}}project.on("rowFilterChanged columnFilterChanged rowSortOrderChanged columnSortOrderChanged datasetChanged",function(){_this.projectUpdated()});this.projectUpdated()};morpheus.HeatMapColorScheme.Predefined={};morpheus.HeatMapColorScheme.Predefined.CN=function(){return{scalingMode:"fixed",values:[-2,-.1,.1,2],colors:["#0000ff","#ffffff","#ffffff","#ff0000"]}};morpheus.HeatMapColorScheme.Predefined.BINARY=function(){return{scalingMode:"fixed",values:[0,1],colors:["#ffffff","black"]}};morpheus.HeatMapColorScheme.Predefined.RELATIVE=function(){return{scalingMode:"relative"}};morpheus.HeatMapColorScheme.Predefined.MAF=function(){return{scalingMode:"fixed",stepped:true,values:[0,1,2,3,4,5,6,7],names:["","Synonymous","In Frame Indel","Other Non-Synonymous","Missense","Splice Site","Frame Shift","Nonsense"],colors:["#ffffff","#4daf4a","#ffff33","#a65628","#377eb8","#984ea3","#ff7f00","#e41a1c"]}};morpheus.HeatMapColorScheme.Predefined.ZS=function(){return{scalingMode:"fixed",values:[-10,-2,2,10],colors:["#0000ff","#ffffff","#ffffff","#ff0000"]}};morpheus.HeatMapColorScheme.ScalingMode={RELATIVE:0,FIXED:1};morpheus.HeatMapConditions=function(){this.array=[]};morpheus.HeatMapConditions.prototype={insert:function(index,c){this.array.splice(index,0,c)},add:function(c){this.array.push(c)},getConditions:function(){return this.array},remove:function(index){this.array.splice(index,1)},copy:function(){var c=new morpheus.HeatMapConditions;this.array.forEach(function(cond){c.array.push(_.clone(cond))});return c}};morpheus.HeatMapColorScheme.prototype={getColors:function(){return this.currentColorSupplier.getColors()},setMissingColor:function(color){this.currentColorSupplier.setMissingColor(color)},getHiddenValues:function(){return this.currentColorSupplier.getHiddenValues?this.currentColorSupplier.getHiddenValues():null},getMissingColor:function(){return this.currentColorSupplier.getMissingColor()},getScalingMode:function(){return this.currentColorSupplier.getScalingMode()},getSizer:function(){return this.currentColorSupplier.getSizer()},getConditions:function(){return this.currentColorSupplier.getConditions()},setScalingMode:function(scalingMode){this.currentColorSupplier.setScalingMode(scalingMode)},getFractions:function(){return this.currentColorSupplier.getFractions()},getNames:function(){return this.currentColorSupplier.getNames()},getMin:function(){return this.currentColorSupplier.getMin()},getMax:function(){return this.currentColorSupplier.getMax()},setMin:function(min){this.currentColorSupplier.setMin(min)},setMax:function(max){this.currentColorSupplier.setMax(max)},isStepped:function(){return this.currentColorSupplier.isStepped()},setFractions:function(options){this.currentColorSupplier.setFractions(options)},setTransformValues:function(options){this.currentColorSupplier.setTransformValues(options);this.cachedRowStats.cachedRow=-1},getTransformValues:function(){return this.currentColorSupplier.getTransformValues()},setStepped:function(stepped){var oldColorSupplier=this.currentColorSupplier;var newColorSupplier=stepped?new morpheus.SteppedColorSupplier:new morpheus.GradientColorSupplier;newColorSupplier.sizer=oldColorSupplier.getSizer();newColorSupplier.array=oldColorSupplier.getConditions();newColorSupplier.setScalingMode(oldColorSupplier.getScalingMode());newColorSupplier.setMin(oldColorSupplier.getMin());newColorSupplier.setMax(oldColorSupplier.getMax());newColorSupplier.setFractions({fractions:oldColorSupplier.getFractions(),colors:oldColorSupplier.getColors()});this.currentColorSupplier=newColorSupplier;this.rowValueToColorSupplier[this.value]=this.currentColorSupplier},toJSON:function(){var json={};var _this=this;if(this.separateColorSchemeForRowMetadataField!=null){json.separateColorSchemeForRowMetadataField=this.separateColorSchemeForRowMetadataField}json.valueToColorScheme={};_.each(_.keys(this.rowValueToColorSupplier),function(key){json.valueToColorScheme[key]=morpheus.AbstractColorSupplier.toJSON(_this.rowValueToColorSupplier[key])});return json},fromJSON:function(json){var _this=this;if(json.separateColorSchemeForRowMetadataField){this.separateColorSchemeForRowMetadataField=json.separateColorSchemeForRowMetadataField;this.vector=this.project.getSortedFilteredDataset().getRowMetadata().getByName(this.separateColorSchemeForRowMetadataField)}this.rowValueToColorSupplier={};var obj=json.valueToColorScheme||json.colorSchemes;if(obj==null){var colorSupplier=morpheus.AbstractColorSupplier.fromJSON(json);_this.rowValueToColorSupplier["null"]=colorSupplier}else{_.each(_.keys(obj),function(key){var colorSupplier=morpheus.AbstractColorSupplier.fromJSON(obj[key]);_this.rowValueToColorSupplier[key]=colorSupplier})}this._ensureColorSupplierExists()},copy:function(project){var _this=this;var c=new morpheus.HeatMapColorScheme(project);c.separateColorSchemeForRowMetadataField=this.separateColorSchemeForRowMetadataField;if(c.separateColorSchemeForRowMetadataField!=null){c.vector=project.getSortedFilteredDataset().getRowMetadata().getByName(c.separateColorSchemeForRowMetadataField)}if(c.vector==null){c.separateColorSchemeForRowMetadataField=null}_.each(_.keys(this.rowValueToColorSupplier),function(key){c.rowValueToColorSupplier[key]=_this.rowValueToColorSupplier[key].copy()});c.value=this.value;c.currentColorSupplier=c.rowValueToColorSupplier[c.value];return c},setSeparateColorSchemeForRowMetadataField:function(separateColorSchemeForRowMetadataField){if(separateColorSchemeForRowMetadataField!=this.separateColorSchemeForRowMetadataField){this.separateColorSchemeForRowMetadataField=separateColorSchemeForRowMetadataField;this.vector=this.project.getSortedFilteredDataset().getRowMetadata().getByName(separateColorSchemeForRowMetadataField);var _this=this;_.each(_.keys(this.rowValueToColorSupplier),function(key){delete _this.rowValueToColorSupplier[key]})}},getProject:function(){return this.project},getSeparateColorSchemeForRowMetadataField:function(){return this.separateColorSchemeForRowMetadataField},getColorByValues:function(){return _.keys(this.rowValueToColorSupplier)},projectUpdated:function(){var dataset=this.project.getSortedFilteredDataset();if(this.separateColorSchemeForRowMetadataField!=null){this.vector=this.project.getSortedFilteredDataset().getRowMetadata().getByName(this.separateColorSchemeForRowMetadataField)}this.cachedRowStats=new morpheus.RowStats(dataset)},setColorSupplierForCurrentValue:function(colorSupplier){this.rowValueToColorSupplier[this.value]=colorSupplier;this.currentColorSupplier=colorSupplier},setCurrentValue:function(value){this.value=value;this._ensureColorSupplierExists()},isSizeBy:function(){this.currentColorSupplier.isSizeBy()},getCurrentColorSupplier:function(){return this.currentColorSupplier},getColor:function(row,column,val){if(this.vector!==undefined){var tmp=this.vector.getValue(row);if(this.value!==tmp){this.value=tmp;this._ensureColorSupplierExists()}}if(this.currentColorSupplier.getScalingMode()===morpheus.HeatMapColorScheme.ScalingMode.RELATIVE){if(this.cachedRowStats.maybeUpdateRelative(row)){this.currentColorSupplier.setMin(this.cachedRowStats.rowCachedMin);this.currentColorSupplier.setMax(this.cachedRowStats.rowCachedMax)}}else if(this.currentColorSupplier.getTransformValues()&&this.cachedRowStats.cachedRow!==row){this.cachedRowStats.cacheTransformValues(row,this.currentColorSupplier.getTransformValues());val=(val-this.cachedRowStats.rowCachedMean)/this.cachedRowStats.rowCachedStandardDeviation}return this.currentColorSupplier.getColor(row,column,val)},_ensureColorSupplierExists:function(){this.currentColorSupplier=this.rowValueToColorSupplier[this.value];if(this.currentColorSupplier===undefined){var cs=morpheus.AbstractColorSupplier.fromJSON({scalingMode:"relative"});this.rowValueToColorSupplier[this.value]=cs;this.currentColorSupplier=cs}}};morpheus.RowStats=function(dataset){this.datasetRowView=new morpheus.DatasetRowView(dataset);this.cachedRow=-1;this.rowCachedMax=0;this.rowCachedMin=0;this.rowCachedStandardDeviation=-1;this.rowCachedMean=-1};morpheus.RowStats.prototype={cacheTransformValues:function(row,transform){var meanFunction=transform===morpheus.AbstractColorSupplier.Z_SCORE?morpheus.Mean:morpheus.Median;var stdevFunction=transform===morpheus.AbstractColorSupplier.Z_SCORE?morpheus.StandardDeviation:morpheus.MAD;this.datasetRowView.setIndex(row);this.rowCachedMean=meanFunction(this.datasetRowView);this.rowCachedStandardDeviation=stdevFunction(this.datasetRowView,this.rowCachedMean)},maybeUpdateRelative:function(row){if(this.cachedRow!==row){this.cachedRow=row;this.datasetRowView.setIndex(row);this.rowCachedMax=-Number.MAX_VALUE;this.rowCachedMin=Number.MAX_VALUE;for(var j=0,ncols=this.datasetRowView.size();j<ncols;j++){var d=this.datasetRowView.getValue(j);if(!isNaN(d)){this.rowCachedMax=d>this.rowCachedMax?d:this.rowCachedMax;this.rowCachedMin=d<this.rowCachedMin?d:this.rowCachedMin}}if(this.rowCachedMin===this.rowCachedMax){this.rowCachedMin--}return true}return false}};morpheus.HeatMapSynchronizer=function(){this.controllers=[]};morpheus.HeatMapSynchronizer.prototype={firing:false,getProject:function(){return this.controllers[0].getProject()},zoom:function(){this.controllers[0].zoom.apply(this.controllers[0],arguments)},setTrackVisible:function(){this.controllers[0].setTrackVisible.apply(this.controllers[0],arguments)},revalidate:function(){this.controllers[0].revalidate.apply(this.controllers[0],arguments)},add:function(heatMap){var that=this;this.controllers.push(heatMap);heatMap.on("change",function(event){if(!that.firing){var source=event.source;var method=event.name;that.firing=true;_.each(that.controllers,function(c){if(c!==source){c[method].apply(c,event.arguments)}});that.firing=false}})}};morpheus.HeatMapElementCanvas=function(project){morpheus.AbstractCanvas.call(this,true);var _this=this;this.colorScheme=null;this.project=project;this.dataset=null;this.columnPositions=new morpheus.Positions;this.rowPositions=new morpheus.Positions;this.lastPosition={left:-1,right:-1,top:-1,bottom:-1};this.selectionBox=null;this.selectedRowElements=[];this.selectedColumnElements=[];project.getElementSelectionModel().on("selectionChanged",function(e){_this.repaint()});this.gridColor=morpheus.HeatMapElementCanvas.GRID_COLOR;this.gridThickness=.1;this.elementDrawCallback=null;this.drawCallback=null;this.drawValuesFormat=morpheus.Util.createNumberFormat(".2f")};morpheus.HeatMapElementCanvas.GRID_COLOR="#808080";morpheus.HeatMapElementCanvas.prototype={drawGrid:true,drawValues:false,setPropertiesFromParent:function(parentHeatMapElementCanvas){this.drawGrid=parentHeatMapElementCanvas.drawGrid;this.gridThickness=parentHeatMapElementCanvas.gridThickness;this.gridColor=parentHeatMapElementCanvas.gridColor;this.drawValues=parentHeatMapElementCanvas.drawValues},updateRowSelectionCache:function(repaint){this.selectedRowElements=morpheus.HeatMapElementCanvas.getSelectedSpans(this.project.getRowSelectionModel().getViewIndices());if(repaint){this.repaint()}},updateColumnSelectionCache:function(repaint){this.selectedColumnElements=morpheus.HeatMapElementCanvas.getSelectedSpans(this.project.getColumnSelectionModel().getViewIndices());if(repaint){this.repaint()}},setGridColor:function(gridColor){this.gridColor=gridColor},getGridColor:function(){return this.gridColor},setGridThickness:function(gridThickness){this.gridThickness=gridThickness},getGridThickness:function(){return this.gridThickness},getColorScheme:function(){return this.colorScheme},isDrawGrid:function(){return this.drawGrid},setDrawGrid:function(drawGrid){this.drawGrid=drawGrid},getDrawValuesFormat:function(){return this.drawValuesFormat},setDrawValuesFormat:function(f){if(typeof f==="object"){f=morpheus.Util.createNumberFormat(f.pattern)}this.drawValuesFormat=f},setDrawValues:function(drawValues){this.drawValues=drawValues},isDrawValues:function(){return this.drawValues},setColorScheme:function(colorScheme){this.colorScheme=colorScheme},setDataset:function(dataset){this.dataset=dataset;this.columnPositions.setLength(this.dataset.getColumnCount());this.rowPositions.setLength(this.dataset.getRowCount());this.updateRowSelectionCache(false);this.updateColumnSelectionCache(false)},getColumnPositions:function(){return this.columnPositions},getRowPositions:function(){return this.rowPositions},getPreferredSize:function(context){var w=Math.ceil(this.columnPositions.getPosition(this.columnPositions.getLength()-1)+this.columnPositions.getItemSize(this.columnPositions.getLength()-1));var h=Math.ceil(this.rowPositions.getPosition(this.rowPositions.getLength()-1)+this.rowPositions.getItemSize(this.rowPositions.getLength()-1));return{width:w,height:h}},prePaint:function(clip,context){var lastPosition=this.lastPosition;var columnPositions=this.columnPositions;var rowPositions=this.rowPositions;var left=morpheus.Positions.getLeft(clip,columnPositions);var right=morpheus.Positions.getRight(clip,columnPositions);var top=morpheus.Positions.getTop(clip,rowPositions);var bottom=morpheus.Positions.getBottom(clip,rowPositions);if(this.invalid||left!==lastPosition.left||right!==lastPosition.right||top!==lastPosition.top||bottom!==lastPosition.bottom){lastPosition.right=right;lastPosition.left=left;lastPosition.top=top;lastPosition.bottom=bottom;this.invalid=true}},postPaint:function(clip,context){morpheus.CanvasUtil.resetTransform(context);var project=this.project;context.strokeStyle="Grey";context.lineWidth=1;var rowPositions=this.getRowPositions();var columnPositions=this.getColumnPositions();if(project.getHoverColumnIndex()>=0||project.getHoverRowIndex()>=0){var height=rowPositions.getItemSize(project.getHoverColumnIndex());var width=columnPositions.getItemSize(project.getHoverColumnIndex());var y=project.getHoverRowIndex()===-1?rowPositions.getPosition(rowPositions.getLength()-1):rowPositions.getPosition(project.getHoverRowIndex());var x=project.getHoverColumnIndex()===-1?columnPositions.getPosition(0):columnPositions.getPosition(project.getHoverColumnIndex());if(project.getHoverColumnIndex()!==-1){context.strokeRect(x-clip.x,0,width,this.getUnscaledHeight())}if(project.getHoverRowIndex()!==-1){context.strokeRect(0,y-clip.y,this.getUnscaledWidth(),height)}if(project.getHoverColumnIndex()!==-1&&project.getHoverRowIndex()!==-1){context.strokeStyle="black";context.lineWidth=3;context.strokeRect(x-clip.x+1.5,y-clip.y+1.5,width-1.5,height-1.5);if(project.isSymmetric()){var y2=rowPositions.getPosition(project.getHoverColumnIndex());var x2=columnPositions.getPosition(project.getHoverRowIndex());context.strokeRect(x2-clip.x+1.5,y2-clip.y+1.5,width-1.5,height-1.5)}}}var left=morpheus.Positions.getLeft(clip,columnPositions);var right=morpheus.Positions.getRight(clip,columnPositions);var top=morpheus.Positions.getTop(clip,rowPositions);var bottom=morpheus.Positions.getBottom(clip,rowPositions);context.strokeStyle="rgb(0,0,0)";context.lineWidth=2;context.translate(-clip.x,-clip.y);var selectedElements=project.getElementSelectionModel().getViewIndices();if(selectedElements!=null){selectedElements.forEach(function(id){var rowIndex=id.getArray()[0];var columnIndex=id.getArray()[1];if(rowIndex>=top&&rowIndex<bottom&&columnIndex>=left&&columnIndex<right){var rowSize=rowPositions.getItemSize(rowIndex);var py=rowPositions.getPosition(rowIndex);var columnSize=columnPositions.getItemSize(columnIndex);var px=columnPositions.getPosition(columnIndex);context.strokeRect(px+1.5,py+1.5,columnSize-1.5,rowSize-1.5)}})}context.strokeStyle="rgb(182,213,253)";var selectedRowElements=this.selectedRowElements;var selectedColumnElements=this.selectedColumnElements;if(!(selectedRowElements.length===0&&selectedColumnElements.length===0)){if(selectedRowElements.length===0){selectedRowElements=[[top,bottom-1]]}if(selectedColumnElements.length===0){selectedColumnElements=[[left,right-1]]}}var nrows=selectedRowElements.length;var ncols=selectedColumnElements.length;if(nrows!==0||ncols!==0){for(var i=0;i<nrows;i++){var r=selectedRowElements[i];var y1=rowPositions.getPosition(r[0]);var y2=rowPositions.getPosition(r[1])+rowPositions.getItemSize(i);for(var j=0;j<ncols;j++){var c=selectedColumnElements[j];var x1=columnPositions.getPosition(c[0]);var x2=columnPositions.getPosition(c[1])+columnPositions.getItemSize(j);context.strokeRect(x1,y1,x2-x1,y2-y1)}}}if(this.selectionBox){context.strokeStyle="rgb(0,0,0)";context.lineWidth=2;if(context.setLineDash){context.setLineDash([5])}var x1=columnPositions.getPosition(this.selectionBox.x[0]);var x2=columnPositions.getPosition(this.selectionBox.x[1]);if(x2<x1){var tmp=x1;x1=x2;x2=tmp+columnPositions.getItemSize(this.selectionBox.x[0])}else{x2+=columnPositions.getItemSize(this.selectionBox.x[1])}var y1=rowPositions.getPosition(this.selectionBox.y[0]);var y2=rowPositions.getPosition(this.selectionBox.y[1]);if(y2<y1){var tmp=y1;y1=y2;y2=tmp+rowPositions.getItemSize(this.selectionBox.y[0])}else{y2+=rowPositions.getItemSize(this.selectionBox.y[1])}context.strokeRect(x1,y1,x2-x1,y2-y1);if(context.setLineDash){context.setLineDash([])}context.lineWidth=1}},setElementDrawCallback:function(elementDrawCallback){this.elementDrawCallback=elementDrawCallback},setSelectionBox:function(selectionBox){this.selectionBox=selectionBox},setDrawCallback:function(drawCallback){this.drawCallback=drawCallback},draw:function(clip,context){var columnPositions=this.columnPositions;var rowPositions=this.rowPositions;var left=morpheus.Positions.getLeft(clip,columnPositions);var right=morpheus.Positions.getRight(clip,columnPositions);var top=morpheus.Positions.getTop(clip,rowPositions);var bottom=morpheus.Positions.getBottom(clip,rowPositions);context.translate(-clip.x,-clip.y);this._draw({left:left,right:right,top:top,bottom:bottom,context:context});context.translate(clip.x,clip.y);if(this.drawCallback){this.drawCallback({clip:clip,context:context})}},_draw:function(options){var left=options.left;var right=options.right;var top=options.top;var bottom=options.bottom;var context=options.context;var fontFamily=morpheus.CanvasUtil.getFontFamily(context);var columnPositions=this.columnPositions;var rowPositions=this.rowPositions;morpheus.CanvasUtil.forceSubPixelRendering(context);context.textAlign="center";context.textBaseline="middle";var dataset=this.dataset;var colorScheme=this.colorScheme;var drawGrid=this.drawGrid;var elementDrawCallback=this.elementDrawCallback;var hasElementDrawCallback=elementDrawCallback!=null;var drawValues=this.drawValues&&columnPositions.getSize()>7&&rowPositions.getSize()>7;var nf;if(drawValues){nf=this.drawValuesFormat;var fontSize=columnPositions.getSize();context.font=fontSize+"px "+fontFamily;var textWidth=context.measureText("-99.9").width;fontSize=(columnPositions.getSize()-1)/textWidth*fontSize;fontSize=Math.min(fontSize,17);context.font=fontSize+"px "+morpheus.CanvasUtil.getFontFamily(context)}var seriesNameToIndex={};for(var i=0;i<dataset.getSeriesCount();i++){seriesNameToIndex[dataset.getName(i)]=i}var sizer;var sizeBySeriesName;var sizeBySeriesIndex;var conditions;var conditionSeriesIndices;var sizeFractionRemapper=d3.scale.linear().domain([0,1]).range([.2,1]);for(var row=top;row<bottom;row++){var rowSize=rowPositions.getItemSize(row);var py=rowPositions.getPosition(row);for(var column=left;column<right;column++){var columnSize=columnPositions.getItemSize(column);var px=columnPositions.getPosition(column);var value=dataset.getValue(row,column);context.fillStyle=colorScheme.getColor(row,column,value);if(column===left){sizer=colorScheme.getSizer();sizeBySeriesName=sizer.getSeriesName();sizeBySeriesIndex=sizeBySeriesName!=null?seriesNameToIndex[sizeBySeriesName]:undefined;conditionSeriesIndices=[];conditions=colorScheme.getConditions().getConditions();for(var ci=0,nconditions=conditions.length;ci<nconditions;ci++){conditionSeriesIndices.push(seriesNameToIndex[conditions[ci].seriesName])}}var yoffset=0;var xoffset=0;var cellRowSize=rowSize;var cellColumnSize=columnSize;if(sizeBySeriesIndex!==undefined){var sizeByValue=dataset.getValue(row,column,sizeBySeriesIndex);if(!isNaN(sizeByValue)){var sizeFraction=sizeFractionRemapper(sizer.valueToFraction(sizeByValue));cellRowSize=cellRowSize*sizeFraction;yoffset=(rowSize-cellRowSize)/2;cellColumnSize=cellColumnSize*sizeFraction;xoffset=(columnSize-cellColumnSize)/2}}if(conditions.length>0){var condition=null;for(var ci=0,nconditions=conditions.length;ci<nconditions;ci++){var cond=conditions[ci];var condValue=dataset.getValue(row,column,conditionSeriesIndices[ci]);if(!isNaN(condValue)&&cond.accept(condValue)){condition=cond;break}}if(condition!==null){if(condition.shape!=null){if(condition.inheritColor){if(sizeBySeriesIndex===undefined){xoffset=1;yoffset=1;cellRowSize-=2;cellColumnSize-=2}var x=px+xoffset+cellRowSize/2;var y=py+yoffset+cellColumnSize/2;morpheus.CanvasUtil.drawShape(context,condition.shape,x,y,Math.min(cellColumnSize,cellRowSize)/2,true)}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize);var x=px+xoffset+cellRowSize/2;var y=py+yoffset+cellColumnSize/2;context.fillStyle=condition.color;morpheus.CanvasUtil.drawShape(context,condition.shape,x,y,Math.min(cellColumnSize,cellRowSize)/4,true)}}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize)}}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize)}}else{context.fillRect(px+xoffset,py+yoffset,cellColumnSize,cellRowSize)}if(drawValues&&cellColumnSize>7&&cellRowSize>7&&!isNaN(value)){context.fillStyle="rgb(0,0,0)";context.fillText(nf(value),px+xoffset+cellColumnSize/2,py+yoffset+cellRowSize/2,cellColumnSize)}if(hasElementDrawCallback){elementDrawCallback(context,dataset,row,column,px,py,columnSize,rowSize)}}}if(drawGrid&&rowPositions.getSize()>10&&columnPositions.getSize()>10){context.strokeStyle=this.gridColor;context.lineWidth=this.gridThickness;context.beginPath();for(var row=top;row<bottom;row++){var rowSize=rowPositions.getItemSize(row);var py=rowPositions.getPosition(row);for(var column=left;column<right;column++){var columnSize=columnPositions.getItemSize(column);var px=columnPositions.getPosition(column);var grid=columnSize>10&&rowSize>10;if(grid){context.rect(px,py,columnSize,rowSize)}}}context.stroke()}context.lineWidth=1}};morpheus.Util.extend(morpheus.HeatMapElementCanvas,morpheus.AbstractCanvas);morpheus.HeatMapElementCanvas.getSelectedSpans=function(set){var array=[];if(set.size()>0){var index=0;var start=index;var viewIndices=set.values();viewIndices.sort(function(a,b){return a===b?0:a<b?-1:1});var length=viewIndices.length;while(index<length){var prior=index===0?viewIndices[0]:viewIndices[index-1];var current=viewIndices[index];if(current-prior>1){array.push([viewIndices[start],viewIndices[index-1]]);start=index}index++}if(start==0){array.push([viewIndices[0],viewIndices[viewIndices.length-1]])}else{array.push([viewIndices[start],viewIndices[index-1]])}}return array};morpheus.KeyboardCharMap=["","","","CANCEL","","","HELP","","BACKSPACE","TAB","","","CLEAR","ENTER","ENTER_SPECIAL","","SHIFT","CONTROL","ALT","PAUSE","CAPS_LOCK","KANA","EISU","JUNJA","FINAL","HANJA","","Escape","CONVERT","NONCONVERT","ACCEPT","MODECHANGE","Space","Page Up","Page Down","End","Home","Left","Up","Right","Down","SELECT","PRINT","EXECUTE","PRINTSCREEN","INSERT","Delete","","0","1","2","3","4","5","6","7","8","9","COLON","SEMICOLON","LESS_THAN","Equals","GREATER_THAN","QUESTION_MARK","AT","A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z","OS_KEY","","CONTEXT_MENU","","SLEEP","0","1","2","3","4","5","6","7","8","9","MULTIPLY","+","SEPARATOR","SUBTRACT","DECIMAL","DIVIDE","F1","F2","F3","F4","F5","F6","F7","F8","F9","F10","F11","F12","F13","F14","F15","F16","F17","F18","F19","F20","F21","F22","F23","F24","","","","","","","","","NUM_LOCK","SCROLL_LOCK","WIN_OEM_FJ_JISHO","WIN_OEM_FJ_MASSHOU","WIN_OEM_FJ_TOUROKU","WIN_OEM_FJ_LOYA","WIN_OEM_FJ_ROYA","","","","","","","","","","CIRCUMFLEX","EXCLAMATION","DOUBLE_QUOTE","HASH","DOLLAR","PERCENT","AMPERSAND","UNDERSCORE","OPEN_PAREN","CLOSE_PAREN","ASTERISK","Plus","PIPE","-","OPEN_CURLY_BRACKET","CLOSE_CURLY_BRACKET","TILDE","","","","","VOLUME_MUTE","VOLUME_DOWN","VOLUME_UP","","","SEMICOLON","EQUALS","COMMA","MINUS","PERIOD","/","BACK_QUOTE","","","","","","","","","","","","","","","","","","","","","","","","","","","OPEN_BRACKET","BACK_SLASH","CLOSE_BRACKET","QUOTE","","META","ALTGR","","WIN_ICO_HELP","WIN_ICO_00","","WIN_ICO_CLEAR","","","WIN_OEM_RESET","WIN_OEM_JUMP","WIN_OEM_PA1","WIN_OEM_PA2","WIN_OEM_PA3","WIN_OEM_WSCTRL","WIN_OEM_CUSEL","WIN_OEM_ATTN","WIN_OEM_FINISH","WIN_OEM_COPY","WIN_OEM_AUTO","WIN_OEM_ENLW","WIN_OEM_BACKTAB","ATTN","CRSEL","EXSEL","EREOF","PLAY","ZOOM","","PA1","WIN_OEM_CLEAR",""];morpheus.HeatMapKeyListener=function(heatMap){var allActions=heatMap.getActionManager().getActions();var actions=allActions.filter(function(a){return a.cb!=null&&a.which!=null});allActions.sort(function(a,b){a=a.name.toLowerCase();b=b.name.toLowerCase();return a===b?0:a<b?-1:1});var keydown=function(e){var tagName=e.target.tagName;var found=false;var commandKey=morpheus.Util.IS_MAC?e.metaKey:e.ctrlKey;var altKey=e.altKey;var shiftKey=e.shiftKey;var which=e.which;var isInputField=tagName==="INPUT"||tagName==="SELECT"||tagName==="TEXTAREA";var acceptOptions={isInputField:isInputField,heatMap:heatMap};var shortcutMatches=function(sc){if(sc.which.indexOf(which)!==-1&&(sc.commandKey===undefined||commandKey===sc.commandKey)&&(sc.shiftKey===undefined||shiftKey===sc.shiftKey)&&(sc.accept==undefined||sc.accept(acceptOptions))){sc.cb({heatMap:heatMap});return true}};if(!isInputField){for(var i=0,n=actions.length;i<n;i++){var sc=actions[i];if(shortcutMatches(sc)){found=true;break}}}else{for(var i=0,n=actions.length;i<n;i++){var sc=actions[i];if(sc.global&&shortcutMatches(sc)){found=true;break}}}if(found){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();return false}};var $keyelement=heatMap.$tabPanel;$keyelement.on("keydown",keydown);$keyelement.on("dragover.morpheus dragenter.morpheus",function(e){e.preventDefault();e.stopPropagation()}).on("drop.morpheus",function(e){if(heatMap.options.menu.File&&heatMap.options.menu.File.indexOf("Open")!==-1&&e.originalEvent.dataTransfer&&e.originalEvent.dataTransfer.files.length){e.preventDefault();e.stopPropagation();var files=e.originalEvent.dataTransfer.files;for(var i=0;i<files.length;i++){morpheus.HeatMap.showTool(new morpheus.OpenFileTool({file:files[i]}),heatMap)}}});$keyelement.on("paste.morpheus",function(e){if(heatMap.options.toolbar.openFile){var tagName=e.target.tagName;if(tagName=="INPUT"||tagName=="SELECT"||tagName=="TEXTAREA"){return}var text=e.originalEvent.clipboardData.getData("text/plain");if(text!=null&&text.length>0){e.preventDefault();e.stopPropagation();var blob=new Blob([text]);var url=window.URL.createObjectURL(blob);morpheus.HeatMap.showTool(new morpheus.OpenFileTool({file:url}),heatMap)}}});$keyelement.on("mousewheel",function(e){var scrolly=e.deltaY*e.deltaFactor;var scrollx=e.deltaX*e.deltaFactor;var stop=false;if(e.altKey){heatMap.zoom(scrolly>0,{rows:true,columns:true});stop=true}else{if(scrolly!==0){var scrollTop=heatMap.scrollTop();if(heatMap.scrollTop(scrollTop-scrolly)!==scrollTop){stop=true}}if(scrollx!==0){var scrollLeft=heatMap.scrollLeft();if(heatMap.scrollLeft(scrollLeft+scrollx)!==scrollLeft){stop=true}}}if(stop&&heatMap.options.standalone){e.preventDefault();e.stopPropagation()}});function shortcutToString(sc){var s=["<b>"];if(sc.commandKey){s.push(morpheus.Util.COMMAND_KEY)}if(sc.shiftKey){s.push("Shift+")}if(sc.which){s.push(morpheus.KeyboardCharMap[sc.which[0]])}s.push("</b>");return s.join("")}this.showKeyMapReference=function(){var html=[];html.push('<table class="table table-condensed">');allActions.forEach(function(sc){html.push("<tr><td>");html.push(shortcutToString(sc));html.push("</td><td>");if(sc.icon){html.push('<span class="'+sc.icon+'"></span> ')}html.push(sc.name);html.push("</td></tr>")});html.push("</table>");morpheus.FormBuilder.showInModal({title:"Keyboard Shortcuts",html:html.join(""),focus:document.activeElement})}};morpheus.HeatMapOptions=function(heatMap){var items=[{name:"color_by",required:true,help:"Use a different color scheme for distinct row annotation values",type:"select",options:["(None)"].concat(morpheus.MetadataUtil.getMetadataNames(heatMap.getProject().getFullDataset().getRowMetadata())),value:heatMap.heatmap.getColorScheme().getSeparateColorSchemeForRowMetadataField()},{name:"color_by_value",required:true,type:"select",options:[]}];items.push({name:"size_by",required:true,type:"select",options:["(None)"].concat(morpheus.DatasetUtil.getSeriesNames(heatMap.getProject().getFullDataset()))});items.push({name:"size_by_minimum",title:"Size by minimum",required:true,type:"text",style:"max-width: 100px;"});items.push({name:"size_by_maximum",title:"Size by maximum",required:true,type:"text",style:"max-width: 100px;"});items.push({name:"conditional_rendering",required:true,type:"button"});items.push({type:"separator"});var createColorSchemeOptions=function(){var colorSchemeOptions=[{name:"relative",value:"relative"},{name:"binary",value:"binary"},{name:"MAF",value:"MAF"},{name:"fixed (-1.5, -0.1, 0.1, 1.5)",value:"cn"}];var savedColorSchemeKeys=[];if(localStorage.getItem("morpheus-colorScheme")!=null){savedColorSchemeKeys=_.keys(JSON.parse(localStorage.getItem("morpheus-colorScheme")))}if(savedColorSchemeKeys.length>0){colorSchemeOptions.push({divider:true});colorSchemeOptions=colorSchemeOptions.concat(savedColorSchemeKeys)}colorSchemeOptions.push({divider:true});colorSchemeOptions.push("My Computer...");return colorSchemeOptions};items.push([{name:"saved_color_scheme",required:true,type:"bootstrap-select",options:createColorSchemeOptions()},{name:"load_color_scheme",type:"button"},{name:"delete_color_scheme",type:"button"}]);items.push({name:"save_color_scheme",type:"button"});var displayItems=[{disabled:heatMap.getProject().getFullDataset().getColumnCount()!==heatMap.getProject().getFullDataset().getRowCount(),name:"link_rows_and_columns",help:"For square matrices",required:true,type:"checkbox",style:"max-width: 100px;",value:heatMap.getProject().isSymmetric()},{name:"show_row_number",required:true,type:"checkbox",value:heatMap.isShowRowNumber()},{name:"show_grid",required:true,type:"checkbox",value:heatMap.heatmap.isDrawGrid()},{name:"grid_thickness",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.heatmap.getGridThickness())},{name:"grid_color",required:true,type:"color",style:"max-width: 50px;",value:heatMap.heatmap.getGridColor()},{name:"row_size",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.heatmap.getRowPositions().getSize())},{name:"column_size",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.heatmap.getColumnPositions().getSize())},{name:"show_values",required:true,type:"checkbox",value:heatMap.heatmap.isDrawValues()},{name:"number_of_fraction_digits",required:true,type:"number",min:0,step:1,style:"max-width: 100px;",value:morpheus.Util.getNumberFormatPatternFractionDigits(heatMap.heatmap.getDrawValuesFormat().toJSON().pattern)}];if(heatMap.rowDendrogram){displayItems.push({name:"row_dendrogram_line_thickness",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.rowDendrogram?heatMap.rowDendrogram.lineWidth:1)})}if(heatMap.columnDendrogram){displayItems.push({name:"column_dendrogram_line_thickness",required:true,type:"text",style:"max-width: 100px;",value:morpheus.Util.nf(heatMap.columnDendrogram?heatMap.columnDendrogram.lineWidth:1)})}displayItems.push({name:"info_window",required:true,type:"select",style:"max-width:130px;",options:[{name:"Fixed To Top",value:0},{name:"New Window",value:1}],value:heatMap.tooltipMode});displayItems.push({name:"inline_tooltip",required:true,type:"checkbox",value:heatMap.options.inlineTooltip});var colorSchemeFormBuilder=new morpheus.FormBuilder;_.each(items,function(item){colorSchemeFormBuilder.append(item)});var displayFormBuilder=new morpheus.FormBuilder;_.each(displayItems,function(item){displayFormBuilder.append(item)});var colorSchemeChooser=new morpheus.HeatMapColorSchemeChooser({showRelative:true,colorScheme:heatMap.heatmap.getColorScheme()});var updatingSizer=false;function colorSchemeChooserUpdated(){if(heatMap.heatmap.getColorScheme().getSizer&&heatMap.heatmap.getColorScheme().getSizer()!=null){colorSchemeFormBuilder.setValue("size_by",heatMap.heatmap.getColorScheme().getSizer().getSeriesName());colorSchemeFormBuilder.setEnabled("size_by_minimum",heatMap.heatmap.getColorScheme().getSizer().getSeriesName()!=null);colorSchemeFormBuilder.setEnabled("size_by_maximum",heatMap.heatmap.getColorScheme().getSizer().getSeriesName()!=null);if(!updatingSizer){colorSchemeFormBuilder.setValue("size_by_minimum",heatMap.heatmap.getColorScheme().getSizer().getMin());colorSchemeFormBuilder.setValue("size_by_maximum",heatMap.heatmap.getColorScheme().getSizer().getMax())}}}colorSchemeChooser.on("change",function(){colorSchemeChooserUpdated();heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint();colorSchemeChooser.restoreCurrentValue()});function createMetadataField(isColumns){var options=[];var value={};_.each(heatMap.getVisibleTrackNames(isColumns),function(name){value[name]=true});_.each(morpheus.MetadataUtil.getMetadataNames(isColumns?heatMap.getProject().getFullDataset().getColumnMetadata():heatMap.getProject().getFullDataset().getRowMetadata()),function(name){options.push(name)});var field={type:"bootstrap-select",search:options.length>10,name:isColumns?"column_annotations":"row_annotations",multiple:true,value:value,options:options,toggle:true};return field}var annotationsBuilder=new morpheus.FormBuilder;annotationsBuilder.append(createMetadataField(false));annotationsBuilder.append(createMetadataField(true));function annotationsListener($select,isColumns){var names=[];_.each(heatMap.getVisibleTrackNames(isColumns),function(name){names.push(name)});var values=$select.val();var selectedNow=_.difference(values,names);var unselectedNow=_.difference(names,values);var tracks=[];_.each(selectedNow,function(name){tracks.push({name:name,isColumns:isColumns,visible:true})});_.each(unselectedNow,function(name){tracks.push({name:name,isColumns:isColumns,visible:false})});heatMap.setTrackVisibility(tracks);colorSchemeChooser.restoreCurrentValue()}var $ca=annotationsBuilder.$form.find("[name=column_annotations]");$ca.on("change",function(e){annotationsListener($(this),true)});var $ra=annotationsBuilder.$form.find("[name=row_annotations]");$ra.on("change",function(e){annotationsListener($(this),false)});var annotationOptionsTabId=_.uniqueId("morpheus");var heatMapOptionsTabId=_.uniqueId("morpheus");var displayOptionsTabId=_.uniqueId("morpheus");var $metadataDiv=$('<div class="tab-pane" id="'+annotationOptionsTabId+'"></div>');$metadataDiv.append($(annotationsBuilder.$form));var $heatMapDiv=$('<div class="tab-pane active" id="'+heatMapOptionsTabId+'"></div>');$heatMapDiv.append(colorSchemeChooser.$div);$heatMapDiv.append($(colorSchemeFormBuilder.$form));var $displayDiv=$('<div class="tab-pane" id="'+displayOptionsTabId+'"></div>');$displayDiv.append($(displayFormBuilder.$form));displayFormBuilder.setEnabled("grid_thickness",heatMap.heatmap.isDrawGrid());displayFormBuilder.setEnabled("grid_color",heatMap.heatmap.isDrawGrid());displayFormBuilder.$form.find("[name=show_grid]").on("click",function(e){var grid=$(this).prop("checked");displayFormBuilder.setEnabled("grid_thickness",grid);displayFormBuilder.setEnabled("grid_color",grid);heatMap.heatmap.setDrawGrid(grid);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()});var $fractionDigits=displayFormBuilder.$form.find("[name=number_of_fraction_digits]");displayFormBuilder.$form.find("[name=show_values]").on("click",function(e){var drawValues=$(this).prop("checked");heatMap.heatmap.setDrawValues(drawValues);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()});$fractionDigits.on("keyup input",_.debounce(function(){var n=parseInt($(this).val());if(n>=0){heatMap.heatmap.setDrawValuesFormat(morpheus.Util.createNumberFormat("."+n+"f"));heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}},100));displayFormBuilder.$form.find("[name=inline_tooltip]").on("click",function(e){heatMap.options.inlineTooltip=$(this).prop("checked")});displayFormBuilder.$form.find("[name=grid_color]").on("change",function(e){var value=$(this).val();heatMap.heatmap.setGridColor(value);heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()});displayFormBuilder.$form.find("[name=grid_thickness]").on("keyup",_.debounce(function(e){var value=parseFloat($(this).val());if(!isNaN(value)){heatMap.heatmap.setGridThickness(value);heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}},100));displayFormBuilder.$form.find("[name=row_size]").on("keyup",_.debounce(function(e){var value=parseFloat($(this).val());if(!isNaN(value)){heatMap.heatmap.getRowPositions().setSize(value);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()}},100));displayFormBuilder.$form.find("[name=info_window]").on("change",function(e){heatMap.setTooltipMode(parseInt($(this).val()))});displayFormBuilder.find("link_rows_and_columns").on("click",function(e){var checked=$(this).prop("checked");if(checked){heatMap.getProject().setSymmetric(heatMap)}else{heatMap.getProject().setSymmetric(null)}});displayFormBuilder.find("show_row_number").on("click",function(e){var checked=$(this).prop("checked");heatMap.setShowRowNumber(checked);heatMap.revalidate()});var $colorByValue=colorSchemeFormBuilder.$form.find("[name=color_by_value]");var separateSchemesField=heatMap.heatmap.getColorScheme().getSeparateColorSchemeForRowMetadataField();if(separateSchemesField!=null){var v=heatMap.project.getFullDataset().getRowMetadata().getByName(separateSchemesField);if(v!=null){$colorByValue.html(morpheus.Util.createOptions(morpheus.VectorUtil.createValueToIndexMap(v).keys()))}}if(separateSchemesField!=null){colorSchemeChooser.setCurrentValue($colorByValue.val())}if(heatMap.heatmap.getColorScheme().getSizer&&heatMap.heatmap.getColorScheme().getSizer()!=null&&heatMap.heatmap.getColorScheme().getSizer().getSeriesName()){colorSchemeFormBuilder.setValue("size_by",heatMap.heatmap.getColorScheme().getSizer().getSeriesName())}colorSchemeFormBuilder.$form.find("[name=size_by]").on("change",function(e){var series=$(this).val();if(series=="(None)"){series=null}colorSchemeChooser.colorScheme.getSizer().setSeriesName(series);colorSchemeChooser.fireChanged()});colorSchemeFormBuilder.$form.find("[name=size_by_minimum]").on("keyup",_.debounce(function(e){updatingSizer=true;colorSchemeChooser.colorScheme.getSizer().setMin(parseFloat($(this).val()));colorSchemeChooser.fireChanged(true);updatingSizer=false},100));colorSchemeFormBuilder.$form.find("[name=size_by_maximum]").on("keyup",_.debounce(function(e){updatingSizer=true;colorSchemeChooser.colorScheme.getSizer().setMax(parseFloat($(this).val()));colorSchemeChooser.fireChanged(true);updatingSizer=false},100));colorSchemeFormBuilder.$form.find("[name=conditional_rendering]").on("click",function(e){e.preventDefault();var conditionalRenderingUI=new morpheus.ConditionalRenderingUI(heatMap);morpheus.FormBuilder.showInModal({title:"Conditional Rendering",html:conditionalRenderingUI.$div,close:"Close",modalClass:"morpheus-sub-modal"})});colorSchemeFormBuilder.find("save_color_scheme").on("click",function(e){e.preventDefault();var saveColorSchemeFormBuilder=new morpheus.FormBuilder;saveColorSchemeFormBuilder.append({name:"save_to",type:"radio",value:"Browser Storage",options:["Browser Storage","File"]});saveColorSchemeFormBuilder.append({name:"color_scheme_name",type:"text"});saveColorSchemeFormBuilder.append({name:"file_name",type:"text"});saveColorSchemeFormBuilder.setVisible("file_name",false);saveColorSchemeFormBuilder.find("save_to").on("change",function(){var isBrowser=$(this).val()==="Browser Storage";saveColorSchemeFormBuilder.setVisible("file_name",!isBrowser);saveColorSchemeFormBuilder.setVisible("color_scheme_name",isBrowser)});morpheus.FormBuilder.showOkCancel({title:"Save Color Scheme",ok:true,cancel:true,draggable:true,content:saveColorSchemeFormBuilder.$form,appendTo:heatMap.getContentEl(),align:"right",okCallback:function(){var colorSchemeText=JSON.stringify(heatMap.heatmap.getColorScheme().toJSON());if(saveColorSchemeFormBuilder.getValue("save_to")==="Browser Storage"){var name=saveColorSchemeFormBuilder.getValue("color_scheme_name").trim();if(name===""){name="my color scheme"}var colorSchemeObject=localStorage.getItem("morpheus-colorScheme");if(colorSchemeObject==null){colorSchemeObject={}}else{colorSchemeObject=JSON.parse(colorSchemeObject)}colorSchemeObject[name]=colorSchemeText;localStorage.setItem("morpheus-colorScheme",JSON.stringify(colorSchemeObject));colorSchemeFormBuilder.setOptions("saved_color_scheme",createColorSchemeOptions())}else{var name=saveColorSchemeFormBuilder.getValue("file_name").trim();if(name===""){name="color_scheme.json"}var blob=new Blob([colorSchemeText],{type:"application/json"});saveAs(blob,name)}},focus:heatMap.getFocusEl()})});colorSchemeFormBuilder.setEnabled("delete_color_scheme",false);colorSchemeFormBuilder.find("delete_color_scheme").on("click",function(){var key=colorSchemeFormBuilder.getValue("saved_color_scheme");var savedColorSchemes=JSON.parse(localStorage.getItem("morpheus-colorScheme"));delete savedColorSchemes[key];localStorage.setItem("morpheus-colorScheme",JSON.stringify(savedColorSchemes));colorSchemeFormBuilder.setOptions("saved_color_scheme",createColorSchemeOptions())});colorSchemeFormBuilder.find("saved_color_scheme").on("change",function(){colorSchemeFormBuilder.setEnabled("delete_color_scheme",["relative","cn","MAF","binary","My Computer..."].indexOf(colorSchemeFormBuilder.getValue("saved_color_scheme"))===-1)});colorSchemeFormBuilder.find("load_color_scheme").on("click",function(e){var val=colorSchemeFormBuilder.getValue("saved_color_scheme");var repaint=true;if(val==="relative"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.RELATIVE()))}else if(val==="cn"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.CN()))}else if(val==="MAF"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.MAF()))}else if(val==="binary"){heatMap.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(morpheus.HeatMapColorScheme.Predefined.BINARY()))}else if(val==="My Computer..."){repaint=false;var $file=$('<input style="display:none;" type="file">');$file.appendTo(heatMap.getContentEl());$file.click();$file.on("change",function(evt){var files=evt.target.files;morpheus.Util.getText(evt.target.files[0]).done(function(text){var json=JSON.parse($.trim(text));heatMap.heatmap.getColorScheme().fromJSON(json);colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme());heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}).fail(function(){morpheus.FormBuilder.showInModal({title:"Error",html:"Unable to read color scheme."})}).always(function(){$file.remove()})})}else{var savedColorSchemes=JSON.parse(localStorage.getItem("morpheus-colorScheme"));var scheme=JSON.parse(savedColorSchemes[val]);heatMap.heatmap.getColorScheme().fromJSON(scheme)}if(repaint){colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme());heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint()}colorSchemeChooser.restoreCurrentValue()});colorSchemeFormBuilder.$form.find("[name=color_by]").on("change",function(e){var colorByField=$(this).val();if(colorByField=="(None)"){colorByField=null}var colorByValue=null;heatMap.heatmap.getColorScheme().setSeparateColorSchemeForRowMetadataField(colorByField);if(colorByField!=null){$colorByValue.html(morpheus.Util.createOptions(morpheus.VectorUtil.createValueToIndexMap(heatMap.project.getFullDataset().getRowMetadata().getByName(colorByField)).keys()));colorByValue=$colorByValue.val()}else{$colorByValue.html("")}heatMap.heatmap.getColorScheme().setCurrentValue(colorByValue);colorSchemeChooser.setCurrentValue(colorByValue);heatMap.heatmap.setInvalid(true);heatMap.heatmap.repaint();colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme())});$colorByValue.on("change",function(e){if(heatMap.heatmap.getColorScheme().getSeparateColorSchemeForRowMetadataField()==null){colorSchemeChooser.setCurrentValue(null);heatMap.heatmap.getColorScheme().setCurrentValue(null);colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme())}else{colorSchemeChooser.setCurrentValue($colorByValue.val());colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme())}});displayFormBuilder.$form.find("[name=column_size]").on("keyup",_.debounce(function(e){heatMap.heatmap.getColumnPositions().setSize(parseFloat($(this).val()));heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=row_gap_size]").on("keyup",_.debounce(function(e){heatMap.rowGapSize=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=column_gap_size]").on("keyup",_.debounce(function(e){heatMap.columnGapSize=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=squish_factor]").on("keyup",_.debounce(function(e){var f=parseFloat($(this).val());heatMap.heatmap.getColumnPositions().setSquishFactor(f);heatMap.heatmap.getRowPositions().setSquishFactor(f);heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=row_dendrogram_line_thickness]").on("keyup",_.debounce(function(e){heatMap.rowDendrogram.lineWidth=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));displayFormBuilder.$form.find("[name=column_dendrogram_line_thickness]").on("keyup",_.debounce(function(e){heatMap.columnDendrogram.lineWidth=parseFloat($(this).val());heatMap.revalidate();colorSchemeChooser.restoreCurrentValue()},100));var $tab=$('<div class="tab-content"></div>');$metadataDiv.appendTo($tab);$heatMapDiv.appendTo($tab);$displayDiv.appendTo($tab);var $div=$("<div></div>");var $ul=$('<ul class="nav nav-tabs" role="tablist">'+'<li><a href="#'+annotationOptionsTabId+'" role="tab" data-toggle="tab">Annotations</a></li>'+'<li><a href="#'+heatMapOptionsTabId+'" role="tab" data-toggle="tab">Color Scheme</a></li>'+'<li><a href="#'+displayOptionsTabId+'" role="tab" data-toggle="tab">Display</a></li>'+"</ul>");$ul.appendTo($div);$tab.appendTo($div);colorSchemeChooser.setColorScheme(heatMap.heatmap.getColorScheme());colorSchemeChooserUpdated();$ul.find("[role=tab]:eq(1)").tab("show");morpheus.FormBuilder.showInModal({title:"Options",html:$div,close:"Close",focus:heatMap.getFocusEl(),onClose:function(){$div.find("input").off("keyup");$ca.off("change");$ra.off("change");$div.remove();colorSchemeChooser.dispose()}})};morpheus.HeatMapSizer=function(){this.seriesName=null;this.sizeByScale=d3.scale.linear().domain([this.min,this.max]).range([0,1]).clamp(true)};morpheus.HeatMapSizer.prototype={min:0,max:1,copy:function(){var sizer=new morpheus.HeatMapSizer;sizer.seriesName=this.seriesName;sizer.min=this.min;sizer.max=this.max;sizer.sizeByScale=this.sizeByScale.copy();return sizer},valueToFraction:function(value){return this.sizeByScale(value)},setMin:function(min){this.min=min;this.sizeByScale=d3.scale.linear().domain([this.min,this.max]).range([0,1]).clamp(true)},setMax:function(max){this.max=max;this.sizeByScale=d3.scale.linear().domain([this.min,this.max]).range([0,1]).clamp(true)},getMin:function(){return this.min},getMax:function(){return this.max},getSeriesName:function(){return this.seriesName},setSeriesName:function(name){this.seriesName=name}};morpheus.HeatMapToolBar=function(heatMap){this.heatMap=heatMap;this.rowSearchResultModelIndices=[];this.columnSearchResultModelIndices=[];var _this=this;var layout=['<div class="hidden-print">'];layout.push('<div data-name="toolbar"></div>');layout.push('<div data-name="tip" style="white-space:nowrap; border-top: thin solid #e7e7e7;margin-bottom:2px;height: 14px; font-size: 10px;overflow:hidden;"></div>');layout.push("</div>");var $el=$(layout.join(""));var searchHtml=[];var $searchForm=$('<form style="display:inline-block;margin-right:14px;" name="searchForm"'+' class="form'+" form-inline"+' form-compact"'+' role="search"></form>');$searchForm.on("submit",function(e){e.preventDefault()});searchHtml.push('<div title="Toggle'+" Search ("+morpheus.Util.COMMAND_KEY+'/)" class="btn-group"'+' data-toggle="buttons">');searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="rows" type="radio" autocomplete="off" name="searchToggle"'+' type="button"> Rows');searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="columns" type="radio" autocomplete="off" name="searchToggle"> Columns');searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="values" type="radio" autocomplete="off" name="searchToggle">'+" Values");searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="rowDendrogram" type="radio" autocomplete="off"'+' name="searchToggle"> Row Dendrogram');searchHtml.push("</label>");searchHtml.push('<label class="btn btn-default btn-xxs">');searchHtml.push('<input data-search="columnDendrogram" type="radio" autocomplete="off"'+' name="searchToggle"> Column Dendrogram');searchHtml.push("</label>");searchHtml.push("</div>");function createSearchOptionsMenu(){searchHtml.push('<div style="display:inline-block;" class="dropdown">');searchHtml.push('<button type="button" class="btn btn-default btn-xxs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> <span class="fa fa-caret-down"></span></button>');searchHtml.push('<ul data-name="searchOptions" class="dropdown-menu">');searchHtml.push('<li><a data-group="matchMode" data-name="exact" href="#"><span'+' data-type="toggle"></span>Exact'+" Match</a></li>");searchHtml.push('<li><a data-group="matchMode" data-name="contains" href="#"><span'+' data-type="toggle"'+' class="dropdown-checkbox fa fa-check"></span>Contains</a></li>');searchHtml.push('<li role="separator" class="divider"></li>');searchHtml.push('<li><a data-group="searchMode" data-name="matchAny" href="#"><span'+' data-type="toggle"'+' class="dropdown-checkbox fa fa-check"></span>Match Any Search Term</a></li>');searchHtml.push('<li><a data-group="searchMode" data-name="matchAll" href="#"><span'+' data-type="toggle"></span>Match All Search Terms</a></li>');searchHtml.push('<li role="separator" class="divider"></li>');searchHtml.push('<li><a data-name="searchHelp" href="#">Help</a></li>');searchHtml.push("</ul>");searchHtml.push("</div>")}function createSearchMenu(dataName,navigation){searchHtml.push('<div style="display:inline-block;" data-name="'+dataName+'">');searchHtml.push('<div class="form-group">');searchHtml.push('<input type="text" class="form-control input-sm" autocomplete="off"'+' name="search">');searchHtml.push("</div>");searchHtml.push('<div class="form-group">');searchHtml.push('<span data-name="searchResultsWrapper" style="display:none;">');searchHtml.push('<span style="font-size:12px;" data-name="searchResults"></span>');if(navigation){searchHtml.push('<button name="previousMatch" type="button" class="btn btn-default btn-xxs" data-toggle="tooltip" title="Previous"><i class="fa fa-chevron-up"></i></button>');searchHtml.push('<button name="nextMatch" type="button" class="btn btn-default btn-xxs" data-toggle="tooltip" title="Next"><i class="fa fa-chevron-down"></i></button>');searchHtml.push('<button name="matchesToTop" type="button" class="btn btn-default btn-xxs" data-toggle="tooltip" title="Matches To Top"><i class="fa fa-level-up"></i></button>')}searchHtml.push("</span>");searchHtml.push("</div>");searchHtml.push("</div>");searchHtml.push("</div>")}if(heatMap.options.toolbar.searchRows||heatMap.options.toolbar.searchColumns||heatMap.options.toolbar.searchValues){createSearchOptionsMenu()}if(heatMap.options.toolbar.searchRows){createSearchMenu("searchRowsGroup",true)}if(heatMap.options.toolbar.searchColumns){createSearchMenu("searchColumnsGroup",true)}if(heatMap.options.toolbar.searchValues){createSearchMenu("searchValuesGroup",false)}createSearchMenu("searchRowDendrogramGroup",false);createSearchMenu("searchColumnDendrogramGroup",false);if(heatMap.options.toolbar.dimensions){searchHtml.push('<div class="form-group">');searchHtml.push('<h6 style="display: inline; margin-left:10px;" data-name="dim"></h6>');searchHtml.push('<h6 style="display: inline; margin-left:10px;" data-name="selection"></h6>');searchHtml.push("</div>")}var $menus=$('<div style="display: inline-block;margin-right:14px;"></div>');function createMenu(menuName,actions,minWidth){if(!minWidth){minWidth="0px"}var menu=[];var dropdownId=_.uniqueId("morpheus");menu.push('<div class="dropdown morpheus-menu">');menu.push('<a class="dropdown-toggle morpheus-black-link morpheus-black-link-background" type="button"'+' id="'+dropdownId+'" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">');menu.push(menuName);menu.push("</a>");menu.push('<ul style="min-width:'+minWidth+';" class="dropdown-menu" aria-labelledby="'+dropdownId+'">');actions.forEach(function(name){if(name==null){menu.push('<li role="separator" class="divider"></li>')}else{var action=heatMap.getActionManager().getAction(name);if(action!=null){menu.push("<li>");menu.push('<a class="morpheus-menu-item" data-action="'+action.name+'" href="#">');menu.push(action.name);if(action.ellipsis){menu.push("...")}if(action.icon){menu.push('<span class="'+action.icon+' morpheus-menu-item-icon"></span> ')}if(action.which){menu.push('<span class="pull-right">');if(action.commandKey){menu.push(morpheus.Util.COMMAND_KEY)}if(action.shiftKey){menu.push("Shift+")}menu.push(morpheus.KeyboardCharMap[action.which[0]]);menu.push("</span>")}menu.push("</a>");menu.push("</li>")}}});menu.push("</ul>");menu.push("</div>");$(menu.join("")).appendTo($menus)}if(heatMap.options.menu){if(heatMap.options.menu.File){createMenu("File",heatMap.options.menu.File,"240px")}if(heatMap.options.menu.View){createMenu("Edit",heatMap.options.menu.Edit)}if(heatMap.options.menu.View){createMenu("View",heatMap.options.menu.View,"170px")}if(heatMap.options.menu.Tools){createMenu("Tools",heatMap.options.menu.Tools)}if(heatMap.options.menu.Help){createMenu("Help",heatMap.options.menu.Help,"220px")}}$(searchHtml.join("")).appendTo($searchForm);var $lineOneColumn=$el.find("[data-name=toolbar]");$menus.appendTo($lineOneColumn);$searchForm.appendTo($lineOneColumn);var toolbarHtml=['<div style="display: inline;">'];toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.zoom){var dropdownId=_.uniqueId("morpheus");toolbarHtml.push('<div style="display:inline-block;" class="dropdown">');toolbarHtml.push('<a class="dropdown-toggle morpheus-black-link" type="button" id="'+dropdownId+'" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">');toolbarHtml.push('<button type="button"'+' class="btn btn-default btn-xxs"><span class="fa'+' fa-search-plus"></span>');toolbarHtml.push(' <span style="font-size: .8em;" class="fa fa-caret-down"></span>');toolbarHtml.push("</button>");toolbarHtml.push('<ul style="width:200px;" class="dropdown-menu" aria-labelledby="'+dropdownId+'">');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Zoom In">Zoom In<span class="pull-right">+</span></a></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Zoom Out">Zoom'+' Out<span class="pull-right">-</span></a></li>');toolbarHtml.push('<li role="separator" class="divider"></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Fit To Window">Fit To Window<span'+' class="fa'+' fa-compress morpheus-menu-item-icon"></span><span class="pull-right">'+morpheus.Util.COMMAND_KEY+morpheus.KeyboardCharMap[heatMap.getActionManager().getAction("Fit To Window").which[0]]+"</span> </a></li>");toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Fit Rows To Window">Fit Rows To Window</a></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="Fit Columns To Window">Fit Columns To Window</a></li>');toolbarHtml.push('<li role="separator" class="divider"></li>');toolbarHtml.push('<li><a class="morpheus-menu-item" href="#" data-action="100%">100%</a></li>');toolbarHtml.push("</ul>");toolbarHtml.push("</div>")}toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.sort){toolbarHtml.push('<button data-toggle="tooltip" title="Sort" name="Sort" type="button" class="btn'+' btn-default btn-xxs"><span class="fa fa-sort-alpha-asc"></span></button>')}if(heatMap.options.toolbar.options){toolbarHtml.push('<button data-action="Options" data-toggle="tooltip" title="Options" type="button"'+' class="btn btn-default btn-xxs"><span class="fa fa-cog"></span></button>')}toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.openFile){toolbarHtml.push('<button data-action="Open File" data-toggle="tooltip" title="Open File ('+morpheus.Util.COMMAND_KEY+'O)" type="button" class="btn btn-default btn-xxs"><span class="fa fa-folder-open-o"></span></button>')}if(heatMap.options.toolbar.saveImage){toolbarHtml.push('<button data-action="Save Image" data-toggle="tooltip" title="Save Image ('+morpheus.Util.COMMAND_KEY+'S)" type="button" class="btn btn-default btn-xxs"><span class="fa fa-file-image-o"></span></button>')}if(heatMap.options.toolbar.saveDataset){toolbarHtml.push('<button data-action="Save Dataset" data-toggle="tooltip" title="Save Dataset ('+morpheus.Util.COMMAND_KEY+'Shift+S)" type="button" class="btn btn-default btn-xxs"><span class="fa fa-floppy-o"></span></button>')}if(heatMap.options.toolbar.saveSession){toolbarHtml.push('<button data-action="Save Session" data-toggle="tooltip" title="Save Session" type="button"'+' class="btn btn-default btn-xxs"><span class="fa fa-anchor"></span></button>')}toolbarHtml.push('<div class="morpheus-button-divider"></div>');if(heatMap.options.toolbar.filter){toolbarHtml.push('<button data-action="Filter" data-toggle="tooltip" title="Filter" type="button"'+' class="btn btn-default btn-xxs"><span class="fa fa-filter"></span></button>')}if(heatMap.options.toolbar.chart&&typeof echarts!=="undefined"){toolbarHtml.push('<button data-action="Chart" data-toggle="tooltip" title="Chart" type="button" class="btn'+' btn-default btn-xxs"><span class="fa fa-line-chart"></span></button>')}if(heatMap.options.toolbar.colorKey){toolbarHtml.push('<div class="morpheus-button-divider"></div>');toolbarHtml.push('<div class="btn-group">');toolbarHtml.push('<button type="button" class="btn btn-default btn-xxs" data-toggle="dropdown"><span title="Color Key" data-toggle="tooltip" class="fa fa-key"></span></button>');toolbarHtml.push('<ul data-name="key" class="dropdown-menu" role="menu">');toolbarHtml.push('<li data-name="keyContent"></li>');toolbarHtml.push("</ul>");toolbarHtml.push("</div>")}toolbarHtml.push("</div>");var $toolbar=$(toolbarHtml.join(""));$toolbar.find("[data-action]").on("click",function(e){e.preventDefault();heatMap.getActionManager().execute($(this).data("action"))}).on("blur",function(e){if(document.activeElement===document.body){heatMap.focus()}});$menus.on("click","li > a",function(e){e.preventDefault();heatMap.getActionManager().execute($(this).data("action"))}).on("blur",function(e){if(document.activeElement===document.body){heatMap.focus()}});if(heatMap.options.toolbar.$customButtons){heatMap.options.toolbar.$customButtons.appendTo($toolbar)}$toolbar.appendTo($lineOneColumn);$el.prependTo(heatMap.$content);this.$tip=$el.find("[data-name=tip]");$el.find('[data-toggle="tooltip"]').tooltip({placement:"bottom",container:"body",trigger:"hover"}).on("click",function(){$(this).tooltip("hide")});var $key=$el.find("[data-name=key]");var $keyContent=$el.find("[data-name=keyContent]");$key.dropdown().parent().on("show.bs.dropdown",function(){new morpheus.HeatMapColorSchemeLegend(heatMap,$keyContent);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"colorKey"})});var searchHelpHtml=[];searchHelpHtml.push("<h4>Symbols</h4>");searchHelpHtml.push('<table class="table table-bordered">');searchHelpHtml.push("<tr><th>Term</th><th>Description</th></tr>");searchHelpHtml.push("<tr><td><code><strong>*</strong></code></td><td>Quote a search term for an"+" exact"+" match. <br"+' />Example: <code><strong>"root beer"</strong></code></td></tr>');searchHelpHtml.push("<tr><td><code><strong>-</strong></code></td><td>Exclude matches using -"+" modifier.</td></tr>");searchHelpHtml.push("<tr><td><code><strong>..</strong></code></td><td>Separate numbers by two"+" periods"+" without spaces to"+" see numbers that fall within a range.. <br"+" />Example: <code><strong>1..10</strong></code></td></tr>");searchHelpHtml.push("<tr><td><code><strong><= < > >= =</strong></code></td><td>Perform a"+" numeric"+" search."+" <br"+" />Example: <code><strong>>4</strong></code></td></tr>");searchHelpHtml.push("</table>");searchHelpHtml.push("<h4>Search fields</h4>");searchHelpHtml.push('<p>You can restrict your search to any field by typing the field name followed by a colon ":" and then the term you are looking for. For example, to search for matches containing "beer" in the beverage field, you can enter:'+" <code><strong>beverage:beer</strong></code>");searchHelpHtml.push("Note that searches only include metadata fields that are displayed. You"+" can search a hidden field by performing a field search.");searchHelpHtml.push("<p>You can search for an exact list of values by enclosing the list of"+" values in parentheses. For example: <code><strong>pet:(cat dog)</strong></code>"+" searches all pets that are either cats or dogs.</p>");var $searchHelp=$(searchHelpHtml.join(""));$el.find("[data-name=searchHelp]").on("click",function(e){e.preventDefault();morpheus.FormBuilder.showInModal({title:"Search Help",html:$searchHelp,appendTo:heatMap.getContentEl(),focus:heatMap.getFocusEl()})});var $searchRowsGroup=$searchForm.find("[data-name=searchRowsGroup]");var $searchColumnsGroup=$searchForm.find("[data-name=searchColumnsGroup]");var $searchValuesGroup=$searchForm.find("[data-name=searchValuesGroup]");var $searchRowDendrogramGroup=$searchForm.find("[data-name=searchRowDendrogramGroup]");var $searchColumnDendrogramGroup=$searchForm.find("[data-name=searchColumnDendrogramGroup]");this.$searchRowDendrogramGroup=$searchRowDendrogramGroup;this.$searchColumnDendrogramGroup=$searchColumnDendrogramGroup;this.matchMode="contains";this.matchAllPredicates=false;var $searchToggle=$searchForm.find("[name=searchToggle]");var nameToSearchObject={};function getSearchElements($group,searchName,cb){var obj={$group:$group,$search:$group.find("[name=search]"),$searchResultsWrapper:$group.find("[data-name=searchResultsWrapper]"),$searchResults:$group.find("[data-name=searchResults]"),$previousMatch:$group.find("[name=previousMatch]"),$nextMatch:$group.find("[name=nextMatch]"),$matchesToTop:$group.find("[name=matchesToTop]"),$toggleButton:$searchToggle.filter("[data-search="+searchName+"]").parent()};nameToSearchObject[searchName]=obj;return obj}var $searchOptions=$el.find("[data-name=searchOptions]");$searchOptions.on("click","li > a",function(e){e.preventDefault();var $this=$(this);var group=$this.data("group");if(group==="matchMode"){_this.matchMode=$this.data("name")}else{_this.matchAllPredicates=$this.data("name")==="matchAll"}var $searchField;if(_this.rowSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.columnSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.rowDendrogramSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.columnDendrogramSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}else if(_this.valueSearchObject.$search.is(":visible")){$searchField=_this.rowSearchObject.$search}if($searchField){$searchField.trigger($.Event("keyup",{keyCode:13,which:13}))}var $span=$(this).find("span");if($span.data("type")==="toggle"){$searchOptions.find("[data-group="+group+"] > [data-type=toggle]").removeClass("dropdown-checkbox"+" fa"+" fa-check");$span.addClass("dropdown-checkbox fa fa-check")}morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchMatchMode"})});this.rowSearchObject=getSearchElements($searchRowsGroup,"rows",function(){_this.search(true)});this.columnSearchObject=getSearchElements($searchColumnsGroup,"columns",function(){_this.search(false)});this.rowDendrogramSearchObject=getSearchElements($searchRowDendrogramGroup,"rowDendrogram",function(){_this.searchDendrogram(false)});this.columnDendrogramSearchObject=getSearchElements($searchColumnDendrogramGroup,"columnDendrogram",function(){_this.searchDendrogram(false)});this.valueSearchObject=getSearchElements($searchValuesGroup,"values",function(){searchValues()});if(!heatMap.options.toolbar.searchRows){this.rowSearchObject.$toggleButton.hide();this.rowSearchObject.$group.css("display","none")}if(!heatMap.options.toolbar.searchColumns){this.columnSearchObject.$toggleButton.hide();this.columnSearchObject.$group.css("display","none")}if(!heatMap.options.toolbar.searchValues){this.valueSearchObject.$toggleButton.hide();this.valueSearchObject.$group.css("display","none")}this.rowDendrogramSearchObject.$toggleButton.hide();this.rowDendrogramSearchObject.$group.hide();this.columnDendrogramSearchObject.$toggleButton.hide();this.columnDendrogramSearchObject.$group.hide();this.rowDendrogramSearchObject.$searchResultsWrapper.show();this.columnDendrogramSearchObject.$searchResultsWrapper.show();this.valueSearchObject.$searchResultsWrapper.show();this.rowSearchObject.$search.css({"border-top":"3.8px solid #e6e6e6","border-bottom":"3.8px solid #e6e6e6",width:"240px"});this.columnSearchObject.$search.css({"border-right":"3.8px solid #e6e6e6","border-left":"3.8px solid #e6e6e6",width:"240px"});this.$valueSearchResults=$searchValuesGroup.find("[name=searchResults]");this.$valueTextField=$searchValuesGroup.find("[name=search]");this.$dimensionsLabel=$el.find("[data-name=dim]");this.$selectionLabel=$el.find("[data-name=selection]");$searchToggle.on("change",function(e){var search=$(this).data("search");for(var name in nameToSearchObject){var searchObject=nameToSearchObject[name];if(name===search){searchObject.$group.css("display","inline-block");searchObject.$search.focus()}else{searchObject.$group.css("display","none")}}});this.toggleSearch=function(){var $visible=$searchToggle.filter(":visible");var $checked=$searchToggle.filter(":checked");var $next=$visible.eq($visible.index($checked)+1);if(!$next.length){$next=$visible.first()}$next.click()};for(var i=0;i<$searchToggle.length;i++){var $button=$($searchToggle[i]);if($button.parent().css("display")==="block"){$button.click();break}}heatMap.on("dendrogramAnnotated",function(e){if(e.isColumns){_this.rowDendrogramSearchObject.$toggleButton.show()}else{_this.columnDendrogramSearchObject.$toggleButton.show()}});heatMap.on("dendrogramChanged",function(e){if(e.isColumns){_this.rowDendrogramSearchObject.$group.hide();_this.rowDendrogramSearchObject.$toggleButton.hide()}else{_this.columnDendrogramSearchObject.$group.hide();_this.columnDendrogramSearchObject.$toggleButton.hide()}});var project=heatMap.getProject();morpheus.Util.autosuggest({$el:this.rowSearchObject.$search,filter:function(terms,cb){var indices=[];var meta=project.getSortedFilteredDataset().getRowMetadata();heatMap.getVisibleTrackNames(false).forEach(function(name){var index=morpheus.MetadataUtil.indexOf(meta,name);if(index!==-1){indices.push(index)}});meta=new morpheus.MetadataModelColumnView(meta,indices);morpheus.MetadataUtil.autocomplete(meta)(terms,cb)},select:function(){_this.search(true)}});this.rowSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.search(true);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchRows"})},500));morpheus.Util.autosuggest({$el:this.columnSearchObject.$search,filter:function(terms,cb){var indices=[];var meta=project.getSortedFilteredDataset().getColumnMetadata();heatMap.getVisibleTrackNames(true).forEach(function(name){var index=morpheus.MetadataUtil.indexOf(meta,name);if(index!==-1){indices.push(index)}});meta=new morpheus.MetadataModelColumnView(meta,indices);morpheus.MetadataUtil.autocomplete(meta)(terms,cb)},select:function(){_this.search(false)}});this.columnSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.search(false);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchColumns"})},500));morpheus.Util.autosuggest({$el:this.rowDendrogramSearchObject.$search,filter:function(tokens,cb){var d=heatMap.getDendrogram(false);if(!d.searchTerms){cb([])}else{var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);if(token===""){cb([])}else{morpheus.Util.autocompleteArrayMatcher(token,cb,d.searchTerms,null,10)}}},select:function(){_this.searchDendrogram(false)}});this.rowDendrogramSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.searchDendrogram(false);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchRowDendrogram"})},500));morpheus.Util.autosuggest({$el:this.columnDendrogramSearchObject.$search,filter:function(tokens,cb){var d=heatMap.getDendrogram(true);if(!d.searchTerms){cb([])}else{var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);if(token===""){cb([])}else{morpheus.Util.autocompleteArrayMatcher(token,cb,d.searchTerms,null,10)}}},select:function(){_this.searchDendrogram(true)}});this.columnDendrogramSearchObject.$search.on("keyup",_.debounce(function(e){if(e.which===13){e.preventDefault()}_this.searchDendrogram(true);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"searchColumnDendrogram"})},500));function searchValues(){var $searchResultsLabel=_this.$valueSearchResults;var text=$.trim(_this.$valueTextField.val());if(text===""){$searchResultsLabel.html("");project.getElementSelectionModel().setViewIndices(null)}else{var viewIndices=morpheus.DatasetUtil.searchValues({dataset:project.getSortedFilteredDataset(),text:text,matchAllPredicates:_this.matchAllPredicates,defaultMatchMode:_this.matchMode});project.getElementSelectionModel().setViewIndices(viewIndices);$searchResultsLabel.html(viewIndices.size()+" match"+(viewIndices.size()===1?"":"es"))}}morpheus.Util.autosuggest({$el:this.$valueTextField,filter:function(terms,cb){morpheus.DatasetUtil.autocompleteValues(project.getSortedFilteredDataset())(terms,cb)},select:function(){searchValues()}});this.$valueTextField.on("keyup",_.debounce(function(e){if(e.which===13){_this.$valueTextField.autocomplete("close");e.preventDefault()}searchValues()},500));this.toggleControls=function(){if($lineOneColumn.css("display")==="none"){$lineOneColumn.css("display","");_this.rowSearchObject.$search.focus()}else{$lineOneColumn.css("display","none");$(_this.heatMap.heatmap.canvas).focus()}};this.$el=$el;var updateFilterStatus=function(){if(heatMap.getProject().getRowFilter().isEnabled()||heatMap.getProject().getColumnFilter().isEnabled()){_this.$el.find("[name=filterButton]").addClass("btn-primary")}else{_this.$el.find("[name=filterButton]").removeClass("btn-primary")}};updateFilterStatus();this.columnSearchObject.$matchesToTop.on("click",function(e){e.preventDefault();var $this=$(this);$this.toggleClass("btn-primary");_this.setSelectionOnTop({isColumns:true,isOnTop:$this.hasClass("btn-primary"),updateButtonStatus:false});morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"columnMatchesToTop"})});this.rowSearchObject.$matchesToTop.on("click",function(e){e.preventDefault();var $this=$(this);$this.toggleClass("btn-primary");_this.setSelectionOnTop({isColumns:false,isOnTop:$this.hasClass("btn-primary"),updateButtonStatus:false});morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"rowMatchesToTop"})});project.on("rowSortOrderChanged.morpheus",function(e){if(_this.searching){return}_this._updateSearchIndices(false);_this.rowSearchObject.$matchesToTop.removeClass("btn-primary")});project.on("columnSortOrderChanged.morpheus",function(e){if(_this.searching){return}_this._updateSearchIndices(true);_this.columnSearchObject.$matchesToTop.removeClass("btn-primary")});heatMap.getProject().on("rowFilterChanged.morpheus",function(e){_this.search(true);updateFilterStatus()});heatMap.getProject().on("columnFilterChanged.morpheus",function(e){_this.search(false);updateFilterStatus()});heatMap.getProject().on("datasetChanged.morpheus",function(){_this.search(true);_this.search(false);updateFilterStatus()});heatMap.getProject().getRowSelectionModel().on("selectionChanged.morpheus",function(){_this.updateSelectionLabel()});heatMap.getProject().getColumnSelectionModel().on("selectionChanged.morpheus",function(){_this.updateSelectionLabel()});this.rowSearchResultViewIndicesSorted=null;this.currentRowSearchIndex=0;this.columnSearchResultViewIndicesSorted=null;this.currentColumnSearchIndex=-1;this.columnSearchObject.$previousMatch.on("click",function(){_this.currentColumnSearchIndex--;if(_this.currentColumnSearchIndex<0){_this.currentColumnSearchIndex=_this.columnSearchResultViewIndicesSorted.length-1}heatMap.scrollLeft(heatMap.getHeatMapElementComponent().getColumnPositions().getPosition(_this.columnSearchResultViewIndicesSorted[_this.currentColumnSearchIndex]));morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"previousColumnMatch"})});this.rowSearchObject.$previousMatch.on("click",function(){_this.currentRowSearchIndex--;if(_this.currentRowSearchIndex<0){_this.currentRowSearchIndex=_this.rowSearchResultViewIndicesSorted.length-1}heatMap.scrollTop(heatMap.getHeatMapElementComponent().getRowPositions().getPosition(_this.rowSearchResultViewIndicesSorted[_this.currentRowSearchIndex]));morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"previousRowMatch"})});this.columnSearchObject.$nextMatch.on("click",function(){_this.next(true);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"nextColumnMatch"})});this.rowSearchObject.$nextMatch.on("click",function(){_this.next(false);morpheus.Util.trackEvent({eventCategory:"ToolBar",eventAction:"nextRowMatch"})});this.updateDimensionsLabel();this.updateSelectionLabel()};morpheus.HeatMapToolBar.HIGHLIGHT_SEARCH_MODE=0;morpheus.HeatMapToolBar.FILTER_SEARCH_MODE=1;morpheus.HeatMapToolBar.MATCHES_TO_TOP_SEARCH_MODE=2;morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE=3;morpheus.HeatMapToolBar.prototype={quickColumnFilter:false,searching:false,rowSearchMode:morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE,columnSearchMode:morpheus.HeatMapToolBar.SELECT_MATCHES_SEARCH_MODE,_updateSearchIndices:function(isColumns){var project=this.heatMap.getProject();if(isColumns){var viewIndices=[];var modelIndices=this.columnSearchResultModelIndices;for(var i=0,length=modelIndices.length;i<length;i++){var index=project.convertModelColumnIndexToView(modelIndices[i]);if(index!==-1){viewIndices.push(index)}}viewIndices.sort(function(a,b){return a<b?-1:1});this.columnSearchResultViewIndicesSorted=viewIndices;this.currentColumnSearchIndex=-1}else{var viewIndices=[];var modelIndices=this.rowSearchResultModelIndices;for(var i=0,length=modelIndices.length;i<length;i++){var index=project.convertModelRowIndexToView(modelIndices[i]);if(index!==-1){viewIndices.push(index)}}viewIndices.sort(function(a,b){return a<b?-1:1});this.rowSearchResultViewIndicesSorted=viewIndices;this.currentRowSearchIndex=-1}},next:function(isColumns){var heatMap=this.heatMap;if(isColumns){this.currentColumnSearchIndex++;if(this.currentColumnSearchIndex>=this.columnSearchResultViewIndicesSorted.length){this.currentColumnSearchIndex=0}heatMap.scrollLeft(heatMap.getHeatMapElementComponent().getColumnPositions().getPosition(this.columnSearchResultViewIndicesSorted[this.currentColumnSearchIndex]))}else{this.currentRowSearchIndex++;if(this.currentRowSearchIndex>=this.rowSearchResultViewIndicesSorted.length){this.currentRowSearchIndex=0}heatMap.scrollTop(heatMap.getHeatMapElementComponent().getRowPositions().getPosition(this.rowSearchResultViewIndicesSorted[this.currentRowSearchIndex]))}},getSearchField:function(type){if(type===morpheus.HeatMapToolBar.COLUMN_SEARCH_FIELD){return this.columnSearchObject.$search}else if(type===morpheus.HeatMapToolBar.ROW_SEARCH_FIELD){return this.rowSearchObject.$search}else if(type===morpheus.HeatMapToolBar.COLUMN_DENDROGRAM_SEARCH_FIELD){return this.columnDendrogramSearchObject.$search}else if(type===morpheus.HeatMapToolBar.ROW_DENDROGRAM_SEARCH_FIELD){return this.rowDendrogramSearchObject.$search}},setSearchText:function(options){var $tf=options.isColumns?this.columnSearchObject.$search:this.rowSearchObject.$search;var existing=options.append?$.trim($tf.val()):"";if(existing!==""){existing+=" "}if(options.onTop){options.isColumns?this.columnSearchObject.$matchesToTop.addClass("btn-primary"):this.rowSearchObject.$matchesToTop.addClass("btn-primary")}$tf.val(existing+options.text);this.search(!options.isColumns);if(options.scrollTo){this.next(options.isColumns)}},updateDimensionsLabel:function(){var p=this.heatMap.getProject();var d=p.getFullDataset();var f=p.getSortedFilteredDataset();var text=[];if(f.getRowCount()!==d.getRowCount()){text.push("<b>");text.push(morpheus.Util.intFormat(f.getRowCount()));text.push("/");text.push(morpheus.Util.intFormat(d.getRowCount()));text.push("</b>")}else{text.push(morpheus.Util.intFormat(f.getRowCount()))}text.push(" rows by ");if(f.getColumnCount()!==d.getColumnCount()){text.push("<b>");text.push(morpheus.Util.intFormat(f.getColumnCount()));text.push("/");text.push(morpheus.Util.intFormat(d.getColumnCount()));text.push("</b>")}else{text.push(morpheus.Util.intFormat(f.getColumnCount()))}text.push(" columns");this.$dimensionsLabel.html(text.join(""))},updateSelectionLabel:function(){var nc=this.heatMap.getProject().getColumnSelectionModel().count();var nr=this.heatMap.getProject().getRowSelectionModel().count();var text=[];text.push(morpheus.Util.intFormat(nr)+" row");if(nr!==1){text.push("s")}text.push(", ");text.push(morpheus.Util.intFormat(nc)+" column");if(nc!==1){text.push("s")}text.push(" selected");this.$selectionLabel.html(text.join(""))},searchDendrogram:function(isColumns){var searchObject=isColumns?this.columnDendrogramSearchObject:this.rowDendrogramSearchObject;var text=$.trim(searchObject.$search.val());var dendrogram=isColumns?this.heatMap.columnDendrogram:this.heatMap.rowDendrogram;var $searchResults=searchObject.$searchResults;var matches=morpheus.DendrogramUtil.search({rootNode:dendrogram.tree.rootNode,text:text,matchAllPredicates:this.matchAllPredicates,defaultMatchMode:this.matchMode});if(matches===-1){$searchResults.html("")}else{$searchResults.html(matches+" match"+(matches===1?"":"es"))}if(matches<=0){var positions=isColumns?this.heatMap.getHeatMapElementComponent().getColumnPositions():this.heatMap.getHeatMapElementComponent().getRowPositions();positions.setSquishedIndices(null);if(isColumns){this.heatMap.getProject().setGroupColumns([],true)}else{this.heatMap.getProject().setGroupRows([],true)}positions.setSize(isColumns?this.heatMap.getFitColumnSize():this.heatMap.getFitRowSize())}else{morpheus.DendrogramUtil.squishNonSearchedNodes(this.heatMap,isColumns)}this.heatMap.updateDataset();this.heatMap.revalidate()},search:function(isRows){this.searching=true;var isMatchesOnTop=isRows?this.rowSearchObject.$matchesToTop.hasClass("btn-primary"):this.columnSearchObject.$matchesToTop.hasClass("btn-primary");var heatMap=this.heatMap;var project=heatMap.getProject();var sortKeys=isRows?project.getRowSortKeys():project.getColumnSortKeys();sortKeys=sortKeys.filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.toString()==="matches on top")});var dataset=project.getSortedFilteredDataset();var $searchResultsLabel=isRows?this.rowSearchObject.$searchResults:this.columnSearchObject.$searchResults;var searchText=!isRows?$.trim(this.columnSearchObject.$search.val()):$.trim(this.rowSearchObject.$search.val());var metadata=isRows?dataset.getRowMetadata():dataset.getColumnMetadata();var visibleIndices=[];heatMap.getVisibleTrackNames(!isRows).forEach(function(name){var index=morpheus.MetadataUtil.indexOf(metadata,name);if(index!==-1){visibleIndices.push(index)}});var fullModel=metadata;metadata=new morpheus.MetadataModelColumnView(metadata,visibleIndices);var searchResultViewIndices=morpheus.MetadataUtil.search({model:metadata,fullModel:fullModel,text:searchText,isColumns:!isRows,matchAllPredicates:this.matchAllPredicates,defaultMatchMode:this.matchMode});if(searchText===""){$searchResultsLabel.html("");if(isRows){this.rowSearchObject.$searchResultsWrapper.hide()}else{this.columnSearchObject.$searchResultsWrapper.hide()}}else{$searchResultsLabel.html(searchResultViewIndices.length+" match"+(searchResultViewIndices.length===1?"":"es"));if(isRows){this.rowSearchObject.$searchResultsWrapper.show()}else{this.columnSearchObject.$searchResultsWrapper.show()}}var searchResultsModelIndices=[];if(searchResultViewIndices!=null){for(var i=0,length=searchResultViewIndices.length;i<length;i++){var viewIndex=searchResultViewIndices[i];searchResultsModelIndices.push(isRows?project.convertViewRowIndexToModel(viewIndex):project.convertViewColumnIndexToModel(viewIndex))}}if(searchResultViewIndices!==null&&isMatchesOnTop){var key=new morpheus.MatchesOnTopSortKey(project,searchResultsModelIndices,"matches on top",!isRows);searchResultViewIndices=key.indices;sortKeys.splice(0,0,key);if(isRows){project.setRowSortKeys(sortKeys,false)}else{project.setColumnSortKeys(sortKeys,false)}}var searchResultsViewIndicesSet=new morpheus.Set;if(searchResultViewIndices!=null){for(var i=0,length=searchResultViewIndices.length;i<length;i++){var viewIndex=searchResultViewIndices[i];searchResultsViewIndicesSet.add(viewIndex)}}if(searchResultViewIndices==null){searchResultViewIndices=[]}if(isRows){this.rowSearchResultModelIndices=searchResultsModelIndices;this.rowSearchResultViewIndicesSorted=searchResultViewIndices.sort(function(a,b){return a<b?-1:1});this.currentRowSearchIndex=-1}else{this.columnSearchResultModelIndices=searchResultsModelIndices;this.columnSearchResultViewIndicesSorted=searchResultViewIndices.sort(function(a,b){return a<b?-1:1});this.currentColumnSearchIndex=-1}(!isRows?project.getColumnSelectionModel():project.getRowSelectionModel()).setViewIndices(searchResultsViewIndicesSet,true);if(isMatchesOnTop){if(isRows){project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,project.getRowSortKeys()),true)}else{project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,project.getColumnSortKeys()),true)}}this.updateDimensionsLabel();this.updateSelectionLabel();this.searching=false},isSelectionOnTop:function(isColumns){var $btn=isColumns?this.columnSearchObject.$matchesToTop:this.rowSearchObject.$matchesToTop;return $btn.hasClass("btn-primary")},setSelectionOnTop:function(options){if(options.updateButtonStatus){var $btn=options.isColumns?this.columnSearchObject.$matchesToTop:this.rowSearchObject.$matchesToTop;if(options.isOnTop){$btn.addClass("btn-primary")}else{$btn.removeClass("btn-primary")}}var project=this.heatMap.getProject();var sortKeys=options.isColumns?project.getColumnSortKeys():project.getRowSortKeys();sortKeys=sortKeys.filter(function(key){return!(key instanceof morpheus.MatchesOnTopSortKey&&key.name==="matches on top")});if(options.isOnTop){var key=new morpheus.MatchesOnTopSortKey(project,options.isColumns?this.columnSearchResultModelIndices:this.rowSearchResultModelIndices,"matches on top");sortKeys.splice(0,0,key);if(options.isColumns){this.heatMap.scrollLeft(0)}else{this.heatMap.scrollTop(0)}}this.searching=true;if(options.isColumns){project.setColumnSortKeys(sortKeys,true)}else{project.setRowSortKeys(sortKeys,true)}this._updateSearchIndices(options.isColumns);this.searching=false}};morpheus.HeatMapToolBar.COLUMN_SEARCH_FIELD="column";morpheus.HeatMapToolBar.ROW_SEARCH_FIELD="column";morpheus.HeatMapToolBar.COLUMN_DENDROGRAM_SEARCH_FIELD="column_dendrogram";morpheus.HeatMapToolBar.ROW_DENDROGRAM_SEARCH_FIELD="row_dendrogram";morpheus.HeatMapTooltipProvider=function(heatMap,rowIndex,columnIndex,options,separator,quick,tipText){var dataset=heatMap.project.getSortedFilteredDataset();if(!quick){if(options.value){_.each(options.value,function(pair){if(tipText.length>0){tipText.push(separator)}tipText.push(pair.name);tipText.push(": <b>");if(_.isArray(pair.value)){for(var i=0;i<pair.value.length;i++){if(i>0){tipText.push(", ")}tipText.push(pair.value[i])}}else{tipText.push(pair.value)}tipText.push("</b>")})}}if(rowIndex!==-1&&columnIndex!==-1){var tooltipSeriesIndices=options.tooltipSeriesIndices?options.tooltipSeriesIndices:morpheus.Util.sequ32(dataset.getSeriesCount());for(var i=0,nseries=tooltipSeriesIndices.length;i<nseries;i++){morpheus.HeatMapTooltipProvider._matrixValueToString(heatMap,dataset,rowIndex,columnIndex,tooltipSeriesIndices[i],tipText,separator,options.showSeriesNameInTooltip||i>0);if(heatMap.options.symmetric&&dataset.getValue(rowIndex,columnIndex,tooltipSeriesIndices[i])!==dataset.getValue(columnIndex,rowIndex,tooltipSeriesIndices[i])){morpheus.HeatMapTooltipProvider._matrixValueToString(heatMap,dataset,columnIndex,rowIndex,tooltipSeriesIndices[i],tipText,separator,false)}}if(quick){var quickRowTracks=heatMap.rowTracks.filter(function(t){return t.settings.inlineTooltip});morpheus.HeatMapTooltipProvider._tracksToString(quickRowTracks,dataset.getRowMetadata(),rowIndex,tipText,separator);morpheus.HeatMapTooltipProvider._tracksToString(heatMap.columnTracks.filter(function(t){return t.settings.inlineTooltip}),dataset.getColumnMetadata(),columnIndex,tipText,separator)}}else if(quick){if(rowIndex!==-1){morpheus.HeatMapTooltipProvider._tracksToString(heatMap.rowTracks.filter(function(t){return t.settings.inlineTooltip&&options.name!==t.getName()}),dataset.getRowMetadata(),rowIndex,tipText,separator)}if(columnIndex!==-1){morpheus.HeatMapTooltipProvider._tracksToString(heatMap.columnTracks.filter(function(t){return t.settings.inlineTooltip&&options.name!==t.getName()}),dataset.getColumnMetadata(),columnIndex,tipText,separator)}}if(!quick){if(rowIndex!==-1){morpheus.HeatMapTooltipProvider._metadataToString(options,heatMap.rowTracks,dataset.getRowMetadata(),rowIndex,tipText,separator)}if(columnIndex!==-1){morpheus.HeatMapTooltipProvider._metadataToString(options,heatMap.columnTracks,dataset.getColumnMetadata(),columnIndex,tipText,separator)}}else if(options.name!=null){var metadata=rowIndex!==-1?dataset.getRowMetadata():dataset.getColumnMetadata();var vector=metadata.getByName(options.name);var track=heatMap.getTrack(options.name,columnIndex!==-1);var colorByName=track!=null?track.settings.colorByField:null;var additionalVector=colorByName!=null?metadata.getByName(colorByName):null;morpheus.HeatMapTooltipProvider.vectorToString(vector,rowIndex!==-1?rowIndex:columnIndex,tipText,separator,additionalVector)}var rowNodes=[];var columnNodes=[];var selectedRowNodes=[];var selectedColumnNodes=[];if(options.rowNodes){rowNodes=options.rowNodes}if(options.columnNodes){columnNodes=options.columnNodes}if(!quick){if(heatMap.rowDendrogram){selectedRowNodes=_.values(heatMap.rowDendrogram.selectedRootNodeIdToNode)}if(heatMap.columnDendrogram){selectedColumnNodes=_.values(heatMap.columnDendrogram.selectedRootNodeIdToNode)}if(selectedRowNodes.length>0&&rowNodes.length>0){var nodeIds={};_.each(selectedRowNodes,function(n){nodeIds[n.id]=true});rowNodes=_.filter(rowNodes,function(n){return nodeIds[n.id]===undefined})}if(selectedColumnNodes.length>0&&columnNodes.length>0){var nodeIds={};_.each(selectedColumnNodes,function(n){nodeIds[n.id]=true});columnNodes=_.filter(columnNodes,function(n){return nodeIds[n.id]===undefined})}}morpheus.HeatMapTooltipProvider._nodesToString(tipText,rowNodes,null,separator);morpheus.HeatMapTooltipProvider._nodesToString(tipText,columnNodes,null,separator);if(!quick){if(selectedRowNodes.length>0){morpheus.HeatMapTooltipProvider._nodesToString(tipText,selectedRowNodes,heatMap.rowDendrogram._selectedNodeColor,separator)}if(selectedColumnNodes.length>0){morpheus.HeatMapTooltipProvider._nodesToString(tipText,selectedColumnNodes,heatMap.columnDendrogram._selectedNodeColor,separator)}}};morpheus.HeatMapTooltipProvider._matrixValueToString=function(heatMap,dataset,rowIndex,columnIndex,seriesIndex,tipText,separator,showSeriesNameInTooltip){var val=dataset.getValue(rowIndex,columnIndex,seriesIndex);if(val!=null){var nf=heatMap.getHeatMapElementComponent().getDrawValuesFormat();if(val.toObject||!_.isNumber(val)){var obj=val.toObject?val.toObject():val;if(morpheus.Util.isArray(obj)){var v=morpheus.Util.toString(obj);if(tipText.length>0){tipText.push(separator)}if(showSeriesNameInTooltip){tipText.push(dataset.getName(seriesIndex));tipText.push(": ")}tipText.push("<b>");tipText.push(v);tipText.push("</b>")}else{var keys=_.keys(obj);if(keys.length===0){var v=morpheus.Util.toString(obj);if(tipText.length>0){tipText.push(separator)}if(showSeriesNameInTooltip){tipText.push(dataset.getName(seriesIndex));tipText.push(": ")}tipText.push("<b>");tipText.push(v);tipText.push("</b>")}else{for(var i=0,nkeys=keys.length;i<nkeys;i++){var key=keys[i];if(key!=="__v"){var objVal=obj[key];var v;if(morpheus.Util.isArray(objVal)){v=morpheus.Util.arrayToString(objVal,", ")}else{v=morpheus.Util.toString(objVal)}if(tipText.length>0){tipText.push(separator)}tipText.push(key);tipText.push(": <b>");tipText.push(v);tipText.push("</b>")}}if(_.isNumber(val)){tipText.push(separator);tipText.push("Value: <b>");tipText.push(nf(val));tipText.push("</b>")}}}}else{if(tipText.length>0){tipText.push(separator)}if(showSeriesNameInTooltip){tipText.push(dataset.getName(seriesIndex));tipText.push(": ")}tipText.push("<b>");tipText.push(nf(val));tipText.push("</b>")}}};morpheus.HeatMapTooltipProvider.vectorToString=function(vector,index,tipText,separator,additionalVector){var arrayValueToString=function(arrayFieldName,arrayVal){if(arrayVal!=null){if(arrayFieldName!=null){if(tipText.length>0){tipText.push(separator)}tipText.push(arrayFieldName)}if(arrayVal.toObject){tipText.push(" ");var obj=arrayVal.toObject();var keys=_.keys(obj);_.each(keys,function(key){var subVal=obj[key];if(subVal!=null&&subVal!=""){if(tipText.length>0){tipText.push(separator)}tipText.push(key);tipText.push(": <b>");tipText.push(morpheus.Util.toString(subVal));tipText.push("</b>")}})}else{tipText.push(": <b>");tipText.push(morpheus.Util.toString(arrayVal));tipText.push("</b>")}}};if(vector!=null){var primaryVal=vector.getValue(index);if(primaryVal!=null&&primaryVal!=""){var primaryFields=vector.getProperties().get(morpheus.VectorKeys.FIELDS);if(primaryFields!=null){var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);if(visibleFieldIndices===undefined){visibleFieldIndices=morpheus.Util.seq(primaryFields.length)}var additionalFieldNames=additionalVector!=null?additionalVector.getProperties().get(morpheus.VectorKeys.FIELDS):null;var additionalVal=additionalFieldNames!=null?additionalVector.getValue(index):null;if(tipText.length>0){tipText.push(separator)}tipText.push(vector.getName());for(var j=0;j<visibleFieldIndices.length;j++){arrayValueToString(primaryFields[visibleFieldIndices[j]],primaryVal[visibleFieldIndices[j]])}if(additionalVal!=null){if(tipText.length>0){tipText.push(separator)}tipText.push(additionalVector.getName());for(var j=0;j<visibleFieldIndices.length;j++){arrayValueToString(additionalFieldNames[visibleFieldIndices[j]],additionalVal[visibleFieldIndices[j]])}}}else if(primaryVal.summary){if(tipText.length>0){tipText.push(separator)}tipText.push(vector.getName());tipText.push(": ");var obj=primaryVal.summary;var keys=_.keys(obj);for(var i=0,nkeys=keys.length;i<nkeys;i++){var key=keys[i];if(key!=="__v"){var objVal=obj[key];var v;if(morpheus.Util.isArray(objVal)){v=morpheus.Util.arrayToString(objVal,", ")}else{v=morpheus.Util.toString(objVal)}if(tipText.length>0){tipText.push(separator)}tipText.push(key);tipText.push(": <b>");tipText.push(v);tipText.push("</b>")}}}else{if(tipText.length>0){tipText.push(separator)}tipText.push(vector.getName());tipText.push(": <b>");tipText.push(morpheus.Util.toString(primaryVal));tipText.push("</b>")}}}};morpheus.HeatMapTooltipProvider._tracksToString=function(tracks,metadata,index,tipText,separator){for(var i=0;i<tracks.length;i++){morpheus.HeatMapTooltipProvider.vectorToString(metadata.getByName(tracks[i].name),index,tipText,separator)}};morpheus.HeatMapTooltipProvider._metadataToString=function(options,tracks,metadata,index,tipText,separator){var filtered=[];for(var i=0,ntracks=tracks.length;i<ntracks;i++){var track=tracks[i];if(track.isVisible()&&track.isShowTooltip()){if(tracks[i].name===options.name){filtered.splice(0,0,track)}else{filtered.push(track)}}}morpheus.HeatMapTooltipProvider._tracksToString(filtered,metadata,index,tipText,separator)};morpheus.HeatMapTooltipProvider._nodesToString=function(tipText,nodes,color,separator){var renderField=function(name,value){if(value!=null){if(tipText.length>0){tipText.push(separator)}if(color){tipText.push('<span style="color:'+color+'">')}tipText.push(name);tipText.push(": <b>");if(_.isArray(value)){for(var i=0;i<value.length;i++){if(i>0){tipText.push(", ")}tipText.push(morpheus.Util.toString(value[i]))}}else{tipText.push(morpheus.Util.toString(value))}tipText.push("</b>");if(color){tipText.push("</span>")}}};_.each(nodes,function(node){if(node.info){for(var name in node.info){var value=node.info[name];renderField(name,value)}}renderField("height",node.height);renderField("depth",node.depth);var nLeafNodes=1+Math.abs(node.maxIndex-node.minIndex);if(nLeafNodes>0){renderField("# of leaf nodes",nLeafNodes)}})};morpheus.HeatMapTrackColorLegend=function(tracks,colorModel){morpheus.AbstractCanvas.call(this,false);this.tracks=tracks;this.colorModel=colorModel;this.canvas.style.position=""};morpheus.HeatMapTrackColorLegend.prototype={getPreferredSize:function(){var tracks=this.tracks;var colorModel=this.colorModel;var xpix=0;var ypix=0;var maxYPix=0;var canvas=this.canvas;var context=canvas.getContext("2d");context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector(tracks[i].settings.colorByField);if(vector.getProperties().get(morpheus.VectorKeys.DISCRETE)){var map=colorModel.getDiscreteColorScheme(vector);map.forEach(function(color,key){var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}ypix+=14})}else{maxWidth=220;ypix+=40}maxWidth=Math.max(maxWidth,context.measureText(vector.getName()).width);xpix+=maxWidth+10+14;maxYPix=Math.max(maxYPix,ypix)}return{width:xpix,height:maxYPix>0?maxYPix+12:0}},draw:function(clip,context){var tracks=this.tracks;var colorModel=this.colorModel;var xpix=0;for(var i=0;i<tracks.length;i++){var ypix=0;var vector=tracks[i].getVector(tracks[i].settings.colorByField);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);context.textAlign="left";context.textBaseline="top";context.fillText(vector.getName(),xpix,ypix);context.strokeStyle="LightGrey";var maxWidth=0;var textWidth=context.measureText(vector.getName()).width;if(!isNaN(textWidth)){maxWidth=Math.max(0,textWidth)}ypix+=14;if(vector.getProperties().get(morpheus.VectorKeys.DISCRETE)){var toStringFunction=morpheus.VectorTrack.vectorToString(vector);var map=colorModel.getDiscreteColorScheme(vector);var values=map.keys().sort(morpheus.SortKey.ASCENDING_COMPARATOR);values.forEach(function(key){if(key!=null){key=toStringFunction(key);var color=colorModel.getMappedValue(vector,key);var textWidth=context.measureText(key).width;if(!isNaN(textWidth)){maxWidth=Math.max(maxWidth,textWidth)}context.fillStyle=color;var xoffset=0;if(tracks[i].isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){context.fillRect(xpix,ypix,12,12);context.strokeRect(xpix,ypix,12,12);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;xoffset=16}context.fillText(key,xpix+xoffset,ypix);ypix+=14}})}else{var scheme=colorModel.getContinuousColorScheme(vector);context.save();context.translate(xpix,ypix);morpheus.HeatMapColorSchemeLegend.drawColorScheme(context,scheme,200);context.restore();maxWidth=Math.max(maxWidth,220);ypix+=40}xpix+=maxWidth+10+14}}};morpheus.Util.extend(morpheus.HeatMapTrackColorLegend,morpheus.AbstractCanvas);morpheus.HeatMapTrackFontLegend=function(tracks,model){morpheus.AbstractCanvas.call(this,false);this.tracks=tracks;this.model=model;this.canvas.style.position=""};morpheus.HeatMapTrackFontLegend.prototype={getPreferredSize:function(){var tracks=this.tracks;var model=this.model;var canvas=this.canvas;var context=canvas.getContext("2d");context.font="900 12px "+morpheus.CanvasUtil.getFontFamily(context);var xpix=0;var ypix=0;var maxYPix=0;for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector(tracks[i].settings.fontField);var map=model.getMap(vector.getName());map.forEach(function(font,key){if(font!=null&&font.weight!="400"){var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}ypix+=14}});xpix+=maxWidth+6;maxYPix=Math.max(maxYPix,ypix)}return{width:xpix,height:maxYPix>0?maxYPix+30:0}},draw:function(clip,context){var tracks=this.tracks;var model=this.model;var xpix=0;var ypix=0;context.textAlign="left";context.textBaseline="top";context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.strokeStyle="black";var font=context.font;for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var textVector=tracks[i].getVector();var fontVector=tracks[i].getVector(tracks[i].settings.fontField);context.font=font;context.fillText(textVector.getName(),xpix,ypix);maxWidth=Math.max(maxWidth,context.measureText(textVector.getName()).width);ypix+=14;var map=model.getMap(fontVector.getName());var values=map.keys().sort(morpheus.SortKey.ASCENDING_COMPARATOR);values.forEach(function(key){var mappedFont=model.getMappedValue(fontVector,key);if(mappedFont!=null&&mappedFont.weight!="400"){context.font=mappedFont.weight+" "+font;var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}context.fillText(key,xpix,ypix);ypix+=14}});xpix+=maxWidth+6}}};morpheus.Util.extend(morpheus.HeatMapTrackFontLegend,morpheus.AbstractCanvas);morpheus.HeatMapTrackShapeLegend=function(tracks,shapeModel){morpheus.AbstractCanvas.call(this,false);this.tracks=tracks;this.shapeModel=shapeModel;this.canvas.style.position=""};morpheus.HeatMapTrackShapeLegend.prototype={getPreferredSize:function(){var tracks=this.tracks;var shapeModel=this.shapeModel;var canvas=this.canvas;var context=canvas.getContext("2d");var xpix=0;var ypix=0;var maxYPix=0;for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector();var map=shapeModel.getMap(vector.getName());map.forEach(function(color,key){var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}ypix+=14});xpix+=maxWidth+24;maxYPix=Math.max(maxYPix,ypix)}return{width:xpix,height:maxYPix>0?maxYPix+30:0}},draw:function(clip,context){var tracks=this.tracks;var shapeModel=this.shapeModel;var xpix=0;var ypix=0;context.textAlign="left";context.textBaseline="top";context.font="12px "+morpheus.CanvasUtil.getFontFamily(context);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.strokeStyle="black";for(var i=0;i<tracks.length;i++){ypix=0;var maxWidth=0;var vector=tracks[i].getVector();context.fillText(vector.getName(),xpix,ypix);maxWidth=Math.max(maxWidth,context.measureText(vector.getName()).width);ypix+=14;var map=shapeModel.getMap(vector.getName());var values=map.keys().sort(morpheus.SortKey.ASCENDING_COMPARATOR);values.forEach(function(key){var shape=shapeModel.getMappedValue(vector,key);var width=context.measureText(key).width;if(!isNaN(width)){maxWidth=Math.max(maxWidth,width)}morpheus.CanvasUtil.drawShape(context,shape,xpix+8,ypix+6,6);context.fillText(key,xpix+16,ypix);ypix+=14});xpix+=maxWidth+24}}};morpheus.Util.extend(morpheus.HeatMapTrackShapeLegend,morpheus.AbstractCanvas);morpheus.HeatMap=function(options){morpheus.Util.loadTrackingCode();var _this=this;var dontExtend=["parent","columnDendrogram","rowDendrogram"];var cache=[];for(var i=0;i<dontExtend.length;i++){var field=dontExtend[i];cache[i]=options[field];options[field]=null}options=$.extend(true,{},{el:null,dataset:undefined,rowAnnotations:undefined,columnAnnotations:undefined,columnGroupBy:undefined,rowGroupBy:undefined,colorScheme:undefined,rowSortBy:undefined,columnSortBy:undefined,rowDendrogram:undefined,columnDendrogram:undefined,columnDendrogramField:"id",rowDendrogramField:"id",rows:[],columns:[],tools:undefined,rowFilter:undefined,columnFilter:undefined,autohideTabBar:false,closeable:true,rename:true,rowSize:13,columnSize:13,rowGapSize:10,columnGapSize:10,drawGrid:true,gridColor:"#808080",showRowNumber:false,gridThickness:.1,height:"window",width:undefined,focus:true,tooltipMode:0,inheritFromParent:true,inheritFromParentOptions:{transpose:false},tooltip:undefined,structureUrlProvider:undefined,promises:undefined,renderReady:undefined,datasetReady:undefined,tabOpened:undefined,loadedCallback:undefined,name:undefined,rowsSortable:true,columnsSortable:true,popupEnabled:true,symmetric:false,keyboard:true,inlineTooltip:true,standalone:false,$loadingImage:morpheus.Util.createLoadingEl(),menu:{File:["Open",null,"Save Image","Save Dataset","Save Session",null,"Close Tab",null,"Rename"+" Tab"],Tools:["New Heat Map",null,"Hierarchical Clustering","KMeans Clustering",null,"Marker Selection","Nearest Neighbors","Create Calculated Annotation",null,"Adjust","Collapse","Similarity Matrix","Transpose",null,"Chart",null,"Sort/Group","Filter",null,"API"],View:["Zoom In","Zoom Out",null,"Fit To Window","Fit Rows To Window","Fit Columns To Window",null,"100%",null,"Options"],Edit:["Copy Image","Copy Selected Dataset",null,"Move Selected Rows To Top","Annotate Selected Rows","Copy Selected Rows","Invert"+" Selected Rows","Select All Rows","Clear Selected Rows",null,"Move Selected Columns To Top","Annotate Selected Columns","Copy Selected Columns","Invert"+" Selected Columns","Select All Columns","Clear Selected Columns"],Help:["Search Menus",null,"Contact","Configuration","Tutorial","Source Code",null,"Keyboard"+" Shortcuts"]},toolbar:{dimensions:true,zoom:true,searchRows:true,searchColumns:true,searchValues:false,options:true,saveImage:true,filter:true,colorKey:true}},options);for(var i=0;i<dontExtend.length;i++){var field=dontExtend[i];options[field]=cache[i]}if(options.menu==null){options.menu={}}if(options.toolbar==null){options.toolbar={}}this.options=options;this.tooltipProvider=morpheus.HeatMapTooltipProvider;if(!options.el){this.$el=$("<div></div>")}else{this.$el=$(options.el)}this.rowGapSize=options.rowGapSize;this.columnGapSize=options.columnGapSize;this.actionManager=new morpheus.ActionManager;this.actionManager.heatMap=this;this.$el.addClass("morpheus");if(this.options.dataset==null){var datasetFormBuilder=new morpheus.FormBuilder;datasetFormBuilder.append({name:"file",type:"file"});this.options.dataset=$.Deferred();morpheus.FormBuilder.showOkCancel({title:"Dataset",appendTo:this.getContentEl(),focus:this.getFocusEl(),content:datasetFormBuilder.$form,okCallback:function(){var file=datasetFormBuilder.getValue("file");morpheus.DatasetUtil.read(file).done(function(dataset){_this.options.dataset.resolve(dataset)}).fail(function(err){_this.options.dataset.reject(err)})},cancelCallback:function(){_this.options.dataset.reject("Session cancelled.")}})}if(this.options.name==null){this.options.name=morpheus.Util.getBaseFileName(morpheus.Util.getFileName(this.options.dataset.file?this.options.dataset.file:this.options.dataset))}var isPrimary=this.options.parent==null;if(this.options.parent==null){if(!morpheus.Util.isHeadless()){if(this.options.tabManager==null){this.tabManager=new morpheus.TabManager({landingPage:function(){if(_this.options.landingPage==null){_this.options.landingPage=new morpheus.LandingPage({tabManager:_this.tabManager});_this.options.landingPage.$el.prependTo(_this.$el)}return _this.options.landingPage},autohideTabBar:this.options.autohideTabBar})}else{this.tabManager=this.options.tabManager}if(this.options.tabManager==null){this.tabManager.appendTo(this.$el)}}}else{if(this.options.inheritFromParent){this.popupItems=this.options.parent.popupItems;if(!this.options.tabOpened){this.options.tabOpened=this.options.parent.options.tabOpened}this.options.drawCallback=this.options.parent.options.drawCallback}this.tabManager=this.options.parent.tabManager}this.$content=$("<div></div>");this.$content.css({width:"100%","user-select":"none","-webkit-user-select":"none","-webkit-user-drag":"none","-webkit-tap-highlight-color":"rgba(0, 0, 0, 0)","-moz-user-select":"none","-moz-user-drag":"none","-moz-tap-highlight-color":"rgba(0, 0, 0, 0)","-ms-user-select":"none","-ms-user-drag":"none","-ms-tap-highlight-color":"rgba(0, 0, 0, 0)","-o-user-select":"none","-o-user-drag":"none","-o-tap-highlight-color":"rgba(0, 0, 0, 0)","overflow-x":"visible","overflow-y":"visible"});this.$content.on("remove.morpheus",function(){_this.$content.off("remove.morpheus");_this.dispose()});if(!morpheus.Util.isHeadless()){var tab=this.tabManager.add({$el:this.$content,closeable:this.options.closeable,rename:this.options.rename,title:this.options.name,object:this,focus:this.options.focus});this.tabId=tab.id;this.$tabPanel=tab.$panel}if(options.$loadingImage){options.$loadingImage.appendTo(this.$content)}this.options.dataSource=!options.dataset?"":options.dataset.file?options.dataset.file:options.dataset;this._togglingInfoWindow=false;var promises=[];if(options.promises){for(var i=0;i<options.promises.length;i++){promises.push(options.promises[i])}}this.whenLoaded=[];if(options.rowAnnotations){var rowDef=morpheus.DatasetUtil.annotate({annotations:options.rowAnnotations,isColumns:false});rowDef.done(function(callbacks){_this.whenLoaded=_this.whenLoaded.concat(callbacks)});promises.push(rowDef)}if(options.columnAnnotations){var columnDef=morpheus.DatasetUtil.annotate({annotations:options.columnAnnotations,isColumns:true});columnDef.done(function(callbacks){_this.whenLoaded=_this.whenLoaded.concat(callbacks)});promises.push(columnDef)}if(options.rowDendrogram!=null&&_.isString(options.rowDendrogram)){if(options.rowDendrogram[0]==="("){_this.options.rowDendrogram=morpheus.DendrogramUtil.parseNewick(options.rowDendrogram)}else{var rowDendrogramDeferred=morpheus.Util.getText(options.rowDendrogram);rowDendrogramDeferred.done(function(text){_this.options.rowDendrogram=morpheus.DendrogramUtil.parseNewick(text)});promises.push(rowDendrogramDeferred)}}if(options.columnDendrogram!=null&&_.isString(options.columnDendrogram)){if(options.columnDendrogram[0]==="("){_this.options.columnDendrogram=morpheus.DendrogramUtil.parseNewick(options.columnDendrogram)}else{var columnDendrogramDeferred=morpheus.Util.getText(options.columnDendrogram);columnDendrogramDeferred.done(function(text){_this.options.columnDendrogram=morpheus.DendrogramUtil.parseNewick(text)});promises.push(columnDendrogramDeferred)}}var heatMapLoaded=function(){if(typeof window!=="undefined"){$(window).on("orientationchange.morpheus resize.morpheus",_this.resizeListener=function(){_this.revalidate()})}_this.revalidate();if(options.loadedCallback){options.loadedCallback(_this)}if(_this.tabManager){if(_this.options.focus){_this.tabManager.setActiveTab(tab.id);_this.focus()}else if(_this.tabManager.getTabCount()===1){_this.tabManager.setActiveTab(tab.id)}}_this.$el.trigger("heatMapLoaded",_this)};if(morpheus.Util.isArray(options.dataset)){var d=morpheus.DatasetUtil.readDatasetArray(options.dataset);d.fail(function(message){if(_this.options.$loadingImage){_this.options.$loadingImage.remove()}if(_this.options.error){_this.options.error(message)}morpheus.FormBuilder.showInModal({title:"Error",html:message,appendTo:_this.getContentEl(),focus:_this.getFocusEl()})});d.done(function(joined){if(_this.options.$loadingImage){_this.options.$loadingImage.remove()}_this.options.dataset=joined;_this._init();if(joined.getRowMetadata().getByName("Source")!=null&&!_this.options.colorScheme){_this.heatmap.getColorScheme().setSeparateColorSchemeForRowMetadataField("Source")}_.each(options.dataset,function(option){if(option.colorScheme){_this.heatmap.getColorScheme().setCurrentValue(morpheus.Util.getBaseFileName(morpheus.Util.getFileName(option.dataset)));_this.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(option.colorScheme))}else{try{_this.autoDisplay({extension:morpheus.Util.getExtension(morpheus.Util.getFileName(option.dataset)),filename:morpheus.Util.getBaseFileName(morpheus.Util.getFileName(option.dataset))})}catch(x){console.log("Autodisplay errror")}}});heatMapLoaded()})}else{var deferred=options.dataset.file?morpheus.DatasetUtil.read(options.dataset.file,options.dataset.options):morpheus.DatasetUtil.read(options.dataset);deferred.done(function(dataset){_this.options.dataset=dataset});deferred.fail(function(err){_this.options.$loadingImage.remove();var message=["Error opening "+(options.dataset.file?morpheus.Util.getFileName(options.dataset.file):morpheus.Util.getFileName(options.dataset))+"."];if(err.message){message.push("<br />Cause: ");message.push(err.message)}if(_this.options.error){_this.options.error(message)}morpheus.FormBuilder.showInModal({title:"Error",html:message.join(""),appendTo:_this.getContentEl(),focus:_this.getFocusEl()})});promises.push(deferred);var datasetOverlay=null;if(options.datasetOverlay){var d=options.datasetOverlay.file?morpheus.DatasetUtil.read(options.datasetOverlay.file,options.datasetOverlay.options):morpheus.DatasetUtil.read(options.datasetOverlay);d.done(function(dataset){datasetOverlay=dataset});promises.push(d)}$.when.apply($,promises).done(function(){if(_this.options.$loadingImage){_this.options.$loadingImage.remove()}if(_this.options.dataset==null){return _this.tabManager.remove(_this.tabId)}_this._init();if(datasetOverlay){morpheus.DatasetUtil.overlay({dataset:_this.options.dataset,newDataset:datasetOverlay,rowAnnotationName:"id",newRowAnnotationName:"id",columnAnnotationName:"id",newColumnAnnotationName:"id"})}heatMapLoaded()})}};morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS=6;morpheus.HeatMap.showTool=function(tool,heatMap,callback){if(tool.gui){var gui=tool.gui(heatMap.getProject());var formBuilder=new morpheus.FormBuilder;_.each(gui,function(item){formBuilder.append(item)});var tabId=heatMap.getTabManager().getActiveTabId();if(tool.init){tool.init(heatMap.getProject(),formBuilder,{heatMap:heatMap})}heatMap.trigger("beforeToolShown",{tool:tool,formBuilder:formBuilder});var okCallback=function(){var $dialogContent=$("<div><span>"+tool.toString()+'...</span><button class="btn'+' btn-xs btn-default" style="margin-left:6px;display: none;">Cancel</button></div>');var value=null;var $dialog=morpheus.FormBuilder.showInDraggableDiv({$content:$dialogContent,appendTo:heatMap.getContentEl(),width:"auto"});var input={};_.each(gui,function(item){input[item.name]=formBuilder.getValue(item.name)});setTimeout(function(){value=tool.execute({heatMap:heatMap,project:heatMap.getProject(),input:input});if(value instanceof Worker){$dialogContent.find("button").css("display","").on("click",function(){value.terminate()});value.onerror=function(e){value.terminate();morpheus.FormBuilder.showInModal({title:"Error",html:e,close:"Close",focus:heatMap.getFocusEl(),appendTo:heatMap.getContentEl()});if(e.stack){console.log(e.stack)}};var terminate=_.bind(value.terminate,value);value.terminate=function(){terminate();$dialog.remove();if(callback){callback(input)}}}else{if(value!=null&&typeof value.done==="function"){value.always(function(){if(callback){callback(input)}$dialog.remove()})}else{if(callback){callback(input)}$dialog.remove()}}},20);setTimeout(function(){if(!(value instanceof Worker)){$dialog.remove()}},5e3)};var $formDiv;tool.ok=function(){$formDiv.modal("hide");okCallback()};var guiOptions=$.extend({},{ok:true},gui.options);$formDiv=morpheus.FormBuilder.showOkCancel({title:tool.toString(),apply:tool.apply,ok:guiOptions.ok,cancel:guiOptions.cancel,size:guiOptions.size,draggable:true,content:formBuilder.$form,appendTo:heatMap.getContentEl(),align:"right",okCallback:okCallback,focus:heatMap.getFocusEl()})}else{tool.execute({heatMap:heatMap,project:heatMap.getProject(),input:{}});if(callback){callback({})}}};morpheus.HeatMap.getSpaces=function(groupByKeys,length,gapSize){var previousArray=[];var nkeys=groupByKeys.length;for(var keyIndex=0;keyIndex<nkeys;keyIndex++){var key=groupByKeys[keyIndex];previousArray.push(key.getValue(0))}var spaces=[];var sum=0;spaces.push(sum);for(var i=1;i<length;i++){var isEqual=true;for(var keyIndex=0;keyIndex<nkeys;keyIndex++){var key=groupByKeys[keyIndex];var comparator=key.getComparator();var val=key.getValue(i);var c=comparator(val,previousArray[keyIndex]);if(c!==0){isEqual=false;for(var keyIndex2=0;keyIndex2<nkeys;keyIndex2++){previousArray[keyIndex2]=groupByKeys[keyIndex2].getValue(i)}break}}if(!isEqual){sum+=gapSize}spaces.push(sum)}return spaces};morpheus.HeatMap.createGroupBySpaces=function(dataset,groupByKeys,gapSize,isColumns){if(groupByKeys.length>0){var nkeys=groupByKeys.length;for(var keyIndex=0;keyIndex<nkeys;keyIndex++){groupByKeys[keyIndex].init(groupByKeys[keyIndex].isColumns()?new morpheus.TransposedDatasetView(dataset):dataset)}return morpheus.HeatMap.getSpaces(groupByKeys,isColumns?dataset.getColumnCount():dataset.getRowCount(),gapSize)}};morpheus.HeatMap.isDendrogramVisible=function(project,isColumns){var sortKeys=isColumns?project.getColumnSortKeys():project.getRowSortKeys();if(sortKeys.length===0){return true}var size=isColumns?project.getSortedFilteredDataset().getColumnCount():project.getSortedFilteredDataset().getRowCount();for(var i=0;i<sortKeys.length;i++){if(!sortKeys[i].isPreservesDendrogram()||sortKeys[i].nvisible!==size){return false}}return true};morpheus.HeatMap.prototype={updatingScroll:false,getWhitespaceEl:function(){return this.$whitespace},getActionManager:function(){return this.actionManager},autoDisplay:function(options){if(options.filename==null){options.filename=""}var colorScheme;if(options.extension==="segtab"||options.extension==="seg"){colorScheme={scalingMode:"fixed",values:morpheus.HeatMapColorScheme.Predefined.CN().values.map(function(value){return Math.pow(2,1+value)}),colors:morpheus.HeatMapColorScheme.Predefined.CN().colors}}else if(options.extension==="maf"){colorScheme=morpheus.HeatMapColorScheme.Predefined.MAF();var rowMutProfile=this.project.getFullDataset().getRowMetadata().getByName("mutation_summary");var fieldNames=rowMutProfile.getProperties().get(morpheus.VectorKeys.FIELDS);var useMafColorMap=true;if(fieldNames.length!==morpheus.MafFileReader.FIELD_NAMES.length){useMafColorMap=false}else{for(var i=0;i<fieldNames.length;i++){if(fieldNames[i]!==morpheus.MafFileReader.FIELD_NAMES[i]){useMafColorMap=false;break}}}if(!useMafColorMap){colorScheme={scalingMode:"fixed",stepped:true,values:[0],colors:["rgb(255,255,255)"]};for(var i=0;i<fieldNames.length;i++){colorScheme.values.push(i+1);colorScheme.colors.push(morpheus.VectorColorModel.TWENTY_COLORS[i%morpheus.VectorColorModel.TWENTY_COLORS.length]);colorScheme.names.push(fieldNames[i])}}var columnMutationSummaryVectors=[];var columnMutationSummaryNames=["mutation_summary","mutation_summary_selection"];for(var i=0;i<columnMutationSummaryNames.length;i++){var name=columnMutationSummaryNames[i];if(this.project.getFullDataset().getColumnMetadata().getByName(name)){columnMutationSummaryVectors.push(this.project.getFullDataset().getColumnMetadata().getByName(name));track=this.getTrack(name,true);if(track){track.settingFromConfig("stacked_bar");if(name==="mutation_summary_selection"){track.settings.autoscaleAlways=true}}}}var track=this.getTrack("mutation_summary",false);if(track){track.settingFromConfig("stacked_bar")}for(var i=1;i<colorScheme.colors.length;i++){if(rowMutProfile){this.getProject().getRowColorModel().setMappedValue(rowMutProfile,i-1,colorScheme.colors[i])}for(var j=0;j<columnMutationSummaryVectors.length;j++){this.getProject().getColumnColorModel().setMappedValue(columnMutationSummaryVectors[j],i-1,colorScheme.colors[i])}}}else if(options.extension==="gmt"){colorScheme=morpheus.HeatMapColorScheme.Predefined.BINARY()}else if(options.filename==="all_lesions.conf_99"||options.filename==="all_data_by_genes.txt"||options.filename.toLowerCase().indexOf("gistic")!==-1){colorScheme={scalingMode:"fixed",values:[-.5,0,.5],colors:["blue","white","red"]}}else if(options.filename.toLowerCase().indexOf("copynumber")!==-1||options.filename.toLowerCase().indexOf("copy number")!==-1){colorScheme={scalingMode:"fixed",values:[-1.5,0,1.5],colors:["blue","white","red"]}}else if(options.filename.toLowerCase().indexOf("achilles")!==-1){colorScheme={scalingMode:"fixed",values:[-3,-1,1,3],colors:["blue","white","white","red"]}}if(colorScheme&&options.filename&&this.heatmap.getColorScheme()){this.heatmap.getColorScheme().setCurrentValue(options.filename);this.heatmap.getColorScheme().setColorSupplierForCurrentValue(morpheus.AbstractColorSupplier.fromJSON(colorScheme))}return colorScheme},sortBasedOnSelection:function(sortOrder,isColumns,append){var project=this.project;var selectionModel=isColumns?project.getColumnSelectionModel():project.getRowSelectionModel();var modelIndices=selectionModel.toModelIndices();if(modelIndices.length===0){return}var priorSortKeyIndex=-1;if(sortOrder==null){var existingSortKeys=isColumns?project.getRowSortKeys():project.getColumnSortKeys();for(var i=0,length=existingSortKeys.length;i<length;i++){var key=existingSortKeys[i];if(key instanceof morpheus.SortByValuesKey&&morpheus.Util.arrayEquals(key.modelIndices,modelIndices)){priorSortKeyIndex=i;if(key.getSortOrder()===morpheus.SortKey.SortOrder.UNSORTED){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.DESCENDING){sortOrder=morpheus.SortKey.SortOrder.ASCENDING}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){sortOrder=morpheus.SortKey.SortOrder.TOP_N}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.TOP_N){sortOrder=morpheus.SortKey.SortOrder.UNSORTED}break}}}if(sortOrder==null){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}var sortKeys;if(append){sortKeys=!isColumns?project.getColumnSortKeys():project.getRowSortKeys();if(priorSortKeyIndex!==-1){if(sortOrder===morpheus.SortKey.SortOrder.UNSORTED){sortKeys.splice(priorSortKeyIndex,1)}else{sortKeys[priorSortKeyIndex].setSortOrder(sortOrder)}}else{if(sortOrder!==morpheus.SortKey.SortOrder.UNSORTED){sortKeys.push(new morpheus.SortByValuesKey(modelIndices,sortOrder,!isColumns))}}sortKeys=morpheus.SortKey.keepExistingSortKeys(sortKeys,!isColumns?project.getColumnSortKeys():project.getRowSortKeys())}else{var newSortKeys=sortOrder===morpheus.SortKey.SortOrder.UNSORTED?[]:[new morpheus.SortByValuesKey(modelIndices,sortOrder,!isColumns)];sortKeys=morpheus.SortKey.keepExistingSortKeys(newSortKeys,!isColumns?project.getColumnSortKeys():project.getRowSortKeys())}if(!isColumns){project.setColumnSortKeys(sortKeys,true);this.scrollLeft(0)}else{project.setRowSortKeys(sortKeys,true);this.scrollTop(0)}morpheus.Util.trackEvent({eventCategory:"Tool",eventAction:isColumns?"sortRowsBasedOnSelection":"sortColumnsBasedOnSelection"})},getToolbarElement:function(){return this.toolbar.$el},getToolbar:function(){return this.toolbar},setName:function(name){this.options.name=name},getName:function(){return this.options.name},showOptions:function(){new morpheus.HeatMapOptions(this)},getProject:function(){return this.project},getDendrogram:function(isColumns){return isColumns?this.columnDendrogram:this.rowDendrogram},toJSON:function(options){var _this=this;var json={};json.colorScheme=this.heatmap.getColorScheme().toJSON();json.name=this.options.name;json.showRowNumber=this.isShowRowNumber();json.rowShapeModel=this.getProject().getRowShapeModel().toJSON(this.getVisibleTracks(false));json.columnShapeModel=this.getProject().getColumnShapeModel().toJSON(this.getVisibleTracks(true));json.rowFontModel=this.getProject().getRowFontModel().toJSON(this.getVisibleTracks(false));json.columnFontModel=this.getProject().getColumnFontModel().toJSON(this.getVisibleTracks(true));json.rowColorModel=this.getProject().getRowColorModel().toJSON(this.getVisibleTracks(false));json.columnColorModel=this.getProject().getColumnColorModel().toJSON(this.getVisibleTracks(true));json.rows=this.getVisibleTracks(false).map(function(track){var size=morpheus.CanvasUtil.getPreferredSize(_this.getTrackHeaderByIndex(_this.getTrackIndex(track.getName(),false),false));var obj=track.settings;obj.field=track.getName();obj.size={width:size.widthSet?size.width:undefined};return obj});json.columns=this.getVisibleTracks(true).map(function(track){var size=morpheus.CanvasUtil.getPreferredSize(_this.getTrackHeaderByIndex(_this.getTrackIndex(track.getName(),true),true));var obj=track.settings;obj.field=track.getName();obj.size={width:size.widthSet?size.width:undefined,height:size.heightSet?size.height:undefined};return obj});json.rowSortBy=morpheus.SortKey.toJSON(this.getProject().getRowSortKeys());json.columnSortBy=morpheus.SortKey.toJSON(this.getProject().getColumnSortKeys());json.rowGroupBy=morpheus.SortKey.toJSON(this.getProject().getGroupRows());json.columnGroupBy=morpheus.SortKey.toJSON(this.getProject().getGroupColumns());json.rowFilter=morpheus.CombinedFilter.toJSON(this.getProject().getRowFilter());json.columnFilter=morpheus.CombinedFilter.toJSON(this.getProject().getColumnFilter());json.symmetric=this.options.symmetric;json.rowSize=this.heatmap.getRowPositions().getSize();json.columnSize=this.heatmap.getColumnPositions().getSize();json.rowGapSize=this.heatmap.rowGapSize;json.columnGapSize=this.heatmap.columnGapSize;json.drawGrid=this.heatmap.isDrawGrid();json.gridColor=this.heatmap.getGridColor();json.gridThickness=this.heatmap.getGridThickness();json.drawValues=this.heatmap.isDrawValues();json.rowSelection=this.getProject().getRowSelectionModel().toModelIndices();json.columnSelection=this.getProject().getColumnSelectionModel().toModelIndices();json.rowSearchTerm=this.toolbar.getSearchField(morpheus.HeatMapToolBar.ROW_SEARCH_FIELD).val();json.columnSearchTerm=this.toolbar.getSearchField(morpheus.HeatMapToolBar.COLUMN_SEARCH_FIELD).val();if(this.rowDendrogram!=null){var out=[];morpheus.DendrogramUtil.writeNewick(this.rowDendrogram.tree.rootNode,out,function(n){return n.index});json.rowDendrogram=out.join("");json.rowDendrogramField=null}if(this.columnDendrogram!=null){var out=[];morpheus.DendrogramUtil.writeNewick(this.columnDendrogram.tree.rootNode,out,function(n){return n.index});json.columnDendrogram=out.join("");json.columnDendrogramField=null}if(options.dataset){json.dataset=morpheus.Dataset.toJSON(this.getProject().getFullDataset())}return json},setDendrogram:function(tree,isColumns,modelOrder){var dendrogram=isColumns?this.columnDendrogram:this.rowDendrogram;if(dendrogram){dendrogram.dispose();dendrogram=null}if(tree!=null){var size=isColumns?this.project.getFullDataset().getColumnCount():this.project.getFullDataset().getRowCount();if(isColumns){dendrogram=new morpheus.ColumnDendrogram(this,tree,this.heatmap.getColumnPositions(),this.project);dendrogram.filter=this.project.getColumnFilter().shallowClone();this.columnDendrogram=dendrogram;var sortKey=new morpheus.SpecifiedModelSortOrder(modelOrder,modelOrder.length,"dendrogram",true);sortKey.setPreservesDendrogram(true);sortKey.setLockOrder(2);sortKey.setUnlockable(false);this.project.setColumnSortKeys([sortKey],true)}else{dendrogram=new morpheus.RowDendrogram(this,tree,this.heatmap.getRowPositions(),this.project);dendrogram.filter=this.project.getRowFilter().shallowClone();this.rowDendrogram=dendrogram;var sortKey=new morpheus.SpecifiedModelSortOrder(modelOrder,modelOrder.length,"dendrogram",false);sortKey.setPreservesDendrogram(true);sortKey.setLockOrder(2);sortKey.setUnlockable(false);this.project.setRowSortKeys([sortKey],true)}dendrogram.appendTo(this.$parent);dendrogram.$label.appendTo(this.$parent);dendrogram.$squishedLabel.appendTo(this.$parent)}else{var sortKeys=isColumns?this.project.getColumnSortKeys():this.project.getRowSortKeys();for(var i=0;i<sortKeys.length;i++){if(sortKeys[i].isPreservesDendrogram()){sortKeys.splice(i,1);i--}}if(isColumns){this.heatmap.getColumnPositions().setSquishedIndices(null);delete this.columnDendrogram;this.project.setColumnSortKeys(sortKeys,true)}else{delete this.rowDendrogram;this.project.setRowSortKeys(sortKeys,true);this.heatmap.getRowPositions().setSquishedIndices(null)}}this.trigger("dendrogramChanged",{isColumns:isColumns})},getTabManager:function(){return this.tabManager},getSelectedElementsText:function(){var _this=this;var project=this.project;var selectedViewIndices=project.getElementSelectionModel().getViewIndices();if(selectedViewIndices.size()>0){var tipText=[];var dataset=project.getSortedFilteredDataset();var rowTracks=_this.rowTracks.filter(function(t){return t.settings.inlineTooltip});var columnTracks=_this.columnTracks.filter(function(t){return t.settings.inlineTooltip});selectedViewIndices.forEach(function(id){var rowIndex=id.getArray()[0];var columnIndex=id.getArray()[1];tipText.push(morpheus.Util.nf(dataset.getValue(rowIndex,columnIndex)));rowTracks.forEach(function(track){tipText.push("\t");tipText.push(morpheus.Util.toString(dataset.getRowMetadata().getByName(track.name).getValue(rowIndex)))});columnTracks.forEach(function(track){tipText.push("\t");tipText.push(morpheus.Util.toString(dataset.getColumnMetadata().getByName(track.name).getValue(columnIndex)))});tipText.push("\n")});return tipText.join("")}},_init:function(){var _this=this;morpheus.MetadataUtil.renameFields(this.options.dataset,this.options);var dataset=this.options.dataset;var rowDendrogram=this.options.rowDendrogram;var columnDendrogram=this.options.columnDendrogram;_.each(this.whenLoaded,function(f){f(_this.options.dataset)});if(this.options.datasetReady){var updatedDataset=this.options.datasetReady(dataset);if(updatedDataset){dataset=updatedDataset}}this.project=new morpheus.Project(dataset);if(this.tabManager){this.tabManager.setTabTitle(this.tabId,this.project.getFullDataset().getRowCount()+" row"+morpheus.Util.s(this.project.getFullDataset().getRowCount())+" x "+this.project.getFullDataset().getColumnCount()+" column"+morpheus.Util.s(this.project.getFullDataset().getColumnCount()))}if(this.options.inheritFromParent&&this.options.parent!=null){morpheus.HeatMap.copyFromParent(this.project,this.options)}if(this.options.rowFilter){morpheus.CombinedFilter.fromJSON(_this.project.getRowFilter(),this.options.rowFilter);_this.project.setRowFilter(_this.project.getRowFilter(),true)}if(this.options.columnFilter){morpheus.CombinedFilter.fromJSON(_this.project.getColumnFilter(),this.options.columnFilter);_this.project.setColumnFilter(_this.project.getColumnFilter(),true)}this.whenLoaded=null;this.$parent=$("<div></div>").css("position","relative");this.$parent.appendTo(this.$content);if(!morpheus.Util.isHeadless()){this.toolbar=new morpheus.HeatMapToolBar(this)}this.vscroll=new morpheus.ScrollBar(true);this.vscroll.appendTo(this.$parent);this.vscroll.on("scroll",function(){if(_this.updatingScroll){return}_this.paintAll({paintRows:true,paintColumns:false,invalidateRows:true,invalidateColumns:false})});this.beforeColumnTrackDivider=new morpheus.Divider(false);this.beforeColumnTrackDivider.appendTo(this.$parent);var dragStartHeight=0;this.beforeColumnTrackDivider.on("resizeStart",function(e){dragStartHeight=_this.columnDendrogram.getUnscaledHeight()}).on("resize",function(e){var newHeight=Math.max(8,dragStartHeight+e.delta);_this.columnDendrogram.setPrefHeight(newHeight);_this.revalidate()}).on("resizeEnd",function(){dragStartHeight=0});this.afterRowDendrogramDivider=new morpheus.Divider(true);this.afterRowDendrogramDivider.appendTo(this.$parent);var rowDendrogramStartWidth=0;this.afterRowDendrogramDivider.on("resizeStart",function(e){rowDendrogramStartWidth=_this.rowDendrogram.getUnscaledWidth()}).on("resize",function(e){var newWidth=Math.max(8,rowDendrogramStartWidth+e.delta);_this.rowDendrogram.setPrefWidth(newWidth);_this.revalidate()}).on("resizeEnd",function(){rowDendrogramStartWidth=0});this.afterVerticalScrollBarDivider=new morpheus.Divider(true);this.afterVerticalScrollBarDivider.appendTo(this.$parent);var resizeStartHeatMapWidth=0;this.afterVerticalScrollBarDivider.on("resizeStart",function(e){resizeStartHeatMapWidth=_this.heatmap.getUnscaledWidth()}).on("resize",function(e){_this.heatmap.prefWidth=resizeStartHeatMapWidth+e.delta;_this.revalidate()});this.hscroll=new morpheus.ScrollBar(false);this.hscroll.appendTo(this.$parent);this.hscroll.on("scroll",function(){if(_this.updatingScroll){return}_this.paintAll({paintRows:false,paintColumns:true,invalidateRows:false,invalidateColumns:true})});this.$whitespace=$('<div style="position: absolute;"></div>');this.$whitespace.appendTo(this.$parent);var heatmap=new morpheus.HeatMapElementCanvas(this.project);if(this.options.drawCallback){heatmap.setDrawCallback(this.options.drawCallback)}$(heatmap.canvas).on("contextmenu",function(e){var items=[];morpheus.Popup.showPopup([{name:"Copy Image",class:"copy"},{name:"Save Image ("+morpheus.Util.COMMAND_KEY+"S)"},{separator:true},{name:"Show Inline Tooltip",checked:_this.options.inlineTooltip}],{x:e.pageX,y:e.pageY},e.target,function(event,item){if(item==="Show Inline Tooltip"){_this.options.inlineTooltip=!_this.options.inlineTooltip}else if(item==="Save Image ("+morpheus.Util.COMMAND_KEY+"S)"){_this.getActionManager().execute("Save Image")}else if(item==="Copy Selection"){var text=_this.getSelectedElementsText();if(text!==""){event.clipboardData.setData("text/plain",text)}}else if(item==="Copy Image"){_this.getActionManager().execute("Copy Image",{event:event})}else{console.log(item+" unknown.")}});e.preventDefault();e.stopPropagation();e.stopImmediatePropagation()});heatmap.appendTo(this.$parent);this.heatmap=heatmap;var rowDendrogramSortKey=null;if(rowDendrogram!=null){var tree=rowDendrogram;if(tree.leafNodes.length!==this.project.getSortedFilteredDataset().getRowCount()){throw"# leaf nodes in row dendrogram "+tree.leafNodes.length+" != "+this.project.getSortedFilteredDataset().getRowCount()}var rowIndices=null;if(this.options.rowDendrogramField!=null){var vector=dataset.getRowMetadata().getByName(this.options.rowDendrogramField);rowIndices=[];var map=new morpheus.Map;var re=/[,:]/g;for(var j=0,size=vector.size();j<size;j++){var key=vector.getValue(j);map.set(key.replace(re,""),j)}for(var i=0,length=tree.leafNodes.length;i<length;i++){var index=map.get(tree.leafNodes[i].name);if(index===undefined){throw"Unable to find row dendrogram id "+tree.leafNodes[i].name+" in row annotations"}rowIndices.push(index)}}else{}this.rowDendrogram=new morpheus.RowDendrogram(this,tree,heatmap.getRowPositions(),this.project,true);this.rowDendrogram.appendTo(this.$parent);this.rowDendrogram.$label.appendTo(this.$parent);this.rowDendrogram.$squishedLabel.appendTo(this.$parent);if(rowIndices!=null){rowDendrogramSortKey=new morpheus.SpecifiedModelSortOrder(rowIndices,rowIndices.length,"dendrogram");rowDendrogramSortKey.setLockOrder(2);rowDendrogramSortKey.setUnlockable(false);rowDendrogramSortKey.setPreservesDendrogram(true)}}var columnDendrogramSortKey=null;if(columnDendrogram!=null){var tree=columnDendrogram;if(tree.leafNodes.length!==this.project.getSortedFilteredDataset().getColumnCount()){throw"# leaf nodes "+tree.leafNodes.length+" != "+this.project.getSortedFilteredDataset().getColumnCount()}var columnIndices=null;if(this.options.columnDendrogramField!=null){columnIndices=[];var vector=dataset.getColumnMetadata().getByName(this.options.columnDendrogramField);var map=new morpheus.Map;var re=/[,:]/g;for(var j=0,size=vector.size();j<size;j++){var key=vector.getValue(j);map.set(key.replace(re,""),j)}for(var i=0,length=tree.leafNodes.length;i<length;i++){var index=map.get(tree.leafNodes[i].name);if(index===undefined){throw"Unable to find column dendrogram id "+tree.leafNodes[i].name+" in column annotations"}columnIndices.push(index)}}else{}this.columnDendrogram=new morpheus.ColumnDendrogram(this,tree,heatmap.getColumnPositions(),this.project,true);this.columnDendrogram.appendTo(this.$parent);this.columnDendrogram.$label.appendTo(this.$parent);this.columnDendrogram.$squishedLabel.appendTo(this.$parent);if(columnIndices!=null){columnDendrogramSortKey=new morpheus.SpecifiedModelSortOrder(columnIndices,columnIndices.length,"dendrogram");columnDendrogramSortKey.setLockOrder(2);columnDendrogramSortKey.setUnlockable(false);columnDendrogramSortKey.setPreservesDendrogram(true)}}if(this.options.drawGrid!=null){this.heatmap.setDrawGrid(this.options.drawGrid)}if(this.options.gridColor!=null){this.heatmap.setGridColor(this.options.gridColor)}if(this.options.gridThickness!=null){this.heatmap.setGridThickness(this.options.gridThickness)}if(this.options.drawValues!=null){this.heatmap.setDrawValues(this.options.drawValues)}if(rowDendrogramSortKey!=null){this.project.setRowSortKeys([rowDendrogramSortKey])}if(columnDendrogramSortKey!=null){this.project.setColumnSortKeys([columnDendrogramSortKey])}if(this.options.rowSortBy&&this.options.rowSortBy.length>0){this.project.setRowSortKeys(morpheus.SortKey.fromJSON(this.project,this.options.rowSortBy),false)}if(this.options.columnSortBy&&this.options.columnSortBy.length>0){this.project.setColumnSortKeys(morpheus.SortKey.fromJSON(this.project,this.options.columnSortBy),false)}if(this.options.rowGroupBy!=null&&this.options.rowGroupBy.length>0){var keys=morpheus.SortKey.fromJSON(this.project,this.options.rowGroupBy);for(var i=0;i<keys.length;i++){this.project.groupRows.push(keys[i])}}if(this.options.columnGroupBy!=null&&this.options.columnGroupBy.length>0){var keys=morpheus.SortKey.fromJSON(this.project,this.options.columnGroupBy);for(var i=0;i<keys.length;i++){this.project.groupColumns.push(keys[i])}}if(this.options.rowSelection!=null&&this.options.rowSelection.length>0){var indices=new morpheus.Set;for(var i=0,length=this.options.rowSelection.length;i<length;i++){indices.add(this.project.convertModelRowIndexToView(this.options.rowSelection[i]))}this.project.getRowSelectionModel().setViewIndices(indices,false)}if(this.options.columnSelection!=null&&this.options.columnSelection.length>0){var indices=new morpheus.Set;for(var i=0,length=this.options.columnSelection.length;i<length;i++){indices.add(this.project.convertModelColumnIndexToView(this.options.columnSelection[i]))}this.project.getColumnSelectionModel().setViewIndices(indices,false)}this.vSortByValuesIndicator=new morpheus.SortByValuesIndicator(this.project,true,heatmap.getRowPositions());this.vSortByValuesIndicator.appendTo(this.$parent);this.hSortByValuesIndicator=new morpheus.SortByValuesIndicator(this.project,false,heatmap.getColumnPositions());this.hSortByValuesIndicator.appendTo(this.$parent);this.verticalSearchBar=new morpheus.ScentedSearch(this.project.getRowSelectionModel(),heatmap.getRowPositions(),true,this.vscroll,this);this.horizontalSearchBar=new morpheus.ScentedSearch(this.project.getColumnSelectionModel(),heatmap.getColumnPositions(),false,this.hscroll,this);this.rowTracks=[];this.rowTrackHeaders=[];this.columnTracks=[];this.columnTrackHeaders=[];if(this.options.rowSize!=null&&this.options.rowSize!=="fit"){this.heatmap.getRowPositions().setSize(this.options.rowSize)}if(this.options.columnSize!=null&&this.options.columnSize!=="fit"){this.heatmap.getColumnPositions().setSize(this.options.columnSize)}var setInitialDisplay=function(isColumns,options){var nameToOption=new morpheus.Map;var displaySpecified=_this.options.parent!=null&&_this.options.inheritFromParent;if(options!=null&&options.length>0){displaySpecified=true;for(var i=0;i<options.length;i++){nameToOption.set(options[i].renameTo!=null?options[i].renameTo:options[i].field,options[i])}}var displayMetadata=isColumns?dataset.getColumnMetadata():dataset.getRowMetadata();if(!displaySpecified){var defaultFieldsToShow=new morpheus.Set;["pert_iname","moa","target","description","cell_id","pert_type"].forEach(function(field){defaultFieldsToShow.add(field)});for(var i=0,metadataCount=displayMetadata.getMetadataCount();i<metadataCount;i++){var v=displayMetadata.get(i);if(defaultFieldsToShow.has(v.getName())&&!nameToOption.has(v.getName())){nameToOption.set(v.getName(),{display:["text"]});displaySpecified=true}}}var isFirst=true;for(var i=0,metadataCount=displayMetadata.getMetadataCount();i<metadataCount;i++){var v=displayMetadata.get(i);var name=v.getName();var option=nameToOption.get(name);if(displaySpecified&&option==null){continue}if(morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS.has(name)&&option==null){continue}var count=isColumns?dataset.getColumnCount():dataset.getRowCount();if(option==null&&!displaySpecified&&count>1&&!morpheus.VectorUtil.containsMoreThanOneValue(v)){continue}if(option==null){option={}}if(option.title){v.getProperties().set(morpheus.VectorKeys.TITLE,option.title)}if(option.display==null){if(name==="pert_iname"||name==="id"||isFirst){option.inlineTooltip=true;option.display=["text"]}else{option.display=isColumns?"color,highlight":"text"}}isFirst=false;var track=_this.addTrack(name,isColumns,option);if(option.size){if(!isColumns&&option.size.width!=null){var header=_this.getTrackHeaderByIndex(_this.getTrackIndex(name,isColumns),isColumns);track.setPrefWidth(option.size.width);header.setPrefWidth(option.size.width)}else if(isColumns&&(option.size.width!=null||option.size.height!=null)){var header=_this.getTrackHeaderByIndex(_this.getTrackIndex(name,isColumns),isColumns);if(option.size.height){track.setPrefHeight(option.size.height);header.setPrefHeight(option.size.height)}if(option.size.width){track.setPrefWidth(option.size.width);header.setPrefWidth(option.size.width)}}}if(option.header&&option.header.font){var header=_this.getTrackHeaderByIndex(_this.getTrackIndex(name,isColumns),isColumns);header.font=option.header.font}if(option.formatter){v.getProperties().set(morpheus.VectorKeys.FORMATTER,morpheus.Util.createNumberFormat(option.formatter))}if(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)&&option.color){var m=isColumns?_this.project.getColumnColorModel():_this.project.getRowColorModel();if(track.getFullVector().getProperties.get(morpheus.VectorKeys.DISCRETE)){_.each(options.color,function(p){m.setMappedValue(v,p.value,p.color)})}else{var cs=m.createContinuousColorMap(v);var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;_.each(options.color,function(p){min=Math.min(min,p.value);max=Math.max(max,p.value)});cs.setMin(min);cs.setMax(max);var valueToFraction=d3.scale.linear().domain([cs.getMin(),cs.getMax()]).range([0,1]).clamp(true);var fractions=[];var colors=[];_.each(options.color,function(p){fractions.push(valueToFraction(p.value));colors.push(p.color)});cs.setFractions({fractions:fractions,colors:colors})}if(track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)&&option.shape){var m=isColumns?_this.project.getColumnShapeModel():_this.project.getRowShapeModel();_.each(options.shape,function(p){m.setMappedValue(v,p.value,p.shape)})}}}};setInitialDisplay(false,this.options.rows);setInitialDisplay(true,this.options.columns);function reorderTracks(array,isColumns){if(array==null||array.length<=1){return}var nameOrderPairs=[];var found=false;array.forEach(function(item,index){var name=item.renameTo||item.field;var order=index;if(item.order!=null){order=item.order;found=true}nameOrderPairs.push({name:name,order:order})});if(!found){array.forEach(function(item,index){var name=item.renameTo||item.field;nameOrderPairs.push({name:name,order:index})})}nameOrderPairs.sort(function(a,b){return a.order===b.order?0:a.order<b.order?-1:1});for(var i=0,counter=0;i<nameOrderPairs.length;i++){var index=_this.getTrackIndex(nameOrderPairs[i].name,isColumns);if(index!==-1){_this.moveTrack(index,counter,isColumns);counter++}}}reorderTracks(this.options.rows,false);reorderTracks(this.options.columns,true);if(this.options.showRowNumber){this.setShowRowNumber(true)}var colorSchemeSpecified=this.options.colorScheme!=null;if(this.options.colorScheme==null){var ext="";if(this.options.dataSource){ext=morpheus.Util.getExtension(morpheus.Util.getFileName(this.options.dataSource))}var colorScheme=this.autoDisplay({filename:morpheus.Util.getBaseFileName(morpheus.Util.getFileName(this.options.dataset)),extension:ext});if(colorScheme==null){colorScheme={type:"relative"}}this.options.colorScheme=colorScheme;var name=this.project.getFullDataset().getName();if(ext==="maf"&&!this.options.rowSortBy){var sortKeys=[];if(this.project.getFullDataset().getRowMetadata().getByName("order")){sortKeys.push(new morpheus.SortKey("order",morpheus.SortKey.SortOrder.ASCENDING))}sortKeys.push(new morpheus.SortKey("id",morpheus.SortKey.SortOrder.ASCENDING));this.project.setRowSortKeys(sortKeys,false)}if(morpheus.DatasetUtil.getSeriesIndex(this.project.getFullDataset(),"allelic_fraction")!==-1){this.options.sizeBy={seriesName:"allelic_fraction",min:0,max:1}}}if(this.options.parent&&this.options.inheritFromParent){this.heatmap.setPropertiesFromParent(this.options.parent.heatmap)}if(this.options.parent&&this.options.inheritFromParent&&!colorSchemeSpecified){heatmap.setColorScheme(this.options.parent.heatmap.getColorScheme().copy(this.project))}else{heatmap.setColorScheme(new morpheus.HeatMapColorScheme(this.project,this.options.colorScheme));if(this.options.dataset.getRowMetadata().getByName("Source")!=null){var sourcesSet=morpheus.VectorUtil.getSet(this.options.dataset.getRowMetadata().getByName("Source"));this.heatmap.getColorScheme().setSeparateColorSchemeForRowMetadataField("Source");sourcesSet.forEach(function(source){_this.autoDisplay({extension:morpheus.Util.getExtension(source),filename:""+source})})}}if(this.options.sizeBy){heatmap.getColorScheme().getSizer().setSeriesName(this.options.sizeBy.seriesName);heatmap.getColorScheme().getSizer().setMin(this.options.sizeBy.min);heatmap.getColorScheme().getSizer().setMax(this.options.sizeBy.max)}this.updateDataset();if(this.options.tabOpened){this.options.tabOpened(this);this.updateDataset()}if(this.options.renderReady){this.options.renderReady(this);this.updateDataset()}if(this.options.rowSize==="fit"){this.heatmap.getRowPositions().setSize(this.getFitRowSize());this.revalidate({paint:false})}if(this.options.columnSize==="fit"){this.heatmap.getColumnPositions().setSize(this.getFitColumnSize());this.revalidate({paint:false})}if(this.options.rowColorModel){this.getProject().getRowColorModel().fromJSON(this.options.rowColorModel)}if(this.options.columnColorModel){this.getProject().getColumnColorModel().fromJSON(this.options.columnColorModel)}if(this.options.rowShapeModel){this.getProject().getRowShapeModel().fromJSON(this.options.rowShapeModel)}if(this.options.columnShapeModel){this.getProject().getColumnShapeModel().fromJSON(this.options.columnShapeModel)}if(this.options.rowFontModel){this.getProject().getRowFontModel().fromJSON(this.options.rowFontModel)}if(this.options.columnFontModel){this.getProject().getColumnFontModel().fromJSON(this.options.columnFontModel)}if(this.options.rowSize==="fit"||this.options.columnSize==="fit"){if(this.options.columnSize==="fit"){this.heatmap.getColumnPositions().setSize(this.getFitColumnSize());this.revalidate({paint:false})}if(this.options.rowSize==="fit"){this.heatmap.getRowPositions().setSize(this.getFitRowSize());this.revalidate({paint:false})}this.paintAll({paintRows:true,paintColumns:true,invalidateRows:true,invalidateColumns:true})}this.options.parent=null;this.$tipFollow=$('<div style="display:none;"'+' class="morpheus-tip-inline"></div>');this.$tipFollow.appendTo(this.$parent);this.$tipInfoWindow=$('<div class="morpheus-tip-dialog"></div>');this.$tipInfoWindow.appendTo(this.$parent);if(!morpheus.Util.isHeadless()){this.$tipInfoWindow.dialog({close:function(event,ui){if(!_this._togglingInfoWindow){_this.toggleInfoWindow()}},autoOpen:false,width:220,height:280,minHeight:38,minWidth:10,collision:"fit",position:{my:"right-30 bottom",at:"right top",of:this.$parent},title:"Info"});this.setTooltipMode(this.options.tooltipMode)}this.getProject().on("rowFilterChanged columnFilterChanged rowGroupByChanged columnGroupByChanged rowSortOrderChanged columnSortOrderChanged datasetChanged",function(e){if(e.type==="datasetChanged"){var dataset=_this.getProject().getFullDataset();for(var i=0;i<_this.rowTracks.length;i++){var track=_this.rowTracks[i];if(!dataset.getRowMetadata().getByName(track.getName())){_this.removeTrack(track.getName(),false);i--}}for(var i=0;i<_this.columnTracks.length;i++){var track=_this.columnTracks[i];if(!dataset.getColumnMetadata().getByName(track.getName())){_this.removeTrack(track.getName(),true);i--}}}_this.updateDataset();_this.revalidate()});this.getProject().on("trackChanged",function(e){var columns=e.columns;_.each(e.vectors,function(v,i){var index=_this.getTrackIndex(v.getName(),columns);if(index===-1){_this.addTrack(v.getName(),columns,e.display[i])}else{var track=_this.getTrackByIndex(index,columns);var display=e.display[i];if(display){track.settingFromConfig(display)}track.setInvalid(true)}});_this.revalidate()});this.getProject().on("rowTrackRemoved",function(e){_this.removeTrack(e.vector.getName(),false);_this.revalidate()});this.getProject().on("columnTrackRemoved",function(e){_this.removeTrack(e.vector.getName(),true);_this.revalidate()});this.getProject().getRowSelectionModel().on("selectionChanged",function(){for(var i=0;i<_this.columnTracks.length;i++){var track=_this.columnTracks[i];if(track.getFullVector().getProperties().get(morpheus.VectorKeys.RECOMPUTE_FUNCTION_SELECTION)){var selectedDataset=_this.getProject().getSelectedDataset({selectedRows:true,selectedColumns:false,emptyToAll:false});var vector=selectedDataset.getColumnMetadata().getByName(track.getName());var f=morpheus.VectorUtil.jsonToFunction(vector,morpheus.VectorKeys.FUNCTION);if(typeof f==="function"){var view=new morpheus.DatasetColumnView(selectedDataset);for(var j=0,size=vector.size();j<size;j++){view.setIndex(j);vector.setValue(j,f(view,selectedDataset,j))}track.setInvalid(true);track.repaint()}}}_this.verticalSearchBar.update();_this.heatmap.updateRowSelectionCache();_this.paintAll({paintRows:true,paintColumns:false,invalidateRows:false,invalidateColumns:false})});this.getProject().getColumnSelectionModel().on("selectionChanged",function(){_this.horizontalSearchBar.update();_this.heatmap.updateColumnSelectionCache();_this.paintAll({paintRows:false,paintColumns:true,invalidateRows:false,invalidateColumns:false})});this.pasteListener=function(e){if(_this.isActiveComponent()){var text=e.originalEvent.clipboardData.getData("text/plain");if(text!=null&&text.length>0){e.preventDefault();e.stopPropagation();var url;if(text.indexOf("http")===0){url=text}else{var blob=new Blob([text],{type:"text/plain"});url=URL.createObjectURL(blob)}morpheus.HeatMap.showTool(new morpheus.OpenFileTool({file:url}),_this)}}};this.beforeCopyListener=function(e){if(_this.isActiveComponent()){e.preventDefault()}};this.copyListener=function(ev){if(_this.isActiveComponent()){var activeComponent=_this.getActiveComponent();var project=_this.project;if(activeComponent==="heatMap"||ev.shiftKey){var bounds=_this.getTotalSize();var height=bounds.height;var width=bounds.width;var canvas=$("<canvas></canvas>")[0];canvas.height=height;canvas.width=width;var context=canvas.getContext("2d");_this.snapshot(context);var url=canvas.toDataURL();ev.originalEvent.clipboardData.setData("text/html",'<img src="'+url+'">');ev.preventDefault();ev.stopImmediatePropagation();return}var dataset=project.getSelectedDataset({emptyToAll:false});var rowsSelected=dataset.getRowCount()>0;var columnsSelected=dataset.getColumnCount()>0;var columnMetadata=dataset.getColumnMetadata();var rowMetadata=dataset.getRowMetadata();var visibleColumnFields=_this.getVisibleTrackNames(true);var columnFieldIndices=[];_.each(visibleColumnFields,function(name){var index=morpheus.MetadataUtil.indexOf(columnMetadata,name);if(index!==-1){columnFieldIndices.push(index)}});columnMetadata=new morpheus.MetadataModelColumnView(columnMetadata,columnFieldIndices);var rowMetadata=dataset.getRowMetadata();var visibleRowFields=_this.getVisibleTrackNames(false);var rowFieldIndices=[];_.each(visibleRowFields,function(name){var index=morpheus.MetadataUtil.indexOf(rowMetadata,name);if(index!==-1){rowFieldIndices.push(index)}});rowMetadata=new morpheus.MetadataModelColumnView(rowMetadata,rowFieldIndices);var text=[];if(rowsSelected&&columnsSelected){text=(new morpheus.GctWriter).write(dataset)}else{var text=[];var model=rowsSelected?rowMetadata:columnMetadata;for(var i=0,count=model.getItemCount();i<count;i++){for(var j=0,nfields=model.getMetadataCount();j<nfields;j++){var v=model.get(j);if(j>0){text.push("\t")}text.push(morpheus.Util.toString(v.getValue(i)))}text.push("\n")}text=text.join("")}ev.originalEvent.clipboardData.setData("text/plain",text);ev.preventDefault();ev.stopImmediatePropagation()}};if(typeof window!=="undefined"){$(window).on("paste.morpheus",this.pasteListener).on("beforecopy.morpheus",this.beforeCopyListener).on("copy.morpheus",this.copyListener)}if(this.options.keyboard&&!morpheus.Util.isHeadless()){new morpheus.HeatMapKeyListener(this)}if(this.options.symmetric){this.getProject().setSymmetric(this)}var dragStartScrollTop;var dragStartScrollLeft;var panstartMousePosition;this.hammer=morpheus.Util.hammer(_this.heatmap.canvas,["pan","pinch","tap","swipe"]).on("swipe",this.swipe=function(event){event.preventDefault()}).on("panend",this.panend=function(event){_this.panning=false;if(panstartMousePosition){panstartMousePosition=null;_this.heatmap.setSelectionBox(null);_this.heatmap.repaint()}event.preventDefault()}).on("panmove",this.panmove=function(event){if(panstartMousePosition){var pos=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.scrollLeft(),_this.scrollTop());var rowIndex=_this.heatmap.getRowPositions().getIndex(pos.y,false);var columnIndex=_this.heatmap.getColumnPositions().getIndex(pos.x,false);_this.updatingScroll=false;_this.heatmap.setSelectionBox({y:[panstartMousePosition.rowIndex,rowIndex],x:[panstartMousePosition.columnIndex,columnIndex]});var rowIndices=new morpheus.Set;for(var i=Math.min(panstartMousePosition.rowIndex,rowIndex),end=Math.max(panstartMousePosition.rowIndex,rowIndex);i<=end;i++){rowIndices.add(i)}var columnIndices=new morpheus.Set;for(var i=Math.min(panstartMousePosition.columnIndex,columnIndex),end=Math.max(panstartMousePosition.columnIndex,columnIndex);i<=end;i++){columnIndices.add(i)}_this.project.getRowSelectionModel().setViewIndices(rowIndices,true);_this.project.getColumnSelectionModel().setViewIndices(columnIndices,true)}else{_this.updatingScroll=true;var rows=false;var columns=false;if(event.deltaY!==0){var pos=dragStartScrollTop+event.deltaY;_this.scrollTop(pos);rows=true}if(event.deltaX!==0){var pos=dragStartScrollLeft+event.deltaX;_this.scrollLeft(pos);columns=true}_this.updatingScroll=false;if(rows||columns){_this.paintAll({paintRows:rows,paintColumns:rows,invalidateRows:rows,invalidateColumns:columns})}}event.preventDefault()}).on("panstart",this.panstart=function(event){_this.panning=true;_this.project.setHoverRowIndex(-1);_this.project.setHoverColumnIndex(-1);if(event.srcEvent.shiftKey){var pos=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.scrollLeft(),_this.scrollTop());panstartMousePosition={rowIndex:_this.heatmap.getRowPositions().getIndex(pos.y,false),columnIndex:_this.heatmap.getColumnPositions().getIndex(pos.x,false)}}else{panstartMousePosition=null;dragStartScrollTop=_this.scrollTop();dragStartScrollLeft=_this.scrollLeft()}event.preventDefault()}).on("tap",this.tap=function(event){if(morpheus.Util.IS_MAC&&event.srcEvent.ctrlKey){return}_this.project.getRowSelectionModel().setViewIndices(new morpheus.Set,true);_this.project.getColumnSelectionModel().setViewIndices(new morpheus.Set,true)}).on("pinch",this.pinch=function(event){var scale=event.scale;_this.heatmap.getRowPositions().setSize(13*scale);_this.heatmap.getColumnPositions().setSize(13*scale);var reval={};if(_this.project.getHoverRowIndex()!==-1){reval.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}if(_this.project.getHoverColumnIndex()!==-1){reval.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}_this.revalidate(reval);event.preventDefault()});var heatMapMouseMoved=function(event){var mouseI,mouseJ;if(event.type==="mouseout"){mouseI=-1;mouseJ=-1}else{var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,_this.scrollLeft(),_this.scrollTop());mouseI=_this.heatmap.getRowPositions().getIndex(position.y,false);mouseJ=_this.heatmap.getColumnPositions().getIndex(position.x,false)}_this.setMousePosition(mouseI,mouseJ,{event:event})};$(_this.heatmap.canvas).on("mouseout",heatMapMouseMoved).on("mousemove",heatMapMouseMoved);_.each(this.options.tools,function(item){var action=_this.getActionManager().getAction(item.name);if(action==null){console.log(item.name+" not found.")}else{var actionGui=action.gui();var gui=actionGui.gui(_this.getProject());var formBuilder=new morpheus.FormBuilder;_.each(gui,function(item){formBuilder.append(item)});var input={};_.each(gui,function(item){input[item.name]=formBuilder.getValue(item.name)});if(item.params){for(var key in item.params){input[key]=item.params[key]}}actionGui.execute({heatMap:_this,project:_this.getProject(),input:input})}})},setMousePosition:function(i,j,options){this.mousePositionOptions=options;var updateColumns=this.project.getHoverColumnIndex()!==j;var updateRows=this.project.getHoverRowIndex()!==i;if(updateColumns||updateRows){if(!this.panning){this.project.setHoverRowIndex(i);this.project.setHoverColumnIndex(j)}this.setToolTip(i,j,options);this.paintAll({paintRows:updateRows,paintColumns:updateColumns,invalidateRows:false,invalidateColumns:false})}else{this._updateTipFollowPosition(options)}this.trigger("change",{name:"setMousePosition",source:this,arguments:arguments})},getContentEl:function(){return this.$content},focus:function(){var scrollTop=document.body.scrollTop;this.$tabPanel.focus();document.body.scrollTop=scrollTop},getFocusEl:function(){return this.$tabPanel},setTooltipMode:function(mode){this._togglingInfoWindow=true;this.options.tooltipMode=mode;this.$tipInfoWindow.html("");this.toolbar.$tip.html("");this.$tipFollow.html("").css({display:"none"});this.toolbar.$tip.css("display",mode===0?"":"none");this.setToolTip(-1,-1);if(this.options.tooltipMode===1){this.$tipInfoWindow.dialog("open")}else{this.$tipInfoWindow.dialog("close")}this._togglingInfoWindow=false},toggleInfoWindow:function(){this.setTooltipMode(this.options.tooltipMode==1?0:1)},_setTipText:function(tipText,tipFollowText,options){if(this.options.tooltipMode===0){this.toolbar.$tip.html(tipText.join(""))}else if(this.options.tooltipMode===1){this.$tipInfoWindow.html(tipText.join(""))}if(tipFollowText!=null){this.tipFollowHidden=false;this.$tipFollow.html(tipFollowText);this._updateTipFollowPosition(options)}else{this.tipFollowHidden=true;this.$tipFollow.empty().css({display:"none"})}this.trigger("change",{name:"setToolTip",source:this,arguments:arguments})},setToolTip:function(rowIndex,columnIndex,options){options=options||{};if(this.options.showSeriesNameInTooltip){options.showSeriesNameInTooltip=true}if(this.options.tooltipSeriesIndices){options.tooltipSeriesIndices=this.options.tooltipSeriesIndices}if(options.heatMapLens){var maxSelectedCount=20;var $wrapper=$("<div></div>");var wrapperHeight=0;var wrapperWidth=0;var found=false;var inline=[];var indicesForLens=[];if(rowIndex!=null&&rowIndex.length>0){for(var hoverIndex=0;hoverIndex<rowIndex.length;hoverIndex++){var row=rowIndex[hoverIndex];if(row>=0&&(row>=this.heatmap.lastPosition.bottom||row<this.heatmap.lastPosition.top)){indicesForLens.push(row)}else{inline.push(row)}}if(indicesForLens.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<indicesForLens.length;hoverIndex++){var row=indicesForLens[hoverIndex];var heatMapWidth=this.heatmap.getUnscaledWidth();var top=row;var bottom=row+1;var startPix=this.heatmap.rowPositions.getPosition(top);var endPix=startPix+this.heatmap.rowPositions.getItemSize(top);var heatMapHeight=endPix-startPix;var canvas=morpheus.CanvasUtil.createCanvas();var trackWidth=0;for(var i=0,ntracks=this.rowTracks.length;i<ntracks;i++){var track=this.rowTracks[i];if(track.isVisible()){trackWidth+=track.getUnscaledWidth()}}var canvasWidth=trackWidth+heatMapWidth+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;canvas.width=canvasWidth*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.width=canvasWidth+"px";canvas.height=heatMapHeight*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.height=heatMapHeight+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);context.save();context.translate(-this.heatmap.lastClip.x,-startPix);context.rect(this.heatmap.lastClip.x,startPix,this.heatmap.lastClip.width,this.heatmap.lastClip.height);context.clip();this.heatmap._draw({left:this.heatmap.lastPosition.left,right:this.heatmap.lastPosition.right,top:top,bottom:bottom,context:context});context.restore();context.translate(heatMapWidth+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS,-startPix);trackWidth=0;for(var i=0,ntracks=this.rowTracks.length;i<ntracks;i++){var track=this.rowTracks[i];if(track.isVisible()){context.save();context.translate(trackWidth,0);context.rect(0,startPix,track.getUnscaledWidth(),track.lastClip.height);context.clip();track._draw({start:top,end:bottom,vector:track.getVector(),context:context,availableSpace:track.getUnscaledWidth()});context.restore();trackWidth+=track.getUnscaledWidth()}}$(canvas).appendTo($wrapper);canvas.style.top=wrapperHeight+"px";wrapperHeight+=parseFloat(canvas.style.height);wrapperWidth=parseFloat(canvas.style.width)}}if(indicesForLens.length>0){if(indicesForLens.length<maxSelectedCount){$wrapper.css({height:wrapperHeight,width:wrapperWidth});var rect=this.$parent[0].getBoundingClientRect();this.$tipFollow.html($wrapper).css({display:"",left:Math.round(parseFloat(this.heatmap.canvas.style.left)-1)+"px",top:options.event.clientY-rect.top-wrapperHeight/2+"px"})}else{this.$tipFollow.html("")}return}else{var tipText=[];var tipFollowText=[];if(inline.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<inline.length;hoverIndex++){this.tooltipProvider(this,inline[hoverIndex],-1,options,this.options.tooltipMode===0?"&nbsp;&nbsp;&nbsp;":"<br />",false,tipText);if(this.options.inlineTooltip){this.tooltipProvider(this,inline[hoverIndex],-1,options,"<br />",true,tipFollowText)}}}var text=tipFollowText.join("");this._setTipText(tipText,text.length===0?null:'<span style="max-width:400px;">'+text+"</span>",options)}}if(columnIndex!=null&&columnIndex.length>0){for(var hoverIndex=0;hoverIndex<columnIndex.length;hoverIndex++){var column=columnIndex[hoverIndex];if(column>=0&&(column>=this.heatmap.lastPosition.right||column<this.heatmap.lastPosition.left)){indicesForLens.push(column)}else{inline.push(column)}}if(indicesForLens.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<indicesForLens.length;hoverIndex++){var column=indicesForLens[hoverIndex];var heatMapHeight=this.heatmap.getUnscaledHeight();var left=column;var right=column+1;var startPix=this.heatmap.columnPositions.getPosition(left);var endPix=startPix+this.heatmap.columnPositions.getItemSize(left);var heatMapWidth=endPix-startPix;var canvas=morpheus.CanvasUtil.createCanvas();var trackHeight=0;for(var i=0,ntracks=this.columnTracks.length;i<ntracks;i++){var track=this.columnTracks[i];if(track.isVisible()){trackHeight+=track.getUnscaledHeight()}}var canvasHeight=trackHeight+heatMapHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;canvas.width=heatMapWidth*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.width=heatMapWidth+"px";canvas.height=canvasHeight*morpheus.CanvasUtil.BACKING_SCALE;canvas.style.height=canvasHeight+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);context.translate(-startPix,0);context.save();context.rect(startPix,trackHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS,this.heatmap.lastClip.width,this.heatmap.lastClip.height+trackHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS);context.clip();context.translate(0,trackHeight+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS-this.heatmap.lastClip.y);this.heatmap._draw({top:this.heatmap.lastPosition.top,bottom:this.heatmap.lastPosition.bottom,left:left,right:right,context:context});context.restore();trackHeight=0;for(var i=0,ntracks=this.columnTracks.length;i<ntracks;i++){var track=this.columnTracks[i];if(track.isVisible()){context.save();context.translate(0,trackHeight);context.rect(startPix,0,track.lastClip.width,track.getUnscaledHeight());context.clip();track._draw({start:left,end:right,vector:track.getVector(),context:context,availableSpace:track.getUnscaledHeight(),clip:{x:track.lastClip.x,y:track.lastClip.y}});context.restore();trackHeight+=track.getUnscaledHeight()}}canvas.style.left=wrapperWidth+"px";wrapperWidth+=parseFloat(canvas.style.width);wrapperHeight=parseFloat(canvas.style.height);$(canvas).appendTo($wrapper)}}if(indicesForLens.length>0){if(indicesForLens.length<maxSelectedCount){$wrapper.css({height:wrapperHeight,width:wrapperWidth});var rect=this.$parent[0].getBoundingClientRect();this.$tipFollow.html($wrapper).css({top:parseFloat(this.heatmap.canvas.style.top)-trackHeight-morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS-1,left:options.event.clientX-rect.left-wrapperWidth/2,display:""})}else{this.$tipFollow.html("")}return}else{var tipText=[];var tipFollowText=[];if(inline.length<maxSelectedCount){for(var hoverIndex=0;hoverIndex<inline.length;hoverIndex++){this.tooltipProvider(this,-1,inline[hoverIndex],options,this.options.tooltipMode===0?"&nbsp;&nbsp;&nbsp;":"<br />",false,tipText);if(this.options.inlineTooltip){this.tooltipProvider(this,-1,inline[hoverIndex],options,"<br />",true,tipFollowText)}}}var text=tipFollowText.join("");this._setTipText(tipText,text===""?null:'<span style="max-width:400px;">'+text+"</span>",options)}}}var tipText=[];this.tooltipProvider(this,rowIndex,columnIndex,options,this.options.tooltipMode===0?"&nbsp;&nbsp;&nbsp;":"<br />",false,tipText);var text=[];var customToolTip=false;var $tipFollowText;if(!this.panning){var tipFollowText=[];if(this.options.inlineTooltip){this.tooltipProvider(this,rowIndex,columnIndex,options,"<br />",true,tipFollowText);if(this.options.tooltip&&rowIndex!==-1&&columnIndex!==-1){tipFollowText.push('<div data-name="tip"></div>')}}text=tipFollowText.join("");$tipFollowText=$('<span style="max-width:400px;">'+text+"</span>");if(this.options.tooltip&&rowIndex!==-1&&columnIndex!==-1){this.options.tooltip(this,rowIndex,columnIndex,$tipFollowText.find("[data-name=tip]"));customToolTip=true}}this._setTipText(tipText,text.length>0||customToolTip?$tipFollowText:null,options)},_updateTipFollowPosition:function(options){if(this.tipFollowHidden){return}var parentRect=this.$parent[0].getBoundingClientRect();var tipRect=this.$tipFollow[0].getBoundingClientRect();var tipWidth=tipRect.width;var tipHeight=tipRect.height;var offset=10;var left=options.event.clientX-parentRect.left+offset;var top=options.event.clientY-parentRect.top+offset;var scrollBarSize=18;if(left+tipWidth>=parentRect.right-parentRect.left-scrollBarSize){left=options.event.clientX-parentRect.left-offset-tipWidth}if(top+tipHeight>=parentRect.bottom-parentRect.top-scrollBarSize){top=options.event.clientY-parentRect.top-offset-tipHeight}this.$tipFollow.css({left:left+"px",top:top+"px",display:""})},setTrackVisibility:function(tracks){var _this=this;_.each(tracks,function(track){var existingTrack=_this.getTrack(track.name,track.isColumns);if(track.visible&&existingTrack!=null&&_.keys(existingTrack.settings).length===0){existingTrack.settingFromConfig("Text")}_this.setTrackVisible(track.name,track.visible,track.isColumns)});this.revalidate();this.trigger("change",{name:"setTrackVisibility",source:this,arguments:arguments})},setTrackVisible:function(name,visible,isColumns){var trackIndex=this.getTrackIndex(name,isColumns);if(trackIndex===-1){if(!visible){return}this.addTrack(name,isColumns)}else{var track=isColumns?this.columnTracks[trackIndex]:this.rowTracks[trackIndex];var header=isColumns?this.columnTrackHeaders[trackIndex]:this.rowTrackHeaders[trackIndex];if(track.isVisible()!==visible){track.setVisible(visible);header.setVisible(visible)}else{return}}this.trigger("change",{name:"setTrackVisible",source:this,arguments:arguments})},addTrack:function(name,isColumns,renderSettings,trackIndex){if(name===undefined){throw"Name not specified"}var tracks=isColumns?this.columnTracks:this.rowTracks;var headers=isColumns?this.columnTrackHeaders:this.rowTrackHeaders;var existingIndex=this.getTrackIndex(name,isColumns);if(existingIndex!==-1){return tracks[existingIndex]}if(renderSettings==null){var metadata=isColumns?this.project.getFullDataset().getColumnMetadata():this.project.getFullDataset().getRowMetadata();renderSettings=morpheus.VectorUtil.getDataType(metadata.getByName(name))==="[number]"?{display:["bar"]}:{display:["text"]}}var positions=isColumns?this.heatmap.getColumnPositions():this.heatmap.getRowPositions();var track=new morpheus.VectorTrack(this.project,name,positions,isColumns,this);track.settingFromConfig(renderSettings);track.appendTo(this.$parent);var header=new morpheus.VectorTrackHeader(this.project,name,isColumns,this);header.appendTo(this.$parent);track._selection=new morpheus.TrackSelection(track,positions,isColumns?this.project.getColumnSelectionModel():this.project.getRowSelectionModel(),isColumns,this);if(trackIndex!=null&&trackIndex>=0){tracks.splice(trackIndex,0,track);headers.splice(trackIndex,0,header)}else{tracks.push(track);headers.push(header)}return track},addPopup:function(item){if(!this.popupItems){this.popupItems=[]}this.popupItems.push(item)},getPopupItems:function(){return this.popupItems||[]},removeTrack:function(name,isColumns){var index=this.getTrackIndex(name,isColumns);var tracks=isColumns?this.columnTracks:this.rowTracks;if(isNaN(index)||index<0||index>=tracks.length){console.log("removeTrack: "+name+" not found.");return}var headers=isColumns?this.columnTrackHeaders:this.rowTrackHeaders;var track=tracks[index];var header=headers[index];track.dispose();header.dispose();tracks.splice(index,1);headers.splice(index,1);this.trigger("change",{name:"removeTrack",source:this,arguments:arguments})},updateDataset:function(){var dataset=this.project.getSortedFilteredDataset();this.verticalSearchBar.update();this.horizontalSearchBar.update();this.heatmap.setDataset(dataset);this.heatmap.getRowPositions().setSpaces(morpheus.HeatMap.createGroupBySpaces(dataset,this.project.getGroupRows(),this.rowGapSize,false));this.heatmap.getColumnPositions().setSpaces(morpheus.HeatMap.createGroupBySpaces(dataset,this.project.getGroupColumns(),this.columnGapSize,true));this.trigger("change",{name:"updateDataset",source:this,arguments:arguments})},zoom:function(isZoomIn,options){options=$.extend({},{rows:true,columns:true},options);if(isZoomIn){if(options.rows){this.heatmap.getRowPositions().setSize(this.heatmap.getRowPositions().getSize()*1.5)}if(options.columns){this.heatmap.getColumnPositions().setSize(this.heatmap.getColumnPositions().getSize()*1.5)}}else{if(options.rows){this.heatmap.getRowPositions().setSize(this.heatmap.getRowPositions().getSize()/1.5)}if(options.columns){this.heatmap.getColumnPositions().setSize(this.heatmap.getColumnPositions().getSize()/1.5)}}var reval={};if(options.rows&&this.project.getHoverRowIndex()!==-1){reval.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}if(options.columns&&this.project.getHoverColumnIndex()!==-1){reval.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}this.revalidate(reval);this.trigger("change",{name:"zoom",source:this,arguments:arguments})},getTrackIndex:function(name,isColumns){var tracks=isColumns?this.columnTracks:this.rowTracks;for(var i=0,length=tracks.length;i<length;i++){if(tracks[i].name!==undefined&&tracks[i].name===name){return i}}return-1},getNumTracks:function(isColumns){return isColumns?this.columnTracks.length:this.rowTracks.length},moveTrack:function(index,newIndex,isColumns){var tracks=isColumns?this.columnTracks:this.rowTracks;var headers=isColumns?this.columnTrackHeaders:this.rowTrackHeaders;var track=tracks[index];tracks.splice(index,1);var header=headers[index];headers.splice(index,1);tracks.splice(newIndex,0,track);headers.splice(newIndex,0,header);this.trigger("change",{name:"moveTrack",source:this,arguments:arguments})},getTrackByIndex:function(index,isColumns){return isColumns?this.columnTracks[index]:this.rowTracks[index]},getTrackHeaderByIndex:function(index,isColumns){return isColumns?this.columnTrackHeaders[index]:this.rowTrackHeaders[index]},getTrack:function(name,isColumns){var index=this.getTrackIndex(name,isColumns);if(index===-1){return undefined}return isColumns?this.columnTracks[index]:this.rowTracks[index]},isActiveComponent:function(){var active=document.activeElement;var tagName=active.tagName;if(tagName=="INPUT"||tagName=="SELECT"||tagName=="TEXTAREA"){return false}return this.$tabPanel[0].contains(active)},getActiveComponent:function(){var active=document.activeElement;if(active.tagName==="CANVAS"){for(var i=0,ntracks=this.columnTracks.length;i<ntracks;i++){if(this.columnTracks[i].canvas===active){return"columnTrack"}}for(var i=0,ntracks=this.rowTracks.length;i<ntracks;i++){if(this.rowTracks[i].canvas===active){return"rowTrack"}}if(this.heatmap.canvas===active){return"heatMap"}}return""},dispose:function(){if(this.project==null){return}this.project.off();this.$tipInfoWindow.dialog("destroy");this.rowTrackHeaders.forEach(function(header){header.dispose()});this.columnTrackHeaders.forEach(function(header){header.dispose()});this.rowTracks.forEach(function(track){track.dispose()});this.columnTracks.forEach(function(track){track.dispose()});if(this.rowDendrogram!=null){this.rowDendrogram.dispose()}if(this.columnDendrogram!=null){this.columnDendrogram.dispose()}this.beforeColumnTrackDivider.dispose();this.afterRowDendrogramDivider.dispose();this.afterVerticalScrollBarDivider.dispose();this.hscroll.dispose();this.vscroll.dispose();this.hammer.off("swipe",this.swipe).off("panmove",this.panmove).off("panstart",this.panstart).off("tap",this.tap).off("pinch",this.pinch).off("panend",this.panend);this.hammer.destroy();if(typeof window!=="undefined"){$(window).off("paste.morpheus",this.pasteListener).off("beforecopy.morpheus",this.beforeCopyListener).off("copy.morpheus",this.copyListener).off("orientationchange.morpheus resize.morpheus",this.resizeListener)}},getVisibleTrackNames:function(isColumns){return this.getVisibleTracks(isColumns).map(function(track){return track.name})},getVisibleTracks:function(isColumns){var tracks=isColumns?this.columnTracks:this.rowTracks;return tracks.filter(function(track){return track.isVisible()&&!track.getFullVector().getProperties().has(morpheus.VectorKeys.IS_INDEX)})},isShowRowNumber:function(){return this.options.showRowNumber},setShowRowNumber:function(visible){this.options.showRowNumber=visible;if(!visible){this.removeTrack("#",false)}else{var track=this.addTrack("#",false,{popupEnabled:false,display:["text"]},0);track.getVector=function(name){var v=new morpheus.AbstractVector("#",this.project.getSortedFilteredDataset().getRowCount());v.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});v.getValue=function(index){return index+1};return v};track.getFullVector=function(){var v=new morpheus.AbstractVector("#",this.project.getFullDataset().getRowCount());v.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"i"});v.getValue=function(index){return index+1};return v};track.showPopup=function(e,isHeader){if(e.preventDefault){e.preventDefault()}}}},resizeTrack:function(name,width,height,isColumns){var index=this.getTrackIndex(name,isColumns);if(index===-1){throw name+" not found in resize track"}var heatMapPrefWidth=null;if(!isColumns){var track=this.rowTracks[index];var header=this.rowTrackHeaders[index];track.setPrefWidth(width);header.setPrefWidth(width)}else{var track=this.columnTracks[index];var header=this.columnTrackHeaders[index];if(height){track.setPrefHeight(height);header.setPrefHeight(height)}if(width){for(var i=0;i<this.columnTracks.length;i++){this.columnTracks[i].setPrefWidth(width);this.columnTrackHeaders[i].setPrefWidth(width)}}}this.revalidate();this.trigger("change",{name:"resizeTrack",source:this,arguments:arguments})},isDendrogramVisible:function(isColumns){var dendrogram=isColumns?this.columnDendrogram:this.rowDendrogram;if(dendrogram!==undefined){return morpheus.HeatMap.isDendrogramVisible(this.project,isColumns)}},paintAll:function(options){var unscaledHeight=this.heatmap.getUnscaledHeight();var unscaledWidth=this.heatmap.getUnscaledWidth();var y=this.scrollTop();var x=this.scrollLeft();this.hscroll.paint();this.vscroll.paint();var rows=options.paintRows;var columns=options.paintColumns;var invalidateRows=options.invalidateRows;var invalidateColumns=options.invalidateColumns;this.hSortByValuesIndicator.setInvalid(invalidateRows||invalidateColumns);this.hSortByValuesIndicator.paint({x:x,y:0,width:unscaledWidth,height:this.hSortByValuesIndicator.getUnscaledHeight()});this.vSortByValuesIndicator.setInvalid(invalidateRows||invalidateColumns);this.vSortByValuesIndicator.paint({x:0,y:y,width:this.vSortByValuesIndicator.getUnscaledWidth(),height:unscaledHeight});if(rows){for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];track.setInvalid(invalidateRows);if(track.isVisible()){track.paint({x:0,y:y,height:unscaledHeight,width:unscaledWidth});this.rowTrackHeaders[i].paint()}}if(this.rowDendrogram!=null){this.rowDendrogram.setInvalid(invalidateRows);if(this.isDendrogramVisible(false)){this.rowDendrogram.setVisible(true);this.rowDendrogram.paint({x:0,y:y,height:unscaledHeight,width:this.rowDendrogram.getUnscaledWidth()})}else{this.rowDendrogram.setVisible(false)}}}if(columns){for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];track.setInvalid(invalidateColumns);track.paint({x:x,y:0,width:unscaledWidth,height:track.getUnscaledHeight()});this.columnTrackHeaders[i].paint()}if(this.columnDendrogram!=null){this.columnDendrogram.setInvalid(invalidateColumns);if(this.isDendrogramVisible(true)){this.columnDendrogram.setVisible(true);this.columnDendrogram.paint({x:x,y:0,width:unscaledWidth,height:this.columnDendrogram.getUnscaledHeight()})}else{this.columnDendrogram.setVisible(false)}}}if(invalidateRows||invalidateColumns){this.heatmap.setInvalid(true)}this.heatmap.paint({x:x,y:y,width:unscaledWidth,height:unscaledHeight});this.trigger("change",{name:"paintAll",source:this,arguments:arguments})},scrollTop:function(pos){if(pos===undefined){return this.vscroll.getValue()}if(isNaN(pos)){pos=0}if(this.vscroll.getVisibleExtent()===this.vscroll.getTotalExtent()){pos=0}pos=Math.max(pos,0);pos=Math.min(this.vscroll.getMaxValue(),pos);if(pos!==this.vscroll.getValue()){this.vscroll.setValue(pos,true);this.trigger("change",{name:"scrollTop",source:this,arguments:arguments})}return pos},scrollLeft:function(pos){if(pos===undefined){return this.hscroll.getValue()}if(isNaN(pos)){pos=0}if(this.hscroll.getVisibleExtent()===this.hscroll.getTotalExtent()){pos=0}pos=Math.max(pos,0);pos=Math.min(this.hscroll.getMaxValue(),pos);if(pos!==this.hscroll.getValue()){this.trigger("change",{name:"scrollLeft",source:this,arguments:arguments});this.hscroll.setValue(pos,true)}return pos},getSelectedTrackName:function(isColumns){return isColumns?this.selectedColumnTrackName:this.selectedRowTrackName},getLastSelectedTrackInfo:function(){return this.selectedTrackInfo},setSelectedTrack:function(name,isColumns){var previousName=isColumns?this.selectedColumnTrackName:this.selectedRowTrackName;if(name!==previousName){var index=this.getTrackIndex(previousName,isColumns);if(index!==-1){this.getTrackHeaderByIndex(index,isColumns).setSelected(false)}if(isColumns){this.selectedColumnTrackName=name;this.selectedTrackInfo={name:name,isColumns:true}}else{this.selectedRowTrackName=name;this.selectedTrackInfo={name:name,isColumns:false}}var index=this.getTrackIndex(name,isColumns);if(index!==-1){this.getTrackHeaderByIndex(index,isColumns).setSelected(true)}this.trigger("change",{name:"setSelected",source:this,arguments:arguments})}},saveImage:function(file,format){var _this=this;var bounds=this.getTotalSize();if(format==="pdf"){var context=new canvas2pdf.PdfContext(blobStream(),{size:[bounds.width,bounds.height]});this.snapshot(context);context.stream.on("finish",function(){var blob=context.stream.toBlob("application/pdf");saveAs(blob,file,true)});context.end()}else if(format==="svg"){var context=new C2S(bounds.width,bounds.height);this.snapshot(context);var svg=context.getSerializedSvg();var prefix=[];prefix.push('<?xml version="1.0" encoding="utf-8"?>\n');prefix.push('<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"'+' "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n');svg=prefix.join("")+svg;var blob=new Blob([svg],{type:"text/plain;charset=utf-8"});saveAs(blob,file,true)}else{var canvas=$("<canvas></canvas>")[0];var height=bounds.height;var width=bounds.width;var backingScale=morpheus.CanvasUtil.BACKING_SCALE;canvas.height=backingScale*height;canvas.style.height=height+"px";canvas.width=backingScale*width;canvas.style.width=width+"px";var context=canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);this.snapshot(context);var toBlob=canvas.toBlobHD?["toBlobHD"]:"toBlob";canvas[toBlob](function(blob){if(blob==null||blob.size===0){morpheus.FormBuilder.showInModal({title:"Save Image",html:"Image is too large to save.",appendTo:_this.getContentEl(),focus:_this.getFocusEl()});return}saveAs(blob,file,true)})}},getTotalSize:function(options){options=$.extend({},{legend:true},options);var _this=this;var heatmapPrefSize=this.heatmap.getPreferredSize();var totalSize={width:heatmapPrefSize.width,height:heatmapPrefSize.height};if(this.isDendrogramVisible(false)){totalSize.width+=this.rowDendrogram.getUnscaledWidth()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}if(this.isDendrogramVisible(true)){totalSize.height+=this.columnDendrogram.getUnscaledHeight()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}var maxRowHeaderHeight=0;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){var headerSize=this.rowTrackHeaders[i].getPrintSize();totalSize.width+=Math.max(headerSize.width,track.getPrintSize().width);maxRowHeaderHeight=Math.max(maxRowHeaderHeight,headerSize.height)}}var maxColumnHeaderWidth=0;var columnTrackHeightSum=0;for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){columnTrackHeightSum+=track.getPrintSize().height;maxColumnHeaderWidth=Math.max(maxColumnHeaderWidth,this.columnTrackHeaders[i].getPrintSize().width)}}totalSize.height+=Math.max(columnTrackHeightSum,maxRowHeaderHeight)+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;totalSize.width+=maxColumnHeaderWidth+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;if(options.legend){var totalLegendWidth=15;var maxLegendHeight=0;var colorByValues=this.heatmap.getColorScheme().getColorByValues();var ntracks=colorByValues.length;for(var i=0;i<ntracks;i++){var value=colorByValues[i];if(value!=null||ntracks===1){this.heatmap.getColorScheme().setCurrentValue(value);var names=this.heatmap.getColorScheme().getNames();maxLegendHeight=Math.max(maxLegendHeight,names!=null?names.length*14:30);totalLegendWidth+=250}}maxLegendHeight+=10;totalSize.height=totalSize.height+maxLegendHeight;totalSize.width=Math.max(totalSize.width,totalLegendWidth)}var trackLegendSize=new morpheus.HeatMapTrackColorLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getColumnColorModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackColorLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getRowColorModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getColumnShapeModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getRowShapeModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getColumnFontModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);trackLegendSize=new morpheus.HeatMapTrackShapeLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getRowFontModel()).getPreferredSize();totalSize.height+=trackLegendSize.height;totalSize.width=Math.max(totalSize.width,trackLegendSize.width);return totalSize},getHeatMapElementComponent:function(){return this.heatmap},snapshot:function(context,options){options=$.extend({},{legend:true},options);var heatmapPrefSize=this.heatmap.getPreferredSize();var totalSize=this.getTotalSize(options);var legendHeight=0;if(options.legend){var colorByValues=this.heatmap.getColorScheme().getColorByValues();context.save();context.translate(15,0);var ntracks=colorByValues.length;for(var i=0,ntracks=colorByValues.length;i<ntracks;i++){var value=colorByValues[i];if(value!=null||ntracks===1){if(value!="null"){}var trackLegend=new morpheus.ColorSupplierLegend(this.heatmap.getColorScheme(),value);trackLegend.draw({},context);legendHeight=Math.max(legendHeight,trackLegend.getUnscaledHeight());var legendWidth=trackLegend.getUnscaledWidth();context.translate(legendWidth,0)}}legendHeight+=10;context.restore()}var legendOffset=15;var maxLegendHeight=0;context.save();context.translate(legendOffset,legendHeight);var trackLegend=new morpheus.HeatMapTrackColorLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getColumnColorModel());trackLegend.draw({},context);var legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackShapeLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getColumnShapeModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackFontLegend(_.filter(this.columnTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getColumnFontModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackColorLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&(track.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR))}),this.getProject().getRowColorModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackShapeLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)}),this.getProject().getRowShapeModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();context.save();context.translate(legendOffset,legendHeight);trackLegend=new morpheus.HeatMapTrackFontLegend(_.filter(this.rowTracks,function(track){return track.isVisible()&&track.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)}),this.getProject().getRowFontModel());trackLegend.draw({},context);legendSize=trackLegend.getPreferredSize();legendOffset+=legendSize.width;maxLegendHeight=Math.max(maxLegendHeight,legendSize.height);context.restore();legendHeight+=maxLegendHeight;var heatmapY=this.isDendrogramVisible(true)?this.columnDendrogram.getUnscaledHeight()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS:0;heatmapY+=legendHeight;var columnTrackY=heatmapY;var heatmapX=this.isDendrogramVisible(false)?this.rowDendrogram.getUnscaledWidth()+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS:0;var isColumnTrackVisible=false;for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){var header=this.columnTrackHeaders[i];heatmapX=Math.max(heatmapX,header.getPrintSize().width);heatmapY+=track.getPrintSize().height;isColumnTrackVisible=true}}if(isColumnTrackVisible){heatmapY+=morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){var header=this.rowTrackHeaders[i];heatmapY=Math.max(heatmapY,header.getPrintSize().height)}}if(this.isDendrogramVisible(true)){var columnDendrogramClip={x:0,y:0,height:this.columnDendrogram.getUnscaledHeight(),width:heatmapPrefSize.width};context.save();context.translate(heatmapX,legendHeight);this.columnDendrogram.prePaint(columnDendrogramClip,context);this.columnDendrogram.draw(columnDendrogramClip,context);context.restore()}if(this.isDendrogramVisible(false)){var rowDendrogramClip={x:0,y:0,width:this.rowDendrogram.getUnscaledWidth(),height:heatmapPrefSize.height};context.save();context.translate(0,heatmapY);this.rowDendrogram.prePaint(rowDendrogramClip,context);this.rowDendrogram.draw(rowDendrogramClip,context);context.restore()}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){context.save();context.translate(heatmapX,columnTrackY);var trackClip={x:0,y:0,width:heatmapPrefSize.width,height:track.getPrintSize().height};track.print(trackClip,context);context.restore();var header=this.columnTrackHeaders[i];context.save();var headerSize=header.getPrintSize();var headerClip={x:0,y:0,width:headerSize.width,height:trackClip.height};context.translate(heatmapX-2,columnTrackY+trackClip.height);header.print(headerClip,context);context.restore();columnTrackY+=Math.max(headerClip.height,trackClip.height)}}context.save();context.translate(heatmapX,heatmapY);this.heatmap.draw({x:0,y:0,width:heatmapPrefSize.width,height:heatmapPrefSize.height},context);context.restore();var rowTrackWidthSum=0;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){context.save();var tx=morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS+heatmapX+heatmapPrefSize.width+rowTrackWidthSum;var ty=heatmapY;var trackClip={x:0,y:0,width:track.getPrintSize().width,height:heatmapPrefSize.height};context.translate(tx,ty);context.strokeStyle="white";context.rect(0,0,trackClip.width,trackClip.height);context.stroke();context.clip();track.print(trackClip,context);context.restore();var header=this.rowTrackHeaders[i];context.save();var headerSize=header.getPrintSize();var headerClip={x:0,y:0,width:headerSize.width,height:headerSize.height};context.translate(tx,ty-4);header.print(headerClip,context);context.restore();rowTrackWidthSum+=Math.max(headerSize.width,trackClip.width)}}},resetZoom:function(){var heatmap=this.heatmap;var rowSizes=heatmap.getRowPositions();var columnSizes=heatmap.getColumnPositions();rowSizes.setSize(13);columnSizes.setSize(13);var reval={};if(this.project.getHoverRowIndex()!==-1){reval.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}if(this.project.getHoverColumnIndex()!==-1){reval.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}this.revalidate(reval)},getFitColumnSize:function(){var heatmap=this.heatmap;var availablePixels=this.getAvailableWidth();if(availablePixels===-1){return 13}if(this.rowDendrogram){availablePixels-=this.rowDendrogram.getUnscaledWidth()}var trackPixels=12;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){trackPixels+=track.getUnscaledWidth()}}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){trackPixels+=this.columnTrackHeaders[i].getUnscaledWidth();break}}availablePixels-=trackPixels;var positions=heatmap.getColumnPositions();var totalCurrent=positions.getItemSize(positions.getLength()-1)+positions.getPosition(positions.getLength()-1);var size=positions.getSize();size=size*(availablePixels/totalCurrent);size=Math.min(13,size);return size},getFitRowSize:function(){var heatmap=this.heatmap;var availablePixels=this.getAvailableHeight();if(availablePixels===-1){return 13}if(this.columnDendrogram){availablePixels-=this.columnDendrogram.getUnscaledHeight()}var trackPixels=12;for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){trackPixels+=track.getUnscaledHeight()}}availablePixels-=trackPixels;var positions=heatmap.getRowPositions();var totalCurrent=positions.getItemSize(positions.getLength()-1)+positions.getPosition(positions.getLength()-1);var size=positions.getSize();size=size*(availablePixels/totalCurrent);size=Math.min(13,size);return size},fitToWindow:function(options){if(options.fitRows){this.heatmap.getRowPositions().setSize(this.getFitRowSize())}if(options.fitColumns){this.heatmap.getColumnPositions().setSize(this.getFitColumnSize())}if(options.repaint){var revalOptions={};if(options.fitRows){if(this.project.getHoverRowIndex()!==-1){revalOptions.scrollTop=this.heatmap.getRowPositions().getPosition(this.project.getHoverRowIndex())}}if(options.fitColumns){if(this.project.getHoverColumnIndex()!==-1){revalOptions.scrollLeft=this.heatmap.getColumnPositions().getPosition(this.project.getHoverColumnIndex())}}this.revalidate(revalOptions)}},getAvailableHeight:function(){if(_.isNumber(this.options.height)){return this.options.height}var height=$(window).height()-this.$parent.offset().top-24;if(this.options.height==="window"){return height}return Math.max(Math.round(screen.height*.7),height)},getAvailableWidth:function(){if(this.options.width){return this.options.width}return this.tabManager.getWidth()-30},revalidate:function(options){if(morpheus.Util.isHeadless()){for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];track.setInvalid(true);if(track.isVisible()){track.paint({x:0,y:0,height:10,width:10})}}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];track.setInvalid(true);if(track.isVisible()){track.paint({x:0,y:0,height:10,width:10})}}return}options=$.extend({},{paint:true},options);this.updatingScroll=true;var availableHeight=this.getAvailableHeight();var availableWidth=this.getAvailableWidth();var heatmapPrefSize=this.heatmap.getPreferredSize();var columnDendrogramHeight=0;var rowDendrogramWidth=0;if(this.columnDendrogram){columnDendrogramHeight=morpheus.CanvasUtil.getPreferredSize(this.columnDendrogram).height}if(this.rowDendrogram){rowDendrogramWidth=morpheus.CanvasUtil.getPreferredSize(this.rowDendrogram).width}var rowTrackWidthSum=0;for(var i=0,length=this.rowTracks.length;i<length;i++){if(this.rowTracks[i].isVisible()){if(this.rowTracks[i].getPrefWidth()!==undefined){this.rowTrackHeaders[i].setPrefWidth(this.rowTracks[i].getPrefWidth())}rowTrackWidthSum+=Math.max(morpheus.CanvasUtil.getPreferredSize(this.rowTrackHeaders[i]).width,morpheus.CanvasUtil.getPreferredSize(this.rowTracks[i]).width)}}if(availableWidth!==-1&&rowTrackWidthSum+rowDendrogramWidth+heatmapPrefSize.width>availableWidth){rowTrackWidthSum=0;for(var i=0,length=this.rowTracks.length;i<length;i++){if(this.rowTracks[i].isVisible()){var rowTrackHeaderSize=morpheus.CanvasUtil.getPreferredSize(this.rowTrackHeaders[i]);var width=Math.max(rowTrackHeaderSize.width,morpheus.CanvasUtil.getPreferredSize(this.rowTracks[i]).width);if(!rowTrackHeaderSize.widthSet){width=Math.min(400,width);this.rowTracks[i].setPrefWidth(width);this.rowTrackHeaders[i].setPrefWidth(width)}rowTrackWidthSum+=width}}}var ypos=columnDendrogramHeight;var maxHeaderWidth=0;for(var i=0,length=this.columnTracks.length;i<length;i++){if(this.columnTracks[i].isVisible()){if(this.columnTracks[i].getPrefHeight()!==undefined){this.columnTrackHeaders[i].setPrefHeight(this.columnTracks[i].getPrefHeight())}var width=morpheus.CanvasUtil.getPreferredSize(this.columnTrackHeaders[i]).width;maxHeaderWidth=Math.max(maxHeaderWidth,width)}}var xpos=Math.max(rowDendrogramWidth,maxHeaderWidth);var heatMapWidth=heatmapPrefSize.width;var maxHeatMapWidth=Math.max(50,availableWidth===-1?Number.MAX_VALUE:availableWidth-rowTrackWidthSum-xpos-morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS);if(maxHeatMapWidth>0&&heatMapWidth>maxHeatMapWidth){heatMapWidth=maxHeatMapWidth;heatMapWidth=Math.min(heatMapWidth,heatmapPrefSize.width)}if(this.heatmap.prefWidth!==undefined){heatMapWidth=Math.min(heatmapPrefSize.width,this.heatmap.prefWidth)}if(this.columnDendrogram!==undefined){this.columnDendrogram.setBounds({width:heatMapWidth,height:columnDendrogramHeight,left:xpos,top:0});this.columnDendrogram.$label.css("left",xpos+this.columnDendrogram.getUnscaledWidth()+10).css("top",2);this.columnDendrogram.$squishedLabel.css("left",xpos+this.columnDendrogram.getUnscaledWidth()+10).css("top",18);this.beforeColumnTrackDivider.setVisible(true);this.beforeColumnTrackDivider.setBounds({left:xpos-maxHeaderWidth,top:ypos,width:maxHeaderWidth});ypos++}else{this.beforeColumnTrackDivider.setVisible(false)}for(var i=0,length=this.columnTracks.length;i<length;i++){var track=this.columnTracks[i];if(track.isVisible()){var size=morpheus.CanvasUtil.getPreferredSize(track);var headerSize=morpheus.CanvasUtil.getPreferredSize(this.columnTrackHeaders[i]);size.height=Math.max(size.height,headerSize.height);track.setBounds({width:heatMapWidth,height:size.height,left:xpos,top:ypos});this.columnTrackHeaders[i].setBounds({width:maxHeaderWidth,height:size.height,left:xpos-maxHeaderWidth,top:ypos});ypos+=size.height}}this.$whitespace[0].style.left=Math.ceil(xpos+heatMapWidth+10)+"px";this.$whitespace[0].style.top="0px";ypos+=morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS;var heatMapHeight=heatmapPrefSize.height;if(availableHeight!==-1&&heatMapHeight>availableHeight-ypos){heatMapHeight=Math.max(100,Math.min(heatmapPrefSize.height,availableHeight-ypos))}if(ypos<0){ypos=0}if(this.rowDendrogram){this.rowDendrogram.setBounds({width:Math.max(rowDendrogramWidth,maxHeaderWidth),height:heatMapHeight,left:0,top:ypos});this.rowDendrogram.$label.css("left",0).css("top",2);this.afterRowDendrogramDivider.setVisible(true);this.afterRowDendrogramDivider.setBounds({height:heatMapHeight,left:this.rowDendrogram.getUnscaledWidth(),top:ypos});xpos++}else{this.afterRowDendrogramDivider.setVisible(false)}this.heatmap.setBounds({width:heatMapWidth,height:heatMapHeight,left:xpos,top:ypos});this.hSortByValuesIndicator.setBounds({height:4,width:heatMapWidth,left:xpos,top:ypos-4});this.hscroll.setVisible(heatMapWidth<heatmapPrefSize.width);this.hscroll.setExtent(heatMapWidth,heatmapPrefSize.width,options.scrollLeft!==undefined?options.scrollLeft:heatmapPrefSize.width===this.hscroll.getTotalExtent()?this.hscroll.getValue():heatmapPrefSize.width*this.hscroll.getValue()/this.hscroll.getMaxValue());this.hscroll.setBounds({left:xpos,top:ypos+heatMapHeight+2});xpos+=heatMapWidth;var nvisibleRowTracks=0;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){nvisibleRowTracks++;break}}this.vSortByValuesIndicator.setBounds({width:4,height:heatMapHeight,left:xpos,top:ypos});if(nvisibleRowTracks>0){xpos=xpos+morpheus.HeatMap.SPACE_BETWEEN_HEAT_MAP_AND_ANNOTATIONS}var rowAnnotationXStart=xpos;for(var i=0,length=this.rowTracks.length;i<length;i++){var track=this.rowTracks[i];if(track.isVisible()){var size=morpheus.CanvasUtil.getPreferredSize(track);var headerSize=morpheus.CanvasUtil.getPreferredSize(this.rowTrackHeaders[i]);size.width=Math.max(headerSize.width,size.width);size.height=heatMapHeight;track.setBounds({width:size.width,height:size.height,left:xpos,top:ypos});this.rowTrackHeaders[i].setBounds({width:size.width,left:xpos,top:ypos-headerSize.height-5,height:headerSize.height});xpos+=size.width}}this.afterVerticalScrollBarDivider.setVisible(nvisibleRowTracks>0?true:false);this.afterVerticalScrollBarDivider.setBounds({left:rowAnnotationXStart-2,top:ypos-18});this.vscroll.setVisible(heatMapHeight<heatmapPrefSize.height);this.vscroll.setExtent(heatMapHeight,heatmapPrefSize.height,options.scrollTop!==undefined?options.scrollTop:heatmapPrefSize.height===this.vscroll.getTotalExtent()?this.vscroll.getValue():heatmapPrefSize.height*this.vscroll.getValue()/this.vscroll.getMaxValue());xpos+=2;this.vscroll.setBounds({left:xpos,top:ypos});xpos+=this.vscroll.getUnscaledWidth();if(this.hscroll.isVisible()){ypos+=this.hscroll.getUnscaledHeight()+2}var totalHeight=2+ypos+heatMapHeight;if(options.paint){this.paintAll({paintRows:true,paintColumns:true,invalidateRows:true,invalidateColumns:true})}this.$parent.css({height:Math.ceil(totalHeight)+"px",width:availableWidth===-1?Math.ceil(xpos+2)+"px":""});this.updatingScroll=false;this.trigger("change",{name:"revalidate",source:this,arguments:arguments})}};morpheus.HeatMap.copyFromParent=function(project,options){project.rowColorModel=options.parent.getProject().getRowColorModel().copy();project.columnColorModel=options.parent.getProject().getColumnColorModel().copy();project.rowShapeModel=options.parent.getProject().getRowShapeModel().copy();project.columnShapeModel=options.parent.getProject().getColumnShapeModel().copy();project.rowFontModel=options.parent.getProject().getRowFontModel().copy();project.columnFontModel=options.parent.getProject().getColumnFontModel().copy();var parentRowTracks=options.parent.rowTracks||[];var parentColumnTracks=options.parent.columnTracks||[];if(options.inheritFromParentOptions.rows){project.columnShapeModel=project.rowShapeModel;project.columnColorModel=project.rowColorModel;project.columnFontModel=project.rowFontModel;parentColumnTracks=parentRowTracks.slice().reverse()}if(options.inheritFromParentOptions.columns){project.rowShapeModel=project.columnShapeModel;project.rowColorModel=project.columnColorModel;project.rowFontModel=project.columnFontModel;parentRowTracks=parentColumnTracks.slice().reverse()}if(options.inheritFromParentOptions.transpose){var tmp=project.rowShapeModel;project.rowShapeModel=project.columnShapeModel;project.columnShapeModel=tmp;tmp=project.rowColorModel;project.rowColorModel=project.columnColorModel;project.columnColorModel=tmp;tmp=project.rowFontModel;project.rowFontModel=project.columnFontModel;project.columnFontModel=tmp;tmp=parentRowTracks.slice().reverse();parentRowTracks=parentColumnTracks.slice().reverse();parentColumnTracks=tmp}options.rows=options.rows||[];for(var i=0;i<parentRowTracks.length;i++){var track=parentRowTracks[i];if(track.isVisible()){options.rows.push({order:options.rows.length,field:track.getName(),display:$.extend(true,{},track.settings),force:true})}}options.columns=options.columns||[];for(var i=0;i<parentColumnTracks.length;i++){var track=parentColumnTracks[i];if(track.isVisible()){options.columns.push({order:options.columns.length,field:track.getName(),display:$.extend(true,{},track.settings),force:true})}}};morpheus.Util.extend(morpheus.HeatMap,morpheus.Events);morpheus.HelpMenu=function(){var html=[];html.push('<ul class="morpheus-footer-links">');html.push('<li><a href="index.html">Home</a></li>');html.push('<li><a data-name="contact" href="#">Contact</a></li>');html.push('<li><a href="documentation.html">Documentation</a></li>');html.push('<li><a href="tutorial.html">Tutorial</a></li>');html.push('<li><a href="configuration.html">Configuration</a></li>');html.push('<li><a href="https://github.com/cmap/morpheus.js">Source Code</a></li>');html.push('<li><a href="https://github.com/cmap/morpheus.R">R Interface</a></li>');html.push('<li><a href="https://github.com/cmap/morpheus-export">Command Line</a></li>');html.push("</ul>");this.$el=$(html.join(""));this.$el.find("[data-name=contact]").on("click",function(e){morpheus.FormBuilder.showInModal({title:"Contact",html:"Please email us at morpheus@broadinstitute.org",focus:document.activeElement});e.preventDefault()})};morpheus.HistogramLegend=function(dataset,colorScheme,metadataValue){morpheus.AbstractCanvas.call(this,true);this.colorScheme=colorScheme;this.metadataValue=metadataValue;this.dataset=dataset;this.binNumberToOccurences=null;this.setBounds({width:250,height:70});this.name=null;this.canvas.style.position="";this.canvas.style.border="1px solid LightGrey"};morpheus.HistogramLegend.prototype={binSize:0,maxCount:0,total:0,setName:function(name){this.name=name},setBinSize:function(binSize){this.binSize=binSize},buildHistogram:function(){var binSize=this.binSize;var dataset=this.dataset;var metadataValue=this.metadataValue;var colorScheme=this.colorScheme;var min=colorScheme.getMin();var max=colorScheme.getMax();if(min===max){min-=.5;max+=.5}var vector=dataset.getRowMetadata().getByName(colorScheme.getSeparateColorSchemeForRowMetadataField());var numberOfBins=Math.ceil((max-min)/binSize);var binNumberToOccurences=new Uint32Array(numberOfBins);this.binNumberToOccurences=binNumberToOccurences;var index=0;for(var i=0,nrows=dataset.getRowCount();i<nrows;i++){if(vector==null||vector.getValue(i)===metadataValue){for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){var value=dataset.getValue(i,j);if(isNaN(value)){continue}var bin=Math.floor((value-min)/binSize);if(bin<0){bin=0}else if(bin>=numberOfBins){bin=numberOfBins-1}binNumberToOccurences[bin]++}}}var maxCount=0;var total=0;for(var i=0;i<numberOfBins;i++){var count=binNumberToOccurences[i];maxCount=count>=maxCount?count:maxCount;total+=count}this.maxCount=maxCount;this.total=total},draw:function(clip,context){this.buildHistogram();var colorScheme=this.colorScheme;var canvasWidth=this.getUnscaledWidth()-50;var valueToPosition=d3.scale.linear().domain([colorScheme.getMin(),colorScheme.getMax()]).range([0,canvasWidth]).clamp(true);var histogramHeight=30;var countToPosition=d3.scale.linear().domain([0,this.maxCount/this.total]).range([histogramHeight,0]).clamp(true);var binNumberToOccurences=this.binNumberToOccurences;var min=colorScheme.getMin();var binSize=this.binSize;var y0=countToPosition(0);if(this.name!=null){context.font="11px "+morpheus.CanvasUtil.getFontFamily(context);context.fillStyle="black";context.lineWidth=1;context.fillText(this.name,.5,12);context.translate(0,14)}context.lineWidth=.2;context.strokeStyle="#D3D2C2";context.fillStyle="#D3D2C2";context.translate(25,0);context.beginPath();context.moveTo(0,y0);context.lineTo(canvasWidth,y0);context.stroke();context.lineWidth=1;context.strokeStyle="white";for(var i=0,numberOfBins=binNumberToOccurences.length;i<numberOfBins;i++){var count=binNumberToOccurences[i];if(count>0){count/=this.total;var start=min+i*binSize;var end=start+binSize;var x=valueToPosition(start);var width=valueToPosition(end)-x;var y=countToPosition(count);context.rect(x,y0,width,y-y0);context.fill();context.stroke()}}context.translate(0,histogramHeight+1);context.fillStyle="black";morpheus.HeatMapColorSchemeLegend.drawColorScheme(context,this.colorScheme,canvasWidth,false,false,6)}};morpheus.Util.extend(morpheus.HistogramLegend,morpheus.AbstractCanvas);morpheus.LegendWithStops=function(){var _this=this;morpheus.AbstractCanvas.call(this,false);this.setBounds({width:300,height:40});$(this.canvas).on("mousedown",function(event){var position=morpheus.CanvasUtil.getMousePos(event.target,event);_this.selectedIndex=_this.findIndexForPosition(position);_this.trigger("selectedIndex",{selectedIndex:_this.selectedIndex})});this.hammer=morpheus.Util.hammer(this.canvas,["pan"]).on("panmove",this.panmove=function(event){if(_this.selectedIndex!==-1){var position=morpheus.CanvasUtil.getMousePos(event.target,event);var fraction=_this.fractionToStopPix.invert(position.x);fraction=Math.max(0,fraction);fraction=Math.min(1,fraction);_this.trigger("moved",{fraction:fraction})}}).on("panstart",this.panstart=function(event){}).on("panend",this.panend=function(event){_this.selectedIndex=-1});$(this.canvas).on("keydown",function(e){if((e.which==8||e.which==46)&&_this.selectedIndex!==-1){_this.trigger("delete");e.preventDefault();e.stopPropagation();e.stopImmediatePropagation()}})};morpheus.LegendWithStops.prototype={border:7,stopHalfSize:5,selectedIndex:-1,destroy:function(){$(this.canvas).off("keyup").off("mousedown");this.hammer.off("panstart",this.panstart).off("panmove",this.panmove);this.hammer.destroy()},setSelectedIndex:function(index){this.selectedIndex=index},findIndexForPosition:function(position){if(position.y>=22){for(var i=0,length=this.fractions.length;i<length;i++){var pix=this.fractionToStopPix(this.fractions[i]);var start=pix-this.stopHalfSize;var end=pix+this.stopHalfSize;if(position.x>=start&&position.x<=end){return i}}}return-1},draw:function(fractions,colors,stepped,fractionToStopPix){this.fractions=fractions;this.colors=colors;this.stepped=stepped;this.fractionToStopPix=fractionToStopPix;var context=this.canvas.getContext("2d");morpheus.CanvasUtil.resetTransform(context);context.clearRect(0,0,this.getUnscaledWidth(),this.getUnscaledHeight());context.translate(this.border,0);morpheus.HeatMapColorSchemeLegend.draw(context,fractions,colors,this.getUnscaledWidth()-2*this.border,this.getUnscaledHeight()-20,stepped);context.translate(-this.border,0);context.lineWidth=1;context.strokeStyle="Grey";context.strokeRect(this.border,0,this.getUnscaledWidth()-2*this.border,this.getUnscaledHeight()-20);for(var i=0;i<fractions.length;i++){if(i>0&&fractions[i]===fractions[i-1]){continue}context.fillStyle=colors[i];var pix=fractionToStopPix(fractions[i]);context.fillRect(pix-this.stopHalfSize,22,this.stopHalfSize*2,this.stopHalfSize*2);if(this.selectedIndex===i){context.lineWidth=2;context.strokeStyle="black"}else{context.lineWidth=1;context.strokeStyle="Grey"}context.strokeRect(pix-this.stopHalfSize,22,this.stopHalfSize*2,this.stopHalfSize*2)}}};morpheus.Util.extend(morpheus.LegendWithStops,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.LegendWithStops,morpheus.Events);morpheus.Popup={};morpheus.Popup.initted=false;morpheus.Popup.init=function(){if(morpheus.Popup.initted){return}morpheus.Popup.initted=true;morpheus.Popup.$popupDiv=$(document.createElement("div"));morpheus.Popup.$popupDiv.css("position","absolute").css("zIndex",1050).css("overflow","auto").addClass("dropdown clearfix");morpheus.Popup.$contextMenu=$(document.createElement("ul"));morpheus.Popup.$contextMenu.addClass("dropdown-menu").css("display","block").css("position","static").css("margin-bottom","5px");morpheus.Popup.$contextMenu.appendTo(morpheus.Popup.$popupDiv);morpheus.Popup.$contextMenu.on("click","a",function(e){e.preventDefault();var $this=$(this);morpheus.Popup.popupCallback(e,$this.data("name"));morpheus.Popup.hide()})};morpheus.Popup.popupInDom=false;morpheus.Popup.hidePopupMenu=function(e){if(morpheus.Popup.component==e.target){e.preventDefault();e.stopPropagation()}morpheus.Popup.hide()};morpheus.Popup.hide=function(){morpheus.Popup.$popupDiv.hide();$(document.body).off("mousedown",morpheus.Popup.hidePopupMenu);morpheus.Popup.popupCallback=null;morpheus.Popup.component=null};morpheus.Popup.showPopup=function(menuItems,position,component,callback){morpheus.Popup.init();if(morpheus.Popup.component==component){morpheus.Popup.hide();return}morpheus.Popup.popupCallback=callback;morpheus.Popup.component=component;var html=[];for(var i=0,length=menuItems.length;i<length;i++){var item=menuItems[i];if(item.header){html.push('<li role="presentation" class="dropdown-header">'+item.name+"</li>")}else if(item.separator){html.push('<li class="divider"></li>')}else{html.push('<li role="presentation"');if(item.disabled){html.push('class="disabled"')}html.push('><a data-name="'+item.name+'" data-type="popup-item" tabindex="-1" href="#"');if(item.class){html.push(' class="'+item.class+'"')}html.push(">");if(item.checked){html.push('<span class="dropdown-checkbox fa fa-check"></span>')}html.push(item.name);if(item.icon){html.push('<span class="pull-right '+item.icon+'"></span>')}html.push("</a>");html.push("</li>")}}morpheus.Popup.$contextMenu.html(html.join(""));if(!morpheus.Popup.popupInDom){morpheus.Popup.popupInDom=true;morpheus.Popup.$popupDiv.appendTo($(document.body))}var $body=$(document.body);var $window=$(window);var windowWidth=$window.width();var windowHeight=$window.height();var popupWidth=morpheus.Popup.$popupDiv.width();var popupHeight=morpheus.Popup.$popupDiv.height();var left=position.x;var top=position.y;if(left+popupWidth>=windowWidth){left-=popupWidth;left=Math.max(4,left)}if(top+popupHeight>=windowHeight){top-=popupHeight;top=Math.max(4,top)}morpheus.Popup.$popupDiv.css({display:"block",left:left,top:top});morpheus.Popup.$popupDiv.show();$body.off("mousedown",morpheus.Popup.hidePopupMenu);window.setTimeout(function(){$body.on("mousedown",function(e){var $target=$(e.target);if($target[0]!==morpheus.Popup.$popupDiv[0]&&$target.data("type")!=="popup-item"){morpheus.Popup.hidePopupMenu(e)}})},1)};morpheus.RowDendrogram=function(heatMap,tree,positions,project){morpheus.AbstractDendrogram.call(this,heatMap,tree,positions,project,morpheus.AbstractDendrogram.Type.ROW)};morpheus.RowDendrogram.prototype={drawNode:function(context,node){var radius=this.getNodeRadius(node);var pix=this.toPix(node);context.beginPath();context.arc(pix[0],pix[1],radius,Math.PI*2,false);context.fill()},isDragHotSpot:function(p){return Math.abs(this.scale(this.cutHeight)-p.x)<=2},drawCutSlider:function(clip,context){if(context.setLineDash){context.setLineDash([5])}context.strokeStyle="black";var nx=this.scale(this.cutHeight);context.beginPath();context.moveTo(nx,clip.y);context.lineTo(nx,this.getUnscaledHeight());context.stroke();if(context.setLineDash){context.setLineDash([])}},getPreferredSize:function(){return{width:100,height:Math.ceil(this.positions.getPosition(this.positions.getLength()-1)+this.positions.getItemSize(this.positions.getLength()-1))}},paintMouseOver:function(clip,context){if(this.project.getHoverRowIndex()!==-1){morpheus.CanvasUtil.resetTransform(context);context.translate(0,-clip.y);this.drawRowBorder(context,this.positions,this.project.getHoverRowIndex(),this.getUnscaledWidth())}},drawRowBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(0,pix+size);context.lineTo(gridSize,pix+size);context.stroke();context.beginPath();context.moveTo(0,pix);context.lineTo(gridSize,pix);context.stroke()},createScale:function(){return d3.scale.linear().domain([0,this.tree.maxHeight]).range([this.getUnscaledWidth(),0])},getMaxIndex:function(clip){return morpheus.Positions.getBottom(clip,this.positions)},getMinIndex:function(clip){return morpheus.Positions.getTop(clip,this.positions)},toPix:function(node){var min=this.positions.getPosition(node.minIndex)+this.positions.getItemSize(node.minIndex)/2;var max=this.positions.getPosition(node.maxIndex)+this.positions.getItemSize(node.maxIndex)/2;return[this.scale(node.height),(min+max)/2]},drawPathFromNodeToParent:function(context,node){var pix=this.toPix(node);var parentPix=this.toPix(node.parent);context.beginPath();context.moveTo(pix[0],pix[1]);context.lineTo(parentPix[0],pix[1]);context.lineTo(parentPix[0],parentPix[1]);context.stroke()},drawNodePath:function(context,node,minIndex,maxIndex){var children=node.children;var left=children[0];var right=children[1];var ry=this.toPix(right)[1];var rx=this.scale(right.height);var ly=this.toPix(left)[1];var lx=this.scale(left.height);var nx=this.scale(node.height);var x;var y;if(!this.drawLeafNodes){var leftIsLeaf=left.children!==undefined;var rightIsLeaf=right.children!==undefined;if(leftIsLeaf){lx=nx+4}if(rightIsLeaf){rx=nx+4}x=[rx,nx,nx,lx];y=[ry,ry,ly,ly]}else{x=[rx,nx,nx,lx];y=[ry,ry,ly,ly]}context.beginPath();context.moveTo(x[0],y[0]);for(var i=1,length=x.length;i<length;i++){context.lineTo(x[i],y[i])}context.stroke()}};morpheus.Util.extend(morpheus.RowDendrogram,morpheus.AbstractDendrogram);morpheus.ScentedSearch=function(model,positions,isVertical,scrollbar,heatMap){morpheus.AbstractCanvas.call(this,false);this.model=model;this.positions=positions;this.isVertical=isVertical;this.scrollbar=scrollbar;this.heatMap=heatMap;this.searchIndices=[];scrollbar.decorator=this;var _this=this;var mouseMove=function(e){var indices=_this.getSearchIndices(e);document.body.style.cursor=indices.length===0?"default":"pointer";scrollbar.canvas.style.cursor=indices.length===0?"default":"pointer";var tipOptions={event:e,heatMapLens:indices.length>=0};if(isVertical){heatMap.setToolTip(indices.length>=0?indices:null,-1,tipOptions)}else{heatMap.setToolTip(-1,indices.length>=0?indices:null,tipOptions)}};var mouseExit=function(e){document.body.style.cursor="default";scrollbar.canvas.style.cursor="default";heatMap.setToolTip(-1,-1,{event:e})};$(scrollbar.canvas).on("mousemove.morpheus",mouseMove).on("mouseout.morpheus",mouseExit)};morpheus.ScentedSearch.LINE_HEIGHT=3.5;morpheus.ScentedSearch.prototype={mouseMovedIndex:-1,getIndex:function(event){var pix=morpheus.CanvasUtil.getMousePos(event.target,event);var val=pix[this.isVertical?"y":"x"];return this.getIndexForPix(val)},getSearchIndices:function(event){var pix=morpheus.CanvasUtil.getMousePos(event.target,event);var val=pix[this.isVertical?"y":"x"];return this.getSearchIndicesForPix(val)},getSearchIndicesForPix:function(pix){var indices=this.searchIndices;if(indices==null){return[]}var scale=this.scale;var tolerance=morpheus.ScentedSearch.LINE_HEIGHT;var matches=[];for(var i=0,length=indices.length;i<length;i++){var midVal=this.positions.getPosition(indices[i])*scale;if(Math.abs(midVal-pix)<=tolerance){matches.push(indices[i])}}return matches},getIndexForPix:function(pix){var indices=this.searchIndices;if(indices==null){return-1}var tolerance=morpheus.ScentedSearch.LINE_HEIGHT;if(this.mouseMovedIndex>0){var midVal=this.positions.getPosition(indices[this.mouseMovedIndex])*scale;if(Math.abs(midVal-pix)<=tolerance){return this.mouseMovedIndex}}var low=0;var scale=this.scale;var high=indices.length-1;while(low<=high){var mid=low+high>>1;var midVal=this.positions.getPosition(indices[mid])*scale;var cmp=0;if(Math.abs(midVal-pix)<=tolerance){cmp=0}else if(midVal<pix){cmp=-1}else if(midVal>pix){cmp=1}if(cmp<0)low=mid+1;else if(cmp>0)high=mid-1;else return mid}return-1},tap:function(position){var val=position[this.isVertical?"y":"x"];var index=this.getIndexForPix(val);this.scrollbar.canvas.style.cursor=index<0?"default":"pointer";if(index>=0){if(this.isVertical){this.heatMap.scrollTop(this.positions.getPosition(this.searchIndices[index]))}else{this.heatMap.scrollLeft(this.positions.getPosition(this.searchIndices[index]))}return true}return false},update:function(){this.searchIndices=this.model.getViewIndices().values().sort(function(a,b){return a<b?-1:1})},draw:function(clip,context){var width=this.scrollbar.getUnscaledWidth();var height=this.scrollbar.getUnscaledHeight();var availableLength=(this.isVertical?height:width)-morpheus.ScentedSearch.LINE_HEIGHT;this.scale=availableLength/(this.positions.getPosition(this.positions.getLength()-1)+this.positions.getItemSize(this.positions.getLength()-1));context.fillStyle=morpheus.ScentedSearch.TICK_COLOR;context.lineWidth=1;this.drawIndices(context,this.searchIndices);this.drawHoverMatchingValues(context)},drawHoverMatchingValues:function(context){var heatmap=this.heatMap;context.fillStyle=morpheus.ScentedSearch.MATCHING_VALUES_TICK_COLOR;if(heatmap.mousePositionOptions&&heatmap.mousePositionOptions.name!=null){var isColumns=!this.isVertical;var track=heatmap.getTrack(heatmap.mousePositionOptions.name,isColumns);if(track==null){return}if(track.settings.highlightMatchingValues){var hoverIndex=isColumns?heatmap.getProject().getHoverColumnIndex():heatmap.getProject().getHoverRowIndex();if(hoverIndex===-1){return}var vector=track.getVector();var value=vector.getValue(hoverIndex);var valueToModelIndices=track.getFullVector().getProperties().get(morpheus.VectorKeys.VALUE_TO_INDICES);if(!valueToModelIndices){var fullVector=track.getFullVector();valueToModelIndices=morpheus.VectorUtil.createValueToIndicesMap(fullVector);fullVector.getProperties().set(morpheus.VectorKeys.VALUE_TO_INDICES,valueToModelIndices)}var modelIndices=valueToModelIndices.get(value);if(modelIndices==null){console.log("valueToModelIndices error");return}var scale=this.scale;var lineLength=!this.isVertical?this.scrollbar.getUnscaledHeight():this.scrollbar.getUnscaledWidth();var isVertical=this.isVertical;var positions=this.positions;var project=heatmap.getProject();for(var i=0,length=modelIndices.length;i<length;i++){var modelIndex=modelIndices[i];var index=isVertical?project.convertModelRowIndexToView(modelIndex):project.convertModelColumnIndexToView(modelIndex);if(index===-1){continue}var pix=positions.getPosition(index)*scale;if(isVertical){context.fillRect(0,pix,lineLength,morpheus.ScentedSearch.LINE_HEIGHT)}else{context.fillRect(pix,0,morpheus.ScentedSearch.LINE_HEIGHT,lineLength)}}}}},drawIndices:function(context,highlightedIndices){var scale=this.scale;var lineLength=!this.isVertical?this.scrollbar.getUnscaledHeight():this.scrollbar.getUnscaledWidth();var isVertical=this.isVertical;var positions=this.positions;for(var i=0,length=highlightedIndices.length;i<length;i++){var index=highlightedIndices[i];var pix=positions.getPosition(index)*scale;if(isVertical){context.beginPath();context.rect(0,pix,lineLength,morpheus.ScentedSearch.LINE_HEIGHT);context.fill()}else{context.beginPath();context.rect(pix,0,morpheus.ScentedSearch.LINE_HEIGHT,lineLength);context.fill()}}}};morpheus.Util.extend(morpheus.ScentedSearch,morpheus.AbstractCanvas);morpheus.ScentedSearch.MATCHING_VALUES_TICK_COLOR="black";morpheus.ScentedSearch.TICK_COLOR="#3182bd";morpheus.ScrollBar=function(isVertical){morpheus.AbstractCanvas.call(this);this.isVertical=isVertical;$(this.canvas).css("border","1px solid #d8d8d8");if(isVertical){this.setBounds({width:12})}else{this.setBounds({height:12})}this.field=this.isVertical?"y":"x";var that=this;var mouseMove=function(event){if(!morpheus.CanvasUtil.dragging){var position=morpheus.CanvasUtil.getMousePos(event.target,event,true);var mouseOver=position[that.field]>=that.thumbPos&&position[that.field]<=that.thumbPos+that.thumbExtent;if(that.thumbMouseOver!==mouseOver){that.thumbMouseOver=mouseOver;that.repaint()}}};var mouseExit=function(e){if(!morpheus.CanvasUtil.dragging&&that.thumbMouseOver){that.thumbMouseOver=false;that.repaint()}};$(this.canvas).on("mousemove",mouseMove).on("mouseout",mouseExit).on("mouseenter",mouseMove);this.hammer=morpheus.Util.hammer(this.canvas,[this.isVertical?"panv":"panh","tap"]).on("panstart",this.panstart=function(event){var position=morpheus.CanvasUtil.getMousePos(event.target,event,true);if(position[that.field]>=that.thumbPos&&position[that.field]<=that.thumbPos+that.thumbExtent){that.draggingThumb=true;that.dragStartThumbPos=that.thumbPos}else{that.draggingThumb=false}}).on("panend",this.panend=function(event){that.draggingThumb=false}).on("panmove",this.panmove=function(event){if(that.draggingThumb){var position=morpheus.CanvasUtil.getMousePos(event.target,event);var thumbPosPix=that.dragStartThumbPos+(that.isVertical?event.deltaY:event.deltaX);var f=thumbPosPix/(that.visibleExtent-that.thumbExtent);var value=f*that.maxValue;that.setValue(value,true);event.preventDefault();event.srcEvent.stopPropagation();event.srcEvent.stopImmediatePropagation()}}).on("tap doubletap",this.tap=function(event){if(!that.draggingThumb){var position=morpheus.CanvasUtil.getMousePos(event.target,event);if(!that.decorator.tap(position)){var thumbExtentToValue=that.thumbExtent/that.totalExtent*that.totalExtent;that.scrollToTop=position[that.field]<that.thumbPos;that.setValue(that.scrollToTop?that.value-thumbExtentToValue:that.value+thumbExtentToValue,true)}}})};morpheus.ScrollBar.prototype={thumbPos:0,thumbExtent:0,extent:0,value:0,maxValue:0,totalExtent:0,visibleExtent:0,dragStartThumbPos:0,draggingThumb:false,thumbMouseOver:false,dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.hammer.off("panend",this.panend).off("panstart",this.panstart).off("panmove",this.panmove).off("tap",this.tap).off("doubletap",this.tap);this.hammer.destroy()},draw:function(clip,context){var width=this.getUnscaledWidth();var height=this.getUnscaledHeight();if(this.visibleExtent===this.totalExtent){context.clearRect(0,0,width,height)}else{context.fillStyle="rgb(241,241,241)";context.fillRect(0,0,width,height);context.fillStyle=!this.thumbMouseOver?"rgb(137,137,137)":"rgb(100,100,100)";if(this.isVertical){context.fillRect(0,this.thumbPos,width,this.thumbExtent)}else{context.fillRect(this.thumbPos,0,this.thumbExtent,height)}}this.decorator.draw(clip,context)},setThumbPosFromValue:function(){var f=this.maxValue==0?0:this.value/this.maxValue;this.thumbPos=f*(this.visibleExtent-this.thumbExtent);this.thumbPos=Math.max(0,this.thumbPos)},getValue:function(){return this.value},getMaxValue:function(){return this.maxValue},setValue:function(value,trigger){if(isNaN(value)){value=0}if(this.visibleExtent===this.totalExtent){value=0}value=Math.max(value,0);value=Math.min(this.maxValue,value);this.value=value;this.setThumbPosFromValue();if(trigger){this.trigger("scroll",{value:this.value});this.repaint()}return this.value},setTotalExtent:function(totalExtent){this.totalExtent=totalExtent;this._setRange()},getTotalExtent:function(){return this.totalExtent},getVisibleExtent:function(){return this.visibleExtent},_setRange:function(){this.thumbExtent=Math.max(10,this.visibleExtent*(this.visibleExtent/this.totalExtent));this.maxValue=this.totalExtent-this.visibleExtent;this.maxValue=Math.max(0,this.maxValue);if(this.isVertical){this.setBounds({height:this.visibleExtent})}else{this.setBounds({width:this.visibleExtent})}},setExtent:function(visibleExtent,totalExtent,value){this.visibleExtent=visibleExtent;this.totalExtent=totalExtent;this._setRange();this.setValue(value,false)}};morpheus.Util.extend(morpheus.ScrollBar,morpheus.AbstractCanvas);morpheus.Util.extend(morpheus.ScrollBar,morpheus.Events);morpheus.ShapeChooser=function(options){var formBuilder=new morpheus.FormBuilder;var map=options.map;var html=['<select name="valuePicker" class="selectpicker" data-live-search="true">'];map.forEach(function(val,key){html.push("<option");html.push(' value="');html.push(key);html.push('">');html.push(key);html.push("</option>")});html.push("</select>");formBuilder.append({name:"selected_value",type:"custom",value:html.join("")});var shapeField=new morpheus.ShapeField({showNone:true});formBuilder.append({style:"max-width:50px;",name:"selected_shape",type:"custom",value:'<div data-name="shape"></div>'});shapeField.$el.appendTo(formBuilder.$form.find("[data-name=shape]"));var $valuePicker=formBuilder.$form.find("[name=valuePicker]");var selectedVal=$valuePicker.val();var _this=this;shapeField.setShapeValue(map.get(selectedVal));shapeField.on("change",function(e){map.set(selectedVal,e.shape);_this.trigger("change",{value:selectedVal,shape:e.shape})});$valuePicker.selectpicker().change(function(){selectedVal=$valuePicker.val();shapeField.setShapeValue(map.get(selectedVal))});this.$div=formBuilder.$form};morpheus.ShapeChooser.prototype={};morpheus.Util.extend(morpheus.ShapeChooser,morpheus.Events);morpheus.ShapeField=function(options){var shapes=options.shapes||morpheus.VectorShapeModel.SHAPES;var _this=this;var html=[];var size2=8;var x=4;var y=4;html.push('<div style="margin-bottom:1em;" class="btn-group">');html.push('<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown" aria-expanded="false"><span data-name="selection"></span> <span class="fa fa-caret-down"></span></button>');html.push('<ul class="dropdown-menu" role="menu">');if(options.showNone){html.push('<li><a data-name="none" href="#">(None)</a></li>')}for(var i=0;i<shapes.length;i++){var context=new C2S(size2*2,size2*2);context.translate(4,4);morpheus.CanvasUtil.drawShape(context,shapes[i],x,y,size2);var svg=context.getSerializedSvg();html.push('<li><a data-name="'+shapes[i]+'" href="#">'+svg+"</a></li>")}html.push("</ul></div>");var $el=$(html.join(""));var $header=$el.find("[data-name=selection]");$el.on("click","li > a",function(e){e.preventDefault();var shape=$(this).data("name");setShapeValue(shape);_this.trigger("change",{shape:shape})});var setShapeValue=function(val){if(val==="none"){$header.html("(None)")}else{var context=new C2S(size2*2,size2*2);context.translate(4,4);morpheus.CanvasUtil.drawShape(context,val,x,y,size2);$header.html(context.getSerializedSvg())}};this.setShapeValue=setShapeValue;this.$el=$el};morpheus.ShapeField.prototype={};morpheus.Util.extend(morpheus.ShapeField,morpheus.Events);morpheus.SortByValuesIndicator=function(project,isVertical,positions){morpheus.AbstractCanvas.call(this,true);this.project=project;this.isVertical=isVertical;this.positions=positions;this.lastPosition={start:-1,end:-1}};morpheus.SortByValuesIndicator.prototype={prePaint:function(clip,context){var positions=this.positions;var start=0;var end=positions.getLength();if(!this.isVertical){start=morpheus.Positions.getLeft(clip,positions);end=morpheus.Positions.getRight(clip,positions)}else{start=morpheus.Positions.getTop(clip,positions);end=morpheus.Positions.getBottom(clip,positions)}if(this.invalid||start!==this.lastPosition.start||end!==this.lastPosition.end){this.lastPosition.start=start;this.lastPosition.end=end;this.invalid=true}},draw:function(clip,context){var project=this.project;var isVertical=this.isVertical;var positions=this.positions;var sortKeys=isVertical?project.getColumnSortKeys():project.getRowSortKeys();context.translate(-clip.x,-clip.y);context.fillStyle="black";context.textBaseline="top";context.textAlign="left";context.font="8px "+morpheus.CanvasUtil.getFontFamily(context);var start=0;var end=positions.getLength();if(!isVertical){start=morpheus.Positions.getLeft(clip,positions);end=morpheus.Positions.getRight(clip,positions)}else{start=morpheus.Positions.getTop(clip,positions);end=morpheus.Positions.getBottom(clip,positions)}var arrowWidth=3;var arrowHeight=4;for(var i=0;i<sortKeys.length;i++){var key=sortKeys[i];if(key instanceof morpheus.SortByValuesKey){var modelIndices=key.modelIndices;for(var j=0;j<modelIndices.length;j++){var modelIndex=modelIndices[j];var view=isVertical?project.convertModelRowIndexToView(modelIndex):project.convertModelColumnIndexToView(modelIndex);if(view!==-1&&view>=start&&view<end){context.save();var pix=positions.getPosition(view);var size=positions.getItemSize(view);if(!isVertical){context.translate(pix+size/2,0)}else{context.translate(2,pix+size/2)}context.beginPath();if(key.getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight);context.lineTo(-arrowWidth,arrowHeight)}else if(key.getSortOrder()===morpheus.SortKey.SortOrder.DESCENDING){context.moveTo(0,arrowHeight);context.lineTo(arrowWidth,0);context.lineTo(-arrowWidth,0)}else{context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight/2);context.lineTo(0,arrowHeight);context.lineTo(-arrowWidth,arrowHeight/2)}context.fill();context.restore()}}}}}};morpheus.Util.extend(morpheus.SortByValuesIndicator,morpheus.AbstractCanvas);morpheus.SortDialog=function(project){var _this=this;var $chooserDiv=$('<div class="container-fluid"></div>');var $div=$('<div class="container-fluid"></div>');var html=[];html.push('<div style="border-bottom:1px solid LightGrey;margin-bottom:20px;" class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-2"><label class="control-label">Sort</label></div>');html.push('<div class="col-xs-5">');html.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="rows" checked>Rows</label></div>');html.push('<div class="radio"><label><input type="radio" name="rowsOrColumns" value="columns">Columns</label></div>');html.push("</div>");html.push("</form>");html.push("</div>");$chooserDiv.html(html.join(""));function toggle(isColumns){_this.isColumns=isColumns;var $element=_this.build(project,isColumns);$div.empty().html($element);$div.on("click","[data-name=delete]",function(e){var $this=$(this);e.preventDefault();$this.closest("div.row").remove()});$div.on("click","[data-name=add]",function(e){var $this=$(this);var level=[];var $sibling=$this.closest("div.row");_this.createLevel(level,new morpheus.SortKey("",morpheus.SortKey.SortOrder.ASCENDING),_this.fields);$sibling.after($(level.join("")));e.preventDefault()})}$chooserDiv.on("change","[name=rowsOrColumns]",function(e){var $this=$(this);toggle($this.val()==="columns")});toggle(false);var $outer=$("<div></div>");$chooserDiv.appendTo($outer);$div.appendTo($outer);morpheus.FormBuilder.showOkCancel({title:"Sort",content:$outer,okCallback:function(){var $forms=$div.find("form");var sortBy=$forms.find("[name=sortBy]").map(function(){return $(this).val()});var lockOrder=$forms.find("[name=lockOrder]").map(function(){return $(this).prop("checked")});var sortOrder=$forms.find("[name=sortOrder]:checked").map(function(){return $(this).val()});var groupBy=$div.find("[name=groupBy]").val();var newSortKeys=[];var modelIndices=_this.isColumns?project.getRowSelectionModel().toModelIndices():project.getColumnSelectionModel().toModelIndices();var existingSortKeys=_this.isColumns?project.getColumnSortKeys():project.getRowSortKeys();for(var i=0;i<existingSortKeys.length;i++){if(existingSortKeys[i].isUnlockable()){existingSortKeys.splice(i,1);i--}}var newSortKeyFields=new morpheus.Set;for(var i=0;i<sortBy.length;i++){if(!newSortKeyFields.has(sortBy[i])){newSortKeyFields.add(sortBy[i]);var key=null;if(sortBy[i]==="selection"){key=new morpheus.SortByValuesKey(modelIndices,sortOrder[i],_this.isColumns)}else if(sortBy[i]!==""){key=new morpheus.SortKey(sortBy[i],sortOrder[i])}if(key!=null){newSortKeys.push(key);if(lockOrder[i]){key.setLockOrder(1)}}}}var newGroupKeys=[];if(groupBy!=null){for(var i=0;i<groupBy.length;i++){newGroupKeys.push(new morpheus.SortKey(groupBy[i],morpheus.SortKey.SortOrder.UNSORTED))}}if(_this.isColumns){project.setGroupColumns(newGroupKeys,true);project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys(newSortKeys,existingSortKeys),true)}else{project.setGroupRows(newGroupKeys,true);project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys(newSortKeys,existingSortKeys),true)}}})};morpheus.SortDialog.prototype={isColumns:false,build:function(project,isColumns){var fields=morpheus.MetadataUtil.getMetadataNames(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata());this.fields=fields;var html=[];var sortKeys=isColumns?project.getColumnSortKeys():project.getRowSortKeys();this.createLevel0(html);for(var i=0;i<sortKeys.length;i++){if(sortKeys[i].isUnlockable()){this.createLevel(html,sortKeys[i],fields)}}html.push('<div class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-2"><label>Group by</label></div>');html.push('<div class="col-xs-4">');var groupByKeys=(isColumns?project.getGroupColumns():project.getGroupRows()).map(function(key){return key.field});html.push('<select multiple name="groupBy" class="selectpicker form-control">');_.each(fields,function(field){html.push('<option value="'+field+'"');if(_.indexOf(groupByKeys,field)!==-1){html.push(" selected")}html.push(">");html.push(field);html.push("</option>")});html.push("</select>");html.push("</div>");html.push("</div>");var $div=$(html.join(""));$div.find(".selectpicker").selectpicker({iconBase:"fa",tickIcon:"fa-check",style:"btn-default btn-sm"});return $div},createLevel0:function(html){html.push('<div style="border-bottom:1px solid LightGrey;margin-bottom:20px;" class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-8">');html.push('<a data-name="add" href="#">Add sort level</a>');html.push("</div>");html.push("</form>");html.push("</div>")},createLevel:function(html,key,fields){html.push('<div style="border-bottom:1px solid LightGrey;margin-bottom:20px;" class="row">');html.push('<form class="form-horizontal" role="form">');html.push('<div class="col-xs-2"><label class="control-label">Sort by</label></div>');html.push('<div class="col-xs-4">');html.push('<select name="sortBy" class="form-control">');html.push('<option value=""></option>');html.push('<option value="selection"'+(key instanceof morpheus.SortByValuesKey?" selected":"")+">selection</option>");_.each(fields,function(field){html.push('<option value="'+field+'"');if(field==key.toString()){html.push(" selected")}html.push(">");html.push(field);html.push("</option>")});html.push("</select>");html.push("</div>");html.push('<div class="col-xs-5">');html.push('<div class="radio"><label><input type="radio" name="sortOrder" value="ascending"'+(morpheus.SortKey.SortOrder.ASCENDING==key.getSortOrder()?" checked":"")+">Ascending</label></div>");html.push('<div class="radio"><label><input type="radio" name="sortOrder" value="descending"'+(morpheus.SortKey.SortOrder.DESCENDING==key.getSortOrder()?" checked":"")+">Descending</label></div>");html.push("</div>");html.push('<div class="col-xs-1">');html.push('<a data-name="delete">Delete</a>');html.push("</div>");html.push('<div class="col-xs-12">');html.push('<div class="checkbox"><label><input name="lockOrder" type="checkbox"'+(key.getLockOrder()!==0?" checked":"")+"> Lock sort level</label></div>");html.push("</div>");html.push('<div class="col-xs-12">');html.push("<br />");html.push('<a data-name="add" href="#">Add sort level</a>');html.push("</div>");html.push("</form>");html.push("</div>")}};morpheus.SteppedColorSupplier=function(){morpheus.AbstractColorSupplier.call(this);this.hiddenValue=0;this.hiddenValues=new morpheus.Set;this.stepped=true};morpheus.SteppedColorSupplier.linearScale=function(value,input0,input1,pix0,pix1){return(value-input0)/(input1-input0)*(pix1-pix0)+pix0};morpheus.SteppedColorSupplier.prototype={createInstance:function(){return new morpheus.SteppedColorSupplier},isStepped:function(){return true},getHiddenValues:function(){return this.hiddenValues},getIndexForFraction:function(f){var fractions=this.fractions;if(f<=fractions[0]){return 0}if(f>=fractions[fractions.length-1]){return fractions.length-1}for(var i=0;i<fractions.length-1;i++){var left=fractions[i];var right=fractions[i+1];if(f>=left&&f<right){return i}}return fractions.length-1},getColor:function(row,column,value){if(this.hiddenValues.has(value)){value=this.hiddenValue}if(isNaN(value)){return this.missingColor}var min=this.min;var max=this.max;var colors=this.colors;if(value<=min){return colors[0]}else if(value>=max){return colors[colors.length-1]}var fraction=morpheus.SteppedColorSupplier.linearScale(value,min,max,0,100)/100;return colors[this.getIndexForFraction(fraction)]}};morpheus.Util.extend(morpheus.SteppedColorSupplier,morpheus.AbstractColorSupplier);morpheus.TabManager=function(options){this.options=$.extend({},{autohideTabBar:false,rename:true},options);var _this=this;this.activeTabObject=null;this.activeTabId=null;this.idToTabObject=new morpheus.Map;this.$nav=$('<ul class="nav nav-tabs compact morpheus-nav"></ul>');this.$nav.sortable({containment:"parent",axis:"x",helper:"clone",cancel:"li:not(.morpheus-sortable)",items:"li.morpheus-sortable"});this.$nav.sortable("disable");this.$nav.on("click","li > a",function(e){var tabId=$(this).data("link");if(tabId!=null){e.preventDefault();if(_this.activeTabId!==tabId){$(this).tab("show")}}});if(this.options.autohideTabBar){this.$nav.css("display","none")}if(options.dropTab){var html=[];html.push('<li class="morpheus-tab-addon dropdown pull-right tabdrop">');html.push('<div class="btn-group">');html.push('<button type="button" class="morpheus-drop-tab-toggle btn btn-link'+' dropdown-toggle"'+' data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">');html.push(' <span class="fa fa-angle-double-down"></span>');html.push("</button>");html.push('<ul class="dropdown-menu dropdown-menu-right" role="menu">');html.push("</ul>");html.push("</div>");html.push("</li>");var $tabDrop=$(html.join(""));var $tabDropMenu=$tabDrop.find(".dropdown-menu");$tabDrop.appendTo(this.$nav);var updateDropTab=function(){var totalWith=_this.$nav.width()-17;var sum=0;var tabDropItems=[];_this.$nav.find("> li").each(function(){var $li=$(this);var $a=$li.find("a");if(!$li.hasClass("morpheus-tab-addon")){var title=$a.contents().first().text();var isActive=$li.hasClass("active");var href=$a.attr("href");tabDropItems.push('<li class="'+(isActive?"active":"")+'"><a data-link="'+href.substring(1)+'" data-toggle="tab"'+' href="'+href+'">'+title+"</a></li>");sum+=$li.outerWidth();if(sum>=totalWith){$li.css("display","none")}else{$li.css("display","")}}});$tabDrop.css("display",tabDropItems.length>0?"":"none");$tabDropMenu.html(tabDropItems.join(""))};$tabDrop.css("display","none");this.$nav.on("sortstop",function(event,ui){updateDropTab()});$(window).on("resize",updateDropTab);this.$nav.on("remove",function(){$(window).off("resize",updateDropTab)});this.on("add remove rename reorder change",function(){updateDropTab()})}this.$nav.on("dblclick","li > a",function(e){e.preventDefault();var $a=$(this);var $li=$a.parent("li");if($li.hasClass("morpheus-tab-addon")){return}_this.rename($a.data("link"))});this.$nav.on("contextmenu.morpheus","li > a",function(e){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();var $a=$(this);var $li=$a.parent("li");if($li.hasClass("morpheus-tab-addon")){return}var menuItems=[];if($a.data("morpheus-rename")&&_this.options.rename){menuItems.push({name:"Rename"})}if($a.data("morpheus-pin")){menuItems.push({name:"Unpin tab"})}else{menuItems.push({name:"Pin tab"})}if(menuItems.length>0){morpheus.Popup.showPopup(menuItems,{x:e.pageX,y:e.pageY},e.target,function(event,item){if(item==="Rename"){_this.rename($a.data("link"))}else if(item==="Pin tab"){$a.data("morpheus-pin",true);$li.removeClass("morpheus-sortable");$li.detach();_this.$nav.prepend($li);$a.find(".close").hide();_this.$nav.sortable("option","items","li.morpheus-sortable");_this.$nav.sortable("refresh")}else if(item==="Unpin tab"){$a.data("morpheus-pin",false);$li.addClass("morpheus-sortable");$a.find(".close").show();_this.$nav.sortable("option","items","li.morpheus-sortable");_this.$nav.sortable("refresh")}})}return false});this.$nav.on("click","button",function(e){e.preventDefault();var target=$(this).attr("data-target");if(target!=null){target=target.substring(1);_this.remove(target)}});this.$tabContent=$('<div class="tab-content"></div>');this.$nav.on("shown.bs.tab",'a[data-toggle="tab"]',function(e){var previous=_this.activeTabId;_this.activeTabId=$(e.target).data("link");_this.activeTabObject=_this.idToTabObject.get(_this.activeTabId);_this.$nav.find("li").removeClass("active");_this.$nav.find("[data-link="+_this.activeTabId+"]").each(function(){$(this).parent().addClass("active")});var scrollTop=document.body.scrollTop;$("#"+_this.activeTabId).focus();document.body.scrollTop=scrollTop;if(_this.adding){return}_this.trigger("change",{tab:_this.activeTabId,previous:previous})})};morpheus.TabManager.prototype={getTabText:function(id){return this.$nav.find("> li > a").filter("a[data-link="+id+"]").contents().first().text()},getTabCount:function(){return this.idToTabObject.size()},setTabText:function(id,text){this.$nav.find("> li > a").filter("[data-link="+id+"]").contents().first().replaceWith(text+"&nbsp;");this.idToTabObject.get(id).setName(name)},addTask:function(task){},removeTask:function(task){},getWidth:function(){return this.$tabContent.outerWidth()||$(window).width()},getActiveTab:function(){return this.activeTabObject},getActiveTabId:function(){return this.activeTabId},add:function(options){this.adding=true;var id=_.uniqueId("morpheus-tab");this.idToTabObject.set(id,options.object);var li=[];li.push('<li class="morpheus-sortable" role="presentation">');li.push('<a data-morpheus-rename="'+options.rename+'" data-toggle="tab" data-link="'+id+'" href="#'+id+'">');li.push(options.title);li.push('&nbsp;<i style="color:black;"></i>');if(options.closeable){li.push('&nbsp<button style="font-size: 18px;" type="button" class="close"'+' aria-label="Close"'+' data-target="#'+id+'"><span aria-hidden="true">×</span></button>')}li.push("</a></li>");var $link=$(li.join(""));$link.appendTo(this.$nav);var $panel=$('<div tabIndex="0" style="outline:0;cursor:default;" role="tabpanel"'+' class="tab-pane" id="'+id+'"></div>');options.$el.appendTo($panel);$panel.appendTo(this.$tabContent);if(options.enabled===false){$link.addClass("disabled");$link.find("a").addClass("btn disabled")}if(options.focus){this.$nav.find('> li > a[data-toggle="tab"]:last').tab("show");this.activeTabId=id;this.activeTabObject=options.object;$panel.focus()}if(this.options.autohideTabBar){this.$nav.css("display",this.idToTabObject.size()>1?"":"none")}this.getTabCount()<=1?this.$nav.sortable("disable"):this.$nav.sortable("enable");this.adding=false;this.trigger("add");return{$panel:$panel,id:id}},appendTo:function($target){this.$nav.appendTo($target);this.$tabContent.appendTo($target)},remove:function(target){if(target===undefined){target=this.activeTabId}var obj=this.idToTabObject.remove(target);$("#"+target).remove();this.activeTabObject=null;this._getA(target).parent().remove();this.$tabContent.find(target).remove();var $a=this.$nav.find('> li > a[data-toggle="tab"]:last');if($a.length===0){if(this.options.landingPage){if(typeof this.options.landingPage==="function"){this.options.landingPage().show()}else{this.options.landingPage.show()}}}$a.tab("show");if(this.options.autohideTabBar){this.$nav.css("display",this.idToTabObject.size()>1?"":"none")}this.getTabCount()<=1?this.$nav.sortable("disable"):this.$nav.sortable("enable");if(this.idToTabObject.size()>0){$($a.attr("href")).focus()}if(obj!=null&&obj.onRemove){obj.onRemove()}this.trigger("remove",{tab:target})},setOptions:function(options){this.options=options;if(this.options.autohideTabBar){this.$nav.css("display",this.idToTabObject.size()>1?"":"none")}},getOptions:function(){return this.options},setActiveTab:function(id){if(id!==this.activeTabId){var $a=this._getA(id);$a.parent().removeClass("disabled");$a.removeClass("btn disabled");$a.tab("show");var previous=this.activeTabId;this.activeTabId=id;this.activeTabObject=this.idToTabObject.get(this.activeTabId);this.trigger("change",{tab:this.activeTabId,previous:previous})}},setTabTitle:function(id,title){this._getA(id).attr("title",title)},_getA:function(id){if(id[0]==="#"){id=id.substring(1)}return this.$nav.find("> li > a[data-link="+id+"]:first")},setTabEnabled:function(id,enabled){var $a=this._getA(id);if(enabled){$a.parent().removeClass("disabled");$a.removeClass("btn disabled")}else{$a.parent().addClass("disabled");$a.addClass("btn disabled")}},getIdToTabObject:function(){return this.idToTabObject},getTabObject:function(id){return this.idToTabObject.get(id)},rename:function(id){var $a=this._getA(id);var $li=$a.parent();if($li.hasClass("morpheus-tab-addon")){return}if(!$a.data("morpheus-rename")||!this.options.rename){return}var _this=this;var builder=new morpheus.FormBuilder;builder.append({name:"name",type:"text",value:$.trim($a.contents().first().text())});morpheus.FormBuilder.showOkCancel({title:"Rename Tab",content:builder.$form,focus:document.activeElement,okCallback:function(){var name=$.trim(builder.getValue("name"));if(name!==""){if(_this.activeTabObject!=null&&_this.activeTabObject.setName){_this.activeTabObject.setName(name)}$a.contents().first().replaceWith(name+"&nbsp;");_this.trigger("rename")}}})}};morpheus.Util.extend(morpheus.TabManager,morpheus.Events);morpheus.Table=function(options){options=morpheus.Table.createOptions(options);this.options=options;if(!options.width){options.width=options.$el.attr("class")}var _this=this;var height=options.height;var $gridDiv=$('<div class="slick-table'+(options.tableClass?" "+options.tableClass:"")+'" style="width:'+options.fixedWidth+";height:"+height+'"></div>');this.$gridDiv=$gridDiv;$gridDiv.appendTo(options.$el);var columns=options.columns;this.columns=columns;var visibleColumns=columns.filter(function(c){return c.visible});var grid=new morpheus.Grid({gridOptions:{select:options.select,rowHeight:options.rowHeight,autoEdit:false,editable:false,autoHeight:options.height==="auto",enableTextSelectionOnCells:true},$el:$gridDiv,items:options.items,columns:visibleColumns});this.grid=grid;this.searchFunction=null;var searchFilter={isEmpty:function(){return _this.searchFunction==null},init:function(){},accept:function(item){return _this.searchFunction(item)}};this.grid.getFilter().add(searchFilter);var $header=$('<div class="slick-table-header"><div name="top"></div><div style="display: inline-block;" name="left" class="pad-bottom-8 pad-top-8"></div><div name="right" class="pull-right pad-bottom-8'+' pad-top-8"></div></div>');this.$header=$header;var $right=$header.find(".pull-right");if(options.search){var tableSearch=new morpheus.TableSearchUI({$el:$header.find("[name=top]"),$right:$right});tableSearch.setTable(this);this.tableSearch=tableSearch}if(options.columnPicker&&visibleColumns.length!==this.columns.length){var select=[];select.push('<select data-width="90px" data-selected-text-format="static" title="Columns..." multiple class="pad-left-4 selectpicker show-tick">');var sortedColumns=this.columns.slice().sort(function(a,b){a=a.name.toLowerCase();b=b.name.toLowerCase();return a===b?0:a<b?-1:1});sortedColumns.forEach(function(c,i){select.push('<option value="'+i+'"');if(c.visible){select.push(" selected")}select.push(">");select.push(c.name);select.push("</option>")});select.push("</select>");var $select=$(select.join(""));$select.appendTo($right);$select.selectpicker({iconBase:"fa",tickIcon:"fa-check",style:"btn-default btn-xs"});$select.on("change",function(){var oldColumns=grid.getColumns().map(function(c){return c.id});var selectedColumnIndices=$select.val();visibleColumns=[];for(var i=0;i<selectedColumnIndices.length;i++){visibleColumns.push(sortedColumns[parseInt(selectedColumnIndices[i])])}var newColumns=visibleColumns.map(function(c){return c.id});grid.setColumns(visibleColumns);if(newColumns.length>oldColumns.length){var set=new morpheus.Set;for(var i=0;i<newColumns.length;i++){set.add(newColumns[i])}for(var i=0;i<oldColumns.length;i++){set.remove(oldColumns[i])}var added=set.values();grid.setSortColumns([{columnId:added[0],sortAsc:true}])}_this.resize();_this.redraw()})}$header.prependTo(options.$el);var collapsed=false;var lastWidth=-1;var resize=function(){if(!_this.options.responsive){return}var gridWidth=options.$el.width();if(gridWidth===lastWidth){return}lastWidth=gridWidth;$gridDiv.css("width",gridWidth+"px");if(!collapsed&&gridWidth<options.collapseBreakpoint&&visibleColumns.length>1){collapsed=true;$gridDiv.addClass("slick-stacked");_this.grid.grid.getOptions().rowHeight=(options.collapsedRowHeight?options.collapsedRowHeight:options.rowHeight)*visibleColumns.length;_this.grid.grid.setColumns([{id:0,tooltip:function(item,value){var html=[];for(var i=0;i<visibleColumns.length;i++){var text=visibleColumns[i].tooltip(item,visibleColumns[i].getter(item));if(text!=null&&text!==""){html.push(text)}}return html.join("<br />")},collapsed:true,getter:function(item){return item},formatter:function(row,cell,value,columnDef,dataContext){var html=[];html.push('<div class="slick-table-wrapper"><div class="slick-cell-wrapper">');if(options.rowHeader){html.push(options.rowHeader(dataContext));html.push('<div style="height:4px;"></div>')}for(var i=0;i<visibleColumns.length;i++){if(i>0){html.push('<div style="height:4px;"></div>')}var c=visibleColumns[i];html.push(c.name);html.push(":");var s=c.renderer(dataContext,c.getter(dataContext));html.push(s)}html.push("</div></div>");return html.join("")},sortable:false,name:""}]);$gridDiv.find(".slick-header").hide();_this.grid.grid.resizeCanvas();_this.grid.grid.invalidate()}else if(collapsed&&gridWidth>=options.collapseBreakpoint){$gridDiv.removeClass("slick-stacked");collapsed=false;if(options.showHeader){$gridDiv.find(".slick-header").show()}_this.grid.grid.getOptions().rowHeight=options.rowHeight;_this.grid.grid.setColumns(visibleColumns);_this.grid.grid.resizeCanvas();if(options.select){_this.grid.grid.setSelectedRows(_this.grid.grid.getSelectedRows())}_this.grid.grid.invalidate()}else{_this.grid.grid.resizeCanvas();_this.grid.grid.invalidate()}_this.grid.maybeAutoResizeColumns()};if(!options.showHeader){$gridDiv.find(".slick-header").hide()}if(options.responsive){$(window).on("resize orientationchange",resize);$gridDiv.on("remove",function(){$(window).off("resize",resize)});resize()}this.resize=resize;if(visibleColumns.length>1&&options.items!=null&&options.items.length>0){this.setItems(options.items)}if(!$gridDiv.is(":visible")){var $parent=$gridDiv;var observer=new MutationObserver(function(mutations){if(window.getComputedStyle($parent[0]).display!=="none"){observer.disconnect();resize()}});while($parent.length>0){if(window.getComputedStyle($parent[0]).display==="none"){break}$parent=$parent.parent()}if($parent.length>0){observer.observe($parent[0],{attributes:true,childList:false,characterData:false})}}};morpheus.Table.defaultRenderer=function(item,value){if(value==null){return""}else if(_.isNumber(value)){return morpheus.Util.nf(value)}else if(morpheus.Util.isArray(value)){var s=[];for(var i=0,length=value.length;i<length;i++){if(i>0){s.push(", ")}var val=value[i];s.push(value[i])}return s.join("")}else{return""+value}};morpheus.Table.prototype={toText:function(){var text=[];var items=this.getItems();var columns=this.columns.filter(function(c){return c.visible});for(var j=0;j<columns.length;j++){if(j>0){text.push("\t")}text.push(columns[j].name)}text.push("\n");for(var i=0;i<items.length;i++){var item=items[i];for(var j=0;j<columns.length;j++){if(j>0){text.push("\t")}var value=columns[j].getter(item);text.push(morpheus.Util.toString(value))}text.push("\n")}return text.join("")},setHeight:function(height){this.options.height=height;if(height==="auto"){this.$gridDiv.css("height","");this.grid.grid.getOptions().autoHeight=true;this.grid.grid.setOptions(this.grid.grid.getOptions())}else{this.$gridDiv.css("height",height)}this.grid.grid.resizeCanvas();if(height==="auto"){var height=this.getItems().length*this.options.rowHeight+this.options.rowHeight;this.$gridDiv.find(".slick-viewport").css("height",height+"px")}this.grid.grid.invalidate()},setSearchVisible:function(visible){this.$header.find("[name=search]").css("display",visible?"":"none")},autocomplete:function(tokens,response){var matches=[];var token=tokens!=null&&tokens.length>0?tokens[tokens.selectionStartIndex]:"";token=$.trim(token);var columns=this.columns.filter(function(c){return c.searchable&&c.visible||c.alwaysSearch});var ncolumns=columns.length;var showField=ncolumns>1;if(token===""){if(ncolumns<=1){return response(matches)}for(var i=0;i<ncolumns;i++){var field=columns[i].name;matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})}matches.sort(function(a,b){return a.value===b.value?0:a.value<b.value?-1:1});return response(matches)}var field=null;var semi=token.indexOf(":");var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");if(semi>0){if(token.charCodeAt(semi-1)!==92){var possibleField=$.trim(token.substring(0,semi));if(possibleField.length>0&&possibleField[0]==='"'&&possibleField[token.length-1]==='"'){possibleField=possibleField.substring(1,possibleField.length-1)}var columnNameToColumn=new morpheus.Map;var columnNames=columns.map(function(c){return c.name});for(var i=0;i<columnNames.length;i++){columnNameToColumn.set(columnNames[i],columns[i])}var c=columnNameToColumn.get(possibleField);if(c!==undefined){token=$.trim(token.substring(semi+1));columns=[c];ncolumns=1}}}else if(ncolumns>1){var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");for(var j=0;j<ncolumns;j++){var field=columns[j].name;if(regex.test(field)){matches.push({value:field+":",label:'<span style="font-weight:300;">'+field+":</span>",show:true})}}}var set=new morpheus.Set;var regex=new RegExp("^"+morpheus.Util.escapeRegex(token),"i");var items=this.getItems();var dataTypes=[];var filteredColumns=[];columns.forEach(function(c){var dataType=null;for(var i=0,nitems=items.length;i<nitems;i++){var value=c.getter(items[i]);if(value!=null){dataType=morpheus.Util.getDataType(value);break}}if(dataType==="string"||dataType==="[string]"){dataTypes.push(dataType);filteredColumns.push(c)}});columns=filteredColumns;ncolumns=columns.length;var maxSize=matches.length+10;for(var i=0,nitems=items.length;i<nitems;i++){var item=items[i];for(var j=0;j<ncolumns;j++){var field=columns[j].name;var value=columns[j].getter(item);var dataType=dataTypes[j];if(dataType==="[string]"){var nvalues=value==null?0:value.length;for(var k=0;k<nvalues;k++){var val=value[k];if(regex.test(val)&&!set.has(val)){set.add(val);matches.push({value:showField?field+":"+val:val,label:showField?'<span style="font-weight:300;">'+field+":</span>"+'<span style="font-weight:900;">'+val+"</span>":'<span style="font-weight:900;">'+val+"</span>"})}if(matches.length===maxSize){return response(matches)}}}else{if(regex.test(value)&&!set.has(value)){set.add(value);matches.push({value:showField?field+":"+value:value,label:showField?'<span style="font-weight:300;">'+field+":</span>"+'<span style="font-weight:900;">'+value+"</span>":'<span style="font-weight:900;">'+value+"</span>"});if(matches.length===maxSize){return response(matches)}}}}}return response(matches)},searchWithPredicates:function(predicates){if(predicates==null||predicates.length===0){this.searchFunction=null;this.grid.setFilter(this.grid.getFilter());return}var columns=this.columns.filter(function(c){return c.searchable&&c.visible||c.alwaysSearch});var columnNameToColumn=new morpheus.Map;var columnNames=columns.map(function(c){return c.name});for(var i=0;i<columnNames.length;i++){columnNameToColumn.set(columnNames[i],columns[i])}var filteredPredicates=[];var npredicates=predicates.length;for(var i=0;i<npredicates;i++){var predicate=predicates[i];var filterColumnName=predicate.getField();if(filterColumnName!=null){var column=columnNameToColumn.get(filterColumnName);if(column){predicate.column=column;filteredPredicates.push(predicate)}}else{filteredPredicates.push(predicate)}}predicates=filteredPredicates;npredicates=predicates.length;var f=function(item){for(var p=0;p<npredicates;p++){var predicate=predicates[p];var searchColumns;if(predicate.column){searchColumns=[predicate.column]}else{searchColumns=columns}for(var j=0,ncolumns=searchColumns.length;j<ncolumns;j++){var value=searchColumns[j].getter(item);if(morpheus.Util.isArray(value)){var nvalues=value.length;for(var i=0;i<nvalues;i++){if(predicate.accept(value[i])){return true}}}else{var predicate=predicates[p];if(predicate.accept(value)){return true}}}}return false};this.searchFunction=f;this.grid.setFilter(this.grid.getFilter())},search:function(text){if(text===""){this.searchFunction=null;this.grid.setFilter(this.grid.getFilter())}else{var tokens=morpheus.Util.getAutocompleteTokens(text);var columns=this.columns.filter(function(c){return c.searchable&&c.visible||c.alwaysSearch});var columnNames=columns.map(function(c){return c.name});var predicates=morpheus.Util.createSearchPredicates({tokens:tokens,fields:columnNames});this.searchWithPredicates(predicates)}},getSelectedRows:function(){return this.grid.getSelectedRows()},getSelectedItems:function(){return this.grid.getSelectedItems()},getSelectedItem:function(){return this.grid.getSelectedItem()},setSelectedRows:function(rows){this.grid.setSelectedRows(rows)},getItems:function(items){return this.grid.getItems()},getAllItemCount:function(){return this.grid.getAllItemCount()},getFilteredItemCount:function(){return this.grid.getFilteredItemCount()},setFilter:function(f){this.grid.setFilter(f)},getFilter:function(){return this.grid.getFilter()},setItems:function(items){this.grid.setItems(items);this.grid.redraw()},redraw:function(){this.grid.redraw()},on:function(evtStr,handler){this.grid.on(evtStr,handler);return this},off:function(evtStr,handler){this.grid.off(evtStr,handler);return this},trigger:function(evtStr){this.grid.trigger(evtStr)}};morpheus.Table.createOptions=function(options){options=$.extend(true,{},{items:[],height:"564px",collapseBreakpoint:400,showHeader:true,select:true,rowHeader:null,responsive:true,fixedWidth:"320px",columnPicker:true},options);if(!options.columns){options.columns=[{name:""}]}var columns=[];options.columns.forEach(function(c,i){var column=$.extend(true,{},{id:i,tooltip:function(dataContext,value){return morpheus.Table.defaultRenderer(dataContext,value)},formatter:function(row,cell,value,columnDef,dataContext){var html=[];html.push('<div class="slick-table-wrapper"><div class="slick-cell-wrapper">');if(options.rowHeader&&cell===0){html.push(options.rowHeader(dataContext))}html.push(column.renderer(dataContext,value));html.push("</div></div>");return html.join("")},comparator:function(a,b){var aNaN=a==null||_.isNumber(a)&&isNaN(a);var bNaN=b==null||_.isNumber(b)&&isNaN(b);if(aNaN&&bNaN){return 0}if(aNaN){return 1}if(bNaN){return-1}if(a.toLowerCase){a=a.toLowerCase()}if(b.toLowerCase){b=b.toLowerCase()}return a===b?0:a<b?-1:1},sortable:true,searchable:true,width:null,name:c.name,renderer:morpheus.Table.defaultRenderer},c);if(column.visible===undefined){column.visible=true}if(!column.getter){column.getter=column.field==null?function(item){return item}:function(item){return item[c.field]}}columns.push(column)});options.columns=columns;if(options.columns.length===1){options.tableClass="slick-table-compact"}else{options.tableClass="slick-bordered-table"}if(!options.rowHeight){options.rowHeight=22}return options};morpheus.TableSearchUI=function(options){var _this=this;var $search=$('<input name="search" type="text" class="form-control input-sm"'+' placeholder="Search" autocomplete="off">');$search.appendTo(options.$el);this.$search=$search;this.$searchResults=$('<span class="pad-top-2 tableview-rowcount" name="search"></span>');this.$showAll=$('<div style="display:inline-block;min-width:60px;" name="search" class="pad-left-8 text-button-copy tableview-rowcount">Show'+" all</div>");this.$searchResults.appendTo(options.$right);this.$showAll.appendTo(options.$right);this.$showAll.on("click",function(e){e.preventDefault();$search.val("");_this.table.search("");_this.table.trigger("showAll",{table:_this.table})});$search.on("keyup",_.debounce(function(){_this.table.search($.trim($(this).val()))},100));morpheus.Util.autosuggest({$el:$search,suggestWhenEmpty:true,filter:function(tokens,response){_this.table.autocomplete(tokens,response)},select:function(){_this.table.search($.trim($search.val()))}})};morpheus.TableSearchUI.prototype={updateSearchLabel:function(){var text="Showing: "+morpheus.Util.intFormat(this.table.getFilteredItemCount())+" / "+morpheus.Util.intFormat(this.table.getAllItemCount());this.$searchResults.html(text)},setTable:function(table){this.table=table;var _this=this;table.on("filter",function(){_this.updateSearchLabel()})}};morpheus.TrackSelection=function(track,positions,selectionModel,isColumns,heatMap){var canvas=track.canvas;var startIndex=-1;var coord=isColumns?"x":"y";function getPosition(event,useDelta){if(track.settings.squished){var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);var squishFactor=total/(isColumns?track.getUnscaledWidth():track.getUnscaledHeight());var clientXY=morpheus.CanvasUtil.getClientXY(event,useDelta);var p=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,0,0,useDelta);p[coord]*=squishFactor;return p}else{return morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,heatMap.scrollLeft(),heatMap.scrollTop(),useDelta)}}var panning=false;var scrollIntervalId;var lastScrollTime=(new Date).getTime();var _this=this;var throttlePanMove=50;function mouseleave(e){var scroll=function(){var now=(new Date).getTime();var rect=canvas.getBoundingClientRect();var doPan=false;if(!isColumns){if(e.clientY>rect.bottom||e.clientY<rect.top){doPan=true}}else{if(e.clientX>rect.right||e.clientX<rect.left){doPan=true}}if(doPan){_this.panmove(e);scrollIntervalId=setTimeout(scroll,throttlePanMove)}};scrollIntervalId=setTimeout(scroll,throttlePanMove);$(canvas).one("mouseover",mouseover)}function mouseover(){clearTimeout(scrollIntervalId);$(canvas).one("mouseleave",mouseleave)}this.hammer=morpheus.Util.hammer(canvas,["pan","tap","longpress"]).on("longpress",this.longpress=function(event){event.preventDefault();event.srcEvent.stopImmediatePropagation();event.srcEvent.stopPropagation();heatMap.setSelectedTrack(track.name,isColumns);track.showPopup(event.srcEvent)}).on("panend",this.panend=function(event){panning=false;clearInterval(scrollIntervalId);$(canvas).off("mouseover mouseleave")}).on("panmove",this.panmove=function(event){var now=(new Date).getTime();var elapsed=now-lastScrollTime;if(elapsed<throttlePanMove){return}var position=getPosition(event);var endIndex=positions.getIndex(position[coord],false);var commandKey=event.srcEvent==null?false:morpheus.Util.IS_MAC?event.srcEvent.metaKey:event.srcEvent.ctrlKey;var viewIndices=commandKey?selectionModel.getViewIndices():new morpheus.Set;var _startIndex=startIndex;if(startIndex>endIndex){var tmp=endIndex;endIndex=_startIndex;_startIndex=tmp}for(var i=_startIndex;i<=endIndex;i++){viewIndices.add(i)}selectionModel.setViewIndices(viewIndices,true);if(!isColumns){var scrollTop=heatMap.scrollTop();var heatMapHeight=heatMap.heatmap.getUnscaledHeight();var scrollBottom=scrollTop+heatMapHeight;if(position.y>scrollBottom){heatMap.scrollTop(position.y+8-heatMapHeight)}else if(position.y<scrollTop){heatMap.scrollTop(position.y-8)}}else{var scrollLeft=heatMap.scrollLeft();var heatMapWidth=heatMap.heatmap.getUnscaledWidth();var scrollRight=scrollLeft+heatMapWidth;if(position.x>scrollRight){heatMap.scrollLeft(position.x+8-heatMapWidth)}else if(position.x<scrollLeft){heatMap.scrollLeft(position.x-8)}}event.preventDefault();if(event.srcEvent!=null){event.srcEvent.stopPropagation();event.srcEvent.stopImmediatePropagation()}lastScrollTime=(new Date).getTime()}).on("panstart",this.panstart=function(event){heatMap.setSelectedTrack(track.name,isColumns);var position=getPosition(event,true);startIndex=positions.getIndex(position[coord],false);panning=true;$(canvas).one("mouseleave.morpheus",mouseleave)}).on("tap doubletap",this.tap=function(event){var position=getPosition(event);var index=positions.getIndex(position[coord],false);if(event.tapCount>1){if(isColumns&&!heatMap.options.columnsSortable||!isColumns&&!heatMap.options.rowsSortable){return}heatMap.sortBasedOnSelection(null,isColumns,event.srcEvent.shiftKey)}else{heatMap.setSelectedTrack(track.name,isColumns);var commandKey=morpheus.Util.IS_MAC?event.srcEvent.metaKey:event.srcEvent.ctrlKey;if(morpheus.Util.IS_MAC&&event.srcEvent.ctrlKey){return}var viewIndices;if(commandKey){viewIndices=selectionModel.getViewIndices();if(viewIndices.has(index)){viewIndices.remove(index)}else{viewIndices.add(index)}}else if(event.srcEvent.shiftKey){viewIndices=selectionModel.getViewIndices();var min=Number.MAX_VALUE;var max=-Number.MAX_VALUE;viewIndices.forEach(function(viewIndex){min=Math.min(viewIndex,min);max=Math.max(viewIndex,max)});if(index>=max){for(var i=max;i<=index;i++){viewIndices.add(i)}}else{for(var i=Math.min(index,min),max=Math.max(index,min);i<=max;i++){viewIndices.add(i)}}}else{viewIndices=new morpheus.Set;viewIndices.add(index)}selectionModel.setViewIndices(viewIndices,true)}})};morpheus.TrackSelection.prototype={dispose:function(){this.hammer.off("longpress",this.longpress).off("panstart",this.panstart).off("panmove",this.panmove).off("panend",this.panend).off("tap",this.tap).off("doubletap",this.tap);this.hammer.destroy()}};morpheus.VectorTrackHeader=function(project,name,isColumns,heatMap){morpheus.AbstractCanvas.call(this);this.font={weight:"400"};this.project=project;this.name=name;this.isColumns=isColumns;var canvas=this.canvas;this.heatMap=heatMap;this.selectedBackgroundColor="#c8c8c8";this.backgroundColor="rgb(255,255,255)";var vector=(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata()).getByName(name);if(vector&&vector.getProperties().has(morpheus.VectorKeys.TITLE)){this.canvas.setAttribute("title",vector.getProperties().get(morpheus.VectorKeys.TITLE));$(this.canvas).tooltip()}var _this=this;this.setBounds({height:this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET});function getResizeCursor(pos){if(isColumns){if(pos.y<3){return{cursor:"ns-resize",isPrevious:true}}if(pos.y>=_this.getUnscaledHeight()-3){return{cursor:"ns-resize",isPrevious:false}}if(pos.x>=_this.getUnscaledWidth()-3){return{isPrevious:false,cursor:"ew-resize"}}}else{if(pos.x<3&&heatMap.getTrackIndex(name,isColumns)>0){return{cursor:"ew-resize",isPrevious:true}}if(pos.x>=_this.getUnscaledWidth()-3){return{cursor:"ew-resize",isPrevious:false}}}}var mouseMove=function(event){if(!morpheus.CanvasUtil.dragging){var pos=morpheus.CanvasUtil.getMousePos(event.target,event);var resizeCursor=getResizeCursor(pos);canvas.style.cursor=resizeCursor==null?"default":resizeCursor.cursor;_this.isMouseOver=true;_this.repaint()}};var mouseExit=function(e){if(!morpheus.CanvasUtil.dragging){canvas.style.cursor="default"}_this.isMouseOver=false;_this.repaint()};var showPopup=function(e){heatMap.setSelectedTrack(_this.name,isColumns);var track=heatMap.getTrack(_this.name,isColumns);if(!track){throw _this.name+" track not found"}e.preventDefault();if(e.stopPropagation){e.stopPropagation()}if(e.stopImmediatePropagation){e.stopImmediatePropagation()}track.showPopup(e,true);return false};$(this.canvas).css({"background-color":this.backgroundColor}).on("mousemove.morpheus",mouseMove).on("mouseout.morpheus",mouseExit).on("mouseenter.morpheus",mouseMove).on("contextmenu.morpheus",showPopup).addClass("morpheus-track-header "+(isColumns?"morpheus-columns":"morpheus-rows"));var resizeCursor;var dragStartWidth=0;var dragStartHeight=0;var reorderingTrack=false;var dragStartPosition;var resizeTrackName;this.hammer=morpheus.Util.hammer(canvas,["pan","tap","longpress"]).on("longpress",this.longpress=function(event){event.preventDefault();heatMap.setSelectedTrack(_this.name,isColumns);var track=heatMap.getTrack(_this.name,isColumns);track.showPopup(event.srcEvent,true)}).on("panend",this.panend=function(event){_this.isMouseOver=false;morpheus.CanvasUtil.dragging=false;canvas.style.cursor="default";var index=heatMap.getTrackIndex(_this.name,isColumns);var header=heatMap.getTrackHeaderByIndex(index,isColumns);var track=heatMap.getTrackByIndex(index,isColumns);var $canvas=$(track.canvas);$canvas.css("z-index","0");$(header.canvas).css("z-index","0");heatMap.revalidate()}).on("panstart",this.panstart=function(event){_this.isMouseOver=false;if(morpheus.CanvasUtil.dragging){return}if(resizeCursor!=null){morpheus.CanvasUtil.dragging=true;canvas.style.cursor=resizeCursor.cursor;if(resizeCursor.isPrevious){var index=heatMap.getTrackIndex(_this.name,isColumns);index--;if(index===-1){index=0}var header=heatMap.getTrackHeaderByIndex(index,isColumns);dragStartWidth=header.getUnscaledWidth();dragStartHeight=header.getUnscaledHeight();resizeTrackName=header.name}else{resizeTrackName=null;dragStartWidth=_this.getUnscaledWidth();dragStartHeight=_this.getUnscaledHeight()}event.preventDefault();reorderingTrack=false}else{var index=heatMap.getTrackIndex(_this.name,isColumns);if(index==-1){throw _this.name+" not found"}var header=heatMap.getTrackHeaderByIndex(index,isColumns);var track=heatMap.getTrackByIndex(index,isColumns);heatMap.setSelectedTrack(_this.name,isColumns);var $canvas=$(track.canvas);dragStartPosition=$canvas.position();$canvas.css("z-index","100");$(header.canvas).css("z-index","100");morpheus.CanvasUtil.dragging=true;resizeCursor=undefined;reorderingTrack=true}}).on("panmove",this.panmove=function(event){_this.isMouseOver=false;if(resizeCursor!=null){var width;var height;if(resizeCursor.cursor==="ew-resize"){var dx=event.deltaX;width=Math.max(8,dragStartWidth+dx)}if(resizeCursor.cursor==="ns-resize"){var dy=event.deltaY;height=Math.max(8,dragStartHeight+dy)}heatMap.resizeTrack(resizeTrackName==null?_this.name:resizeTrackName,width,height,isColumns)}else if(reorderingTrack){var index=heatMap.getTrackIndex(_this.name,isColumns);var header=heatMap.getTrackHeaderByIndex(index,isColumns);var track=heatMap.getTrackByIndex(index,isColumns);var ntracks=heatMap.getNumTracks(isColumns);var delta=isColumns?event.deltaY:event.deltaX;var newIndex=index+(delta>0?1:-1);newIndex=Math.min(Math.max(0,newIndex),ntracks-1);var prop=isColumns?"top":"left";var w=isColumns?"getUnscaledHeight":"getUnscaledWidth";var trackBounds={};trackBounds[prop]=dragStartPosition[prop]+delta;track.setBounds(trackBounds);header.setBounds(trackBounds);var dragOverTrack=heatMap.getTrackByIndex(newIndex,isColumns);var dragOverWidth=dragOverTrack[w]();var dragOverLeft=$(dragOverTrack.canvas).position()[prop];var dragleft=dragStartPosition[prop]+delta;var dragright=dragleft+track[w]();if(delta>0&&dragright>=dragOverLeft+dragOverWidth/2||delta<0&&dragleft<=dragOverLeft+dragOverWidth/2){if(index!==newIndex){heatMap.moveTrack(index,newIndex,isColumns);var otherHeader=heatMap.getTrackHeaderByIndex(index,isColumns);var otherTrack=heatMap.getTrackByIndex(index,isColumns);var $movedCanvas=$(otherTrack.canvas);var newLeft=$movedCanvas.position()[prop];if(delta<0){newLeft+=track[w]()}else{newLeft-=track[w]()}var otherBounds={};otherBounds[prop]=newLeft;otherTrack.setBounds(otherBounds);otherHeader.setBounds(otherBounds)}}}}).on("tap",this.tap=function(event){if(morpheus.Util.IS_MAC&&event.srcEvent.ctrlKey){return}_this.isMouseOver=false;heatMap.setSelectedTrack(_this.name,isColumns);var vector=(isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata()).getByName(name);if(isColumns&&!heatMap.options.columnsSortable||vector==null){return}if(!isColumns&&!heatMap.options.rowsSortable||vector==null){return}var additionalSort=event.srcEvent.shiftKey;var isGroupBy=false;var existingSortKeyIndex=_this.getSortKeyIndexForColumnName(_this.getSortKeys(),_this.name);var sortOrder;var sortKey;var dataType=morpheus.VectorUtil.getDataType(vector);if(existingSortKeyIndex!=null){sortKey=_this.getSortKeys()[existingSortKeyIndex.index];if(sortKey.getSortOrder()===morpheus.SortKey.SortOrder.UNSORTED){sortOrder=morpheus.SortKey.SortOrder.ASCENDING}else if(sortKey.getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}else if(sortKey.getSortOrder()===morpheus.SortKey.SortOrder.TOP_N){sortOrder=morpheus.SortKey.SortOrder.UNSORTED}else{sortOrder=dataType==="number"||dataType==="[number]"?morpheus.SortKey.SortOrder.TOP_N:morpheus.SortKey.SortOrder.UNSORTED}}else{sortKey=new morpheus.SortKey(_this.name,morpheus.SortKey.SortOrder.ASCENDING);sortOrder=morpheus.SortKey.SortOrder.ASCENDING}if(sortKey!=null){sortKey.setSortOrder(sortOrder);_this.setSortingStatus(_this.getSortKeys(),sortKey,additionalSort,isGroupBy)}});$(this.canvas).on("mousedown",function(event){resizeCursor=getResizeCursor(morpheus.CanvasUtil.getMousePos(event.target,event,true))})};morpheus.VectorTrackHeader.FONT_OFFSET=2;morpheus.VectorTrackHeader.prototype={selected:false,isMouseOver:false,defaultFontHeight:11,dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);this.hammer.off("longpress",this.longpress).off("panend",this.panend).off("panstart",this.panstart).off("panmove",this.panmove).off("tap",this.tap);this.hammer.destroy()},getPreferredSize:function(){var size=this.getPrintSize();size.width+=24;if(!this.isColumns){size.height=this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET}return size},getPrintSize:function(){var context=this.canvas.getContext("2d");context.font=this.fontWeight+" "+this.defaultFontHeight+"px "+morpheus.CanvasUtil.getFontFamily(context);var textWidth=4+context.measureText(this.name).width;return{width:textWidth,height:this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET}},getSortKeys:function(){return this.isColumns?this.project.getColumnSortKeys():this.project.getRowSortKeys()},setOrder:function(sortKeys){if(this.isColumns){this.project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,this.project.getColumnSortKeys()),false)}else{this.project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys(sortKeys,this.project.getRowSortKeys()),false)}},setGroupBy:function(groupBy){var existingGroupBy=this.isColumns?this.project.groupColumns:this.project.groupRows;var index=-1;for(var i=0,length=existingGroupBy.length;i<length;i++){if(existingGroupBy[i].toString()===groupBy.toString()){index=i;break}}var newGroupBy=[groupBy];if(index!==-1){newGroupBy=existingGroupBy;newGroupBy.splice(index,1)}if(this.isColumns){this.project.setGroupColumns(newGroupBy,true)}else{this.project.setGroupRows(newGroupBy,true)}},setSelected:function(selected){if(selected!=this.selected){this.selected=selected;$(this.canvas).css({"background-color":this.selected?this.selectedBackgroundColor:this.backgroundColor})}},setSortingStatus:function(sortKeys,sortKey,additionalSort,isGroupBy){if(!isGroupBy){if(sortKey.getSortOrder()==morpheus.SortKey.SortOrder.UNSORTED&&!additionalSort){this.setOrder([])}else{if(additionalSort&&sortKeys.length==0){additionalSort=false}if(!additionalSort){sortKeys=[sortKey]}else{var sortKeyIndex=this.getSortKeyIndexForColumnName(sortKeys,sortKey.toString());if(sortKeyIndex===null){sortKeys.push(sortKey)}else{sortKeys[sortKeyIndex.index]=sortKey}}this.setOrder(sortKeys)}}if(isGroupBy){this.setGroupBy(sortKey)}else{if(this.isColumns){this.project.trigger("columnSortOrderChanged")}else{this.project.trigger("rowSortOrderChanged")}}},getSortKeyIndexForColumnName:function(sortKeys,columnName){if(sortKeys!=null){var counter=0;for(var i=0,size=sortKeys.length;i<size;i++){if(sortKeys[i].isUnlockable()){counter++}if(sortKeys[i]instanceof morpheus.SortKey&&columnName===sortKeys[i].toString()){return{index:i,number:counter}}}}return null},print:function(clip,context){if(clip.height<=6){return}context.textBaseline="bottom";if(this.isColumns){context.textAlign="right";context.font=this.font.weight+" "+Math.min(this.defaultFontHeight,clip.height-morpheus.VectorTrackHeader.FONT_OFFSET)+"px "+morpheus.CanvasUtil.getFontFamily(context)}else{context.textAlign="left";context.font=clip.height-morpheus.VectorTrackHeader.FONT_OFFSET+"px "+morpheus.CanvasUtil.getFontFamily(context)}context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.fillText(this.name,0,0)},draw:function(clip,context){var sortKeys=this.getSortKeys();var name=this.name;var existingSortKeyIndex=this.getSortKeyIndexForColumnName(sortKeys,name);var unlockableSortKeys=sortKeys.filter(function(key){return key.isUnlockable()});morpheus.CanvasUtil.resetTransform(context);context.clearRect(0,0,this.getUnscaledWidth(),this.getUnscaledHeight());if(this.getUnscaledHeight()<5){return}context.strokeStyle="#ddd";if(this.isColumns){context.beginPath();context.moveTo(0,this.getUnscaledHeight());context.lineTo(this.getUnscaledWidth(),this.getUnscaledHeight());context.stroke();context.textAlign="right"}else{context.beginPath();context.moveTo(this.getUnscaledWidth(),0);context.lineTo(this.getUnscaledWidth(),this.getUnscaledHeight());context.stroke();context.textAlign="left"}var textWidth=context.measureText(name).width;var isColumns=this.isColumns;var xpix=this.isColumns?this.getUnscaledWidth()-2:10;if(isColumns){if(existingSortKeyIndex!=null){xpix-=6;if(sortKeys[existingSortKeyIndex.index].getLockOrder()!==0){xpix-=10}}if(sortKeys.length>1){xpix-=6}}context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;var ypix=this.isColumns?this.getUnscaledHeight()/2:this.getUnscaledHeight()-(this.defaultFontHeight+morpheus.VectorTrackHeader.FONT_OFFSET)/2;context.textBaseline="middle";if(this.isMouseOver){var xdot=xpix-(isColumns?textWidth+4:4);var ydot=ypix-3;for(var i=0;i<2;i++){for(var j=0;j<3;j++){context.fillRect(xdot-i*3,ydot+j*3,1.5,1.5)}}}var fontHeight=Math.min(this.defaultFontHeight,this.getUnscaledHeight()-morpheus.VectorTrackHeader.FONT_OFFSET);fontHeight=Math.min(fontHeight,morpheus.VectorTrack.MAX_FONT_SIZE);context.font=this.font.weight+" "+fontHeight+"px "+morpheus.CanvasUtil.getFontFamily(context);context.fillText(name,xpix,ypix);context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;if(existingSortKeyIndex!==null){context.beginPath();var x=this.isColumns?xpix+4:xpix+textWidth+6;var arrowHeight=Math.min(8,this.getUnscaledHeight()/2-1);var arrowWidth=3;if(sortKeys[existingSortKeyIndex.index].getSortOrder()===morpheus.SortKey.SortOrder.ASCENDING){context.translate(x,ypix-arrowHeight);context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight);context.lineTo(-arrowWidth,arrowHeight)}else if(sortKeys[existingSortKeyIndex.index].getSortOrder()===morpheus.SortKey.SortOrder.DESCENDING){context.translate(x,ypix);context.moveTo(0,arrowHeight);context.lineTo(arrowWidth,0);context.lineTo(-arrowWidth,0)}else{context.translate(x,ypix-arrowHeight/2);context.moveTo(0,0);context.lineTo(arrowWidth,arrowHeight/2);context.lineTo(0,arrowHeight);context.lineTo(-arrowWidth,arrowHeight/2)}context.fill();morpheus.CanvasUtil.resetTransform(context);context.textAlign="left";if(unlockableSortKeys.length>1){context.font="8px "+morpheus.CanvasUtil.getFontFamily(context);var sortIndex=""+existingSortKeyIndex.number;context.fillText(sortIndex,x+4,ypix-2);x+=context.measureText(sortIndex).width}if(sortKeys[existingSortKeyIndex.index].getLockOrder()!==0){context.font=fontHeight+"px FontAwesome";context.fillText("",x+arrowWidth+2,ypix)}}}};morpheus.Util.extend(morpheus.VectorTrackHeader,morpheus.AbstractCanvas);morpheus.VectorTrack=function(project,name,positions,isColumns,heatmap){morpheus.AbstractCanvas.call(this,true);this.preferredSize={width:0,height:0};this.project=project;this.positions=positions;this.isColumns=isColumns;this.name=name;this.visible=true;this.heatmap=heatmap;this.id=_.uniqueId();var _this=this;this.updateSpanMapFunction=function(){_this.spanMap=morpheus.VectorUtil.createSpanMap(_this.getVector())};this.lastPosition={start:-1,end:-1};this.events="rowSortOrderChanged rowFilterChanged datasetChanged";var mouseMoved=function(event){var index=-1;if(event.type!=="mouseout"){var position=morpheus.CanvasUtil.getMousePosWithScroll(event.target,event,heatmap.scrollLeft(),heatmap.scrollTop());if(_this.settings.squished){var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);var squishFactor=total/(isColumns?_this.getUnscaledWidth():_this.getUnscaledHeight());position[isColumns?"x":"y"]*=squishFactor}index=!isColumns?_this.positions.getIndex(position.y,false):_this.positions.getIndex(position.x,false)}if(isColumns){heatmap.setMousePosition(-1,index,{name:_this.name,event:event})}else{heatmap.setMousePosition(index,-1,{name:_this.name,event:event})}};$(this.canvas).on("contextmenu.morpheus",function(e){e.preventDefault();e.stopPropagation();e.stopImmediatePropagation();heatmap.setSelectedTrack(_this.name,isColumns);_this.showPopup(e);return false});this.settings={maxTextWidth:undefined,squished:false,inlineTooltip:false,tooltip:true,highlightMatchingValues:false,colorBarSize:12,stackedBar:false,display:[],selectionColor:"rgb(182,213,253)",colorByField:null,fontField:null,barColor:"#bdbdbd",barSize:40,min:undefined,mid:undefined,max:undefined,autoscaleAlways:false,minMaxReversed:false};$(this.canvas).on("mousemove.morpheus mouseout.morpheus",mouseMoved)};morpheus.VectorTrack.RENDER={TEXT:"text",COLOR:"color",BAR:"bar",MOLECULE:"molecule",TEXT_AND_COLOR:"text_and_color",TEXT_AND_FONT:"text_and_font",SHAPE:"shape",ARC:"arc",BOX_PLOT:"box_plot",HEAT_MAP:"heat_map"};morpheus.VectorTrack.vectorToString=function(vector){var dataType=morpheus.VectorUtil.getDataType(vector);var formatter=vector.getProperties().get(morpheus.VectorKeys.FORMATTER);if(formatter!=null){if(typeof formatter==="object"){formatter=morpheus.Util.createNumberFormat(formatter.pattern);if(dataType==="[number]"){var nf=formatter;formatter=function(v){var s=[];if(v!=null){for(var i=0,arrayLength=v.length;i<arrayLength;i++){s.push(nf(v[i]))}}return s.join(", ")}}vector.getProperties().set(morpheus.VectorKeys.FORMATTER,formatter)}}else if(dataType==="number"){formatter=morpheus.Util.nf}else if(dataType==="[number]"){formatter=function(v){var s=[];if(v!=null){for(var i=0,arrayLength=v.length;i<arrayLength;i++){s.push(morpheus.Util.nf(v[i]))}}return s.join(", ")}}else if(dataType==="[string]"){formatter=function(v){var s=[];if(v!=null){for(var i=0,arrayLength=v.length;i<arrayLength;i++){s.push(v[i])}}return s.join(", ")}}else{formatter=function(v){return""+v}}return formatter};morpheus.VectorTrack.prototype={settingFromConfig:function(conf){var _this=this;var settings=this.settings;var fromString=function(s){settings.display=[];var tokens=s.split(",");for(var i=0,length=tokens.length;i<length;i++){var method=$.trim(tokens[i]);method=method.toUpperCase();var mapped=morpheus.VectorTrack.RENDER[method];if(mapped!==undefined){settings.display.push(mapped)}else if(method==="DISCRETE"){_this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE,true)}else if(method==="CONTINUOUS"){_this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,false)}else if(method==="HIGHLIGHT"){settings.highlightMatchingValues=true}else if(method==="STACKED_BAR"){settings.stackedBar=true;settings.display.push(morpheus.VectorTrack.RENDER.BAR)}else if(method==="TOOLTIP"){settings.inlineTooltip=true}else{console.log(method+" not found.")}}};var fromArray=function(array){settings.display=[];for(var i=0;i<array.length;i++){var method=array[i].toUpperCase();var mapped=morpheus.VectorTrack.RENDER[method];if(mapped!==undefined){settings.display.push(mapped)}else{console.log(method+" not found.")}}};var fromObject=function(obj){settings.display=[];for(var key in obj){if(obj[key]){var method=key.toUpperCase();var mapped=morpheus.VectorTrack.RENDER[method];if(mapped!==undefined){settings.display.push(mapped)}}}};if(conf!=null){if(_.isString(conf)){fromString(conf)}else if(_.isArray(conf)){fromArray(conf)}else{var userSuppliedSettings=conf;if(!_.isArray(conf.display)&&_.isObject(conf.display)){userSuppliedSettings=conf.display}settings=$.extend({},settings,userSuppliedSettings);settings.maxTextWidth=undefined;if(userSuppliedSettings.discrete!=null){_this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE,userSuppliedSettings.discrete)}if(_.isArray(userSuppliedSettings.display)){settings.display=userSuppliedSettings.display}else if(_.isString(userSuppliedSettings.display)){fromString(userSuppliedSettings.display)}if(!_.isArray(settings.render)&&_.isObject(settings.render)){fromObject(settings.render);delete settings.render}}this.settings=settings}if(!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT))){settings.display.push(morpheus.VectorTrack.RENDER.TEXT)}this._update()},setShowTooltip:function(value){this.settings.tooltip=value},isShowTooltip:function(){return this.settings.tooltip},isRenderAs:function(value){return this.settings.display.indexOf(value)!==-1},dispose:function(){morpheus.AbstractCanvas.prototype.dispose.call(this);$(this.canvas).off();this._selection.dispose();this.project.off(this.events,this.updateSpanMapFunction)},getName:function(){return this.name},getVector:function(name){name=name==null?this.name:name;var vector=this.isColumns?this.project.getSortedFilteredDataset().getColumnMetadata().getByName(name):this.project.getSortedFilteredDataset().getRowMetadata().getByName(name);return!vector?new morpheus.Vector(name,0):vector},getFullVector:function(){var vector=this.isColumns?this.project.getFullDataset().getColumnMetadata().getByName(this.name):this.project.getFullDataset().getRowMetadata().getByName(this.name);return!vector?new morpheus.Vector(this.name,0):vector},_updatePreferredSize:function(){var size=this._computePreferredSize();this.preferredSize.width=size.width;this.preferredSize.height=size.height},_computePreferredSize:function(forPrint){var width=0;var height=0;if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)){if(this.positions.getSize()>=6){var context=this.canvas.getContext("2d");var textWidth=morpheus.CanvasUtil.getVectorStringWidth(context,this.getVector(),this.positions,forPrint?-1:this.isColumns?120:100);if(!forPrint){this.settings.maxTextWidth=textWidth}width+=textWidth}else if(!forPrint){this.settings.maxTextWidth=0}}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)){width+=this.settings.barSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){width+=this.settings.colorBarSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){width+=this.settings.colorBarSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){width+=300}if(this.isRenderAs(morpheus.VectorTrack.RENDER.ARC)){width+=this.settings.arcSize}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){width+=100}if(this.isRenderAs(morpheus.VectorTrack.RENDER.HEAT_MAP)){width+=100}var nkeys=this.settings.display.length;if(nkeys>0){width+=(nkeys-1)*2}width=Math.max(0,width);return this.isColumns?{width:height,height:width}:{width:width,height:height}},getPreferredSize:function(){return this.preferredSize},getPrintSize:function(){return this._computePreferredSize(true)},_createDiscreteValueMap:function(){var values=morpheus.VectorUtil.getValues(this.getFullVector());values.sort(morpheus.SortKey.ASCENDING_COMPARATOR);this.discreteValueMap=new morpheus.Map;for(var i=0,length=values.length;i<length;i++){this.discreteValueMap.set(values[i],i+1)}this.settings.min=0;this.settings.mid=0;this.settings.max=values.length},_setChartMinMax:function(){if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){if(!this.settings.stackedBar&&this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)&&!this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){if(!this.discreteValueMap){this._createDiscreteValueMap()}}else{if(this.settings.autoscaleAlways||this.settings.min==null||this.settings.max==null||this.settings.mid==null){var vector=this.getFullVector();var minMax=morpheus.VectorUtil.getMinMax(vector);var min=minMax.min;var max=minMax.max;if(this.settings.minMaxReversed){var tmp=max;max=min;min=tmp}if(this.settings.autoscaleAlways||this.settings.min==null){this.settings.min=Math.min(0,min)}if(this.settings.autoscaleAlways||this.settings.max==null){this.settings.max=Math.max(0,max)}if(this.settings.autoscaleAlways||this.settings.mid==null){this.settings.mid=this.settings.min<0?0:this.settings.min}}}}},_update:function(){if(this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)==null&&(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR))){if((this.isColumns?this.project.getColumnColorModel():this.project.getRowColorModel()).getContinuousColorScheme(this.getFullVector())!=null){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,false);this.settings.highlightMatchingValues=false}else if((this.isColumns?this.project.getColumnColorModel():this.project.getRowColorModel()).getDiscreteColorScheme(this.getFullVector())!=null){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,true);this.settings.highlightMatchingValues=true}else if(this.getFullVector().getProperties().has(morpheus.VectorKeys.FIELDS)||morpheus.VectorUtil.getDataType(this.getFullVector())==="number"||morpheus.VectorUtil.getDataType(this.getFullVector())==="[number]"){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,false);this.settings.highlightMatchingValues=false}}if(this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)==null){this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,true)}if(this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){this.project.off(this.events,this.updateSpanMapFunction)}this._setChartMinMax();if(this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){this.project.on(this.events,this.updateSpanMapFunction);if(!this.moleculeCache){this.moleculeCache={};var _this=this;var valueToModelIndices=this.getFullVector().getProperties().get(morpheus.VectorKeys.VALUE_TO_INDICES);if(!valueToModelIndices){var fullVector=this.getFullVector();valueToModelIndices=morpheus.VectorUtil.createValueToIndicesMap(fullVector);fullVector.getProperties().set(morpheus.VectorKeys.VALUE_TO_INDICES,valueToModelIndices)}if(_this.heatmap.options.structureUrlProvider!==undefined){valueToModelIndices.forEach(function(indices,value){var url=_this.heatmap.options.structureUrlProvider(value);var image=new Image;image.src=url;_this.moleculeCache[value]=image});setTimeout(function(){_this.setInvalid(true);_this.repaint()},2e3)}else{var values=valueToModelIndices.keys();var doRequest=function(smile){$.ajax({contentType:"text/plain",context:{smile:smile},data:{string:smile,representation:"sdf"},url:"http://cactus.nci.nih.gov/chemical/structure"}).done(function(text){_this.moleculeCache[this.smile]=text;if(values.length>0){doRequest(values.pop())}_this.invalid=true;_this.repaint()})};for(var i=0;i<6;i++){doRequest(values.pop())}}this.updateSpanMapFunction()}}this._updatePreferredSize()},postPaint:function(clip,context){context.lineWidth=1;context.strokeStyle="Grey";var project=this.project;var setup=this._setup(context,clip);var vector=setup.vector;var start=setup.start;var end=setup.end;if(this.isColumns){if(project.getHoverColumnIndex()!==-1){this.drawColumnBorder(context,this.positions,project.getHoverColumnIndex(),this.getUnscaledHeight())}}else{if(project.getHoverRowIndex()!==-1){this.drawRowBorder(context,this.positions,project.getHoverRowIndex(),this.getUnscaledWidth())}}this._highlightMatchingValues(context,vector,start,end)},_highlightMatchingValues:function(context,viewVector,start,end){var project=this.project;var positions=this.positions;context.strokeStyle="black";context.lineWidth=3;var hoverIndex=this.isColumns?project.getHoverColumnIndex():project.getHoverRowIndex();var value=viewVector.getValue(hoverIndex);if(this.settings.highlightMatchingValues&&hoverIndex!==-1&&this.heatmap.mousePositionOptions&&this.heatmap.mousePositionOptions.name===viewVector.getName()){var valueToModelIndices=this.getFullVector().getProperties().get(morpheus.VectorKeys.VALUE_TO_INDICES);if(!valueToModelIndices){var fullVector=this.getFullVector();valueToModelIndices=morpheus.VectorUtil.createValueToIndicesMap(fullVector);fullVector.getProperties().set(morpheus.VectorKeys.VALUE_TO_INDICES,valueToModelIndices)}var indices=valueToModelIndices.get(value);if(indices==null){console.log("valueToModelIndices error");return}if(indices.length<=1){return}if(this.isColumns){if(project.getHoverColumnIndex()!==-1){var height=this.getUnscaledHeight();context.beginPath();for(var i=0,nindices=indices.length;i<nindices;i++){var viewIndex=project.convertModelColumnIndexToView(indices[i]);if(viewIndex>=start&&viewIndex<end){var size=positions.getItemSize(viewIndex);var pix=positions.getPosition(viewIndex);context.rect(pix,0,size,height)}}context.stroke()}}else{context.beginPath();var width=this.getUnscaledWidth();var indices=valueToModelIndices.get(value);for(var i=0,nindices=indices.length;i<nindices;i++){var viewIndex=project.convertModelRowIndexToView(indices[i]);if(viewIndex>=start&&viewIndex<end){var size=positions.getItemSize(viewIndex);var pix=positions.getPosition(viewIndex);context.rect(0,pix,width,size)}}context.stroke()}}},drawSelection:function(options){var project=this.project;var positions=this.positions;var context=options.context;var start=options.start;var end=options.end;context.lineWidth=1;context.fillStyle=this.settings.selectionColor;if(this.isColumns){var height=this.getUnscaledHeight();var viewIndices=project.getColumnSelectionModel().getViewIndices();viewIndices.forEach(function(i){if(i>=start&&i<=end){var size=positions.getItemSize(i);var pix=positions.getPosition(i);context.fillRect(pix,0,size,height)}})}else{var width=this.getUnscaledWidth();if(!this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){var viewIndices=project.getRowSelectionModel().getViewIndices();viewIndices.forEach(function(i){if(i>=start&&i<=end){var size=positions.getItemSize(i);var pix=positions.getPosition(i);context.fillRect(0,pix,width,size)}})}}},prePaint:function(clip,context){var project=this.project;var positions=this.positions;var setup=this._setup(context,clip);var start=setup.start;var end=setup.end;this.drawSelection({context:context,start:start,end:end});if(this.invalid||start!==this.lastPosition.start||end!==this.lastPosition.end){this.lastPosition.start=start;this.lastPosition.end=end;this.invalid=true}},drawRowBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(0,pix+size);context.lineTo(gridSize,pix+size);context.stroke();context.beginPath();context.moveTo(0,pix);context.lineTo(gridSize,pix);context.stroke()},drawColumnBorder:function(context,positions,index,gridSize){var size=positions.getItemSize(index);var pix=positions.getPosition(index);context.beginPath();context.moveTo(pix+size,0);context.lineTo(pix+size,gridSize);context.stroke();context.beginPath();context.moveTo(pix,0);context.lineTo(pix,gridSize);context.stroke()},isSquished:function(){return this.settings.squished},_setup:function(context,clip){var start=0;var vector=this.getVector();var end=vector.size();var settings=this.settings;var positions=this.positions;var width=clip.width;var height=clip.height;if(!settings.squished){if(this.isColumns){start=morpheus.Positions.getLeft(clip,positions);end=morpheus.Positions.getRight(clip,positions)}else{start=morpheus.Positions.getTop(clip,positions);end=morpheus.Positions.getBottom(clip,positions)}}if(settings.squished){var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);if(!this.isColumns){var squishFactor=height/total;context.scale(1,squishFactor)}else{var squishFactor=width/total;context.scale(squishFactor,1)}}else{context.translate(-clip.x,-clip.y)}return{start:start,end:end,vector:vector}},draw:function(clip,context){var setup=this._setup(context,clip);this._draw({start:setup.start,end:setup.end,vector:setup.vector,context:context,availableSpace:this.isColumns?this.getUnscaledHeight():this.getUnscaledWidth(),clip:clip})},print:function(clip,context){var vector=this.getVector();this._draw({start:0,end:vector.size(),vector:vector,context:context,availableSpace:this.isColumns?clip.height:clip.width,clip:clip})},_draw:function(options){var _this=this;var context=options.context;var vector=options.vector;var availableSpace=options.availableSpace;var fullAvailableSpace=options.availableSpace;var start=options.start;var end=options.end;var clip=options.clip;var positions=this.positions;if(this.settings.autoscaleAlways){this._setChartMinMax()}context.textAlign="left";context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;var fontSize=Math.min(morpheus.VectorTrack.MAX_FONT_SIZE,positions.getSize()-2);var size=0;context.font=fontSize+"px "+morpheus.CanvasUtil.getFontFamily(context);context.strokeStyle=morpheus.HeatMapElementCanvas.GRID_COLOR;context.lineWidth=.1;if(this.heatmap.heatmap.isDrawGrid()&&!this.settings.squished){if(this.isColumns){var gridSize=availableSpace;context.beginPath();for(var i=start;i<end;i++){var size=positions.getItemSize(i);var pix=positions.getPosition(i);if(size>7){context.moveTo(pix+size,0);context.lineTo(pix+size,gridSize)}}context.stroke()}else{if(!this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){var gridSize=availableSpace;context.beginPath();for(var i=start;i<end;i++){var size=positions.getItemSize(i);var pix=positions.getPosition(i);if(size>7){context.moveTo(0,pix+size);context.lineTo(gridSize,pix+size)}}context.stroke()}}}context.lineWidth=1;var offset=1;if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){this.renderColor(context,vector,start,end,clip,this.isColumns?availableSpace:0,!this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE));offset+=this.settings.colorBarSize+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){this.renderShape(context,vector,start,end,clip,this.isColumns?availableSpace-offset:offset);offset+=this.settings.colorBarSize+2;availableSpace-=offset}if(this.isRenderAs(morpheus.VectorTrack.RENDER.ARC)){this.renderArc(context,vector,start,end,clip,this.settings.arcSize);offset+=this.settings.arcSize+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)){this.renderMolecule(context,vector,start,end,clip,offset,availableSpace)}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){var barSize=!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)?availableSpace-2:this.settings.barSize;offset++;this.renderBoxPlot(context,vector,start,end,clip,offset,barSize);offset+=barSize+2;availableSpace-=offset}if(this.isRenderAs(morpheus.VectorTrack.RENDER.HEAT_MAP)){var barSize=!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)?availableSpace-2:this.settings.barSize;offset++;this.renderHeatMap(context,vector,start,end,clip,barSize);offset+=barSize+2;availableSpace-=offset}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)){var barSize=!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)?availableSpace-1:this.settings.barSize;if(this.settings.stackedBar){this.renderStackedBar(context,vector,start,end,clip,offset,barSize)}else{var fields=vector.getProperties().get(morpheus.VectorKeys.FIELDS);var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);if(fields!=null&&visibleFieldIndices==null){visibleFieldIndices=morpheus.Util.seq(fields.length)}if(fields!=null){this.renderUnstackedBar(context,vector,start,end,clip,offset,barSize,visibleFieldIndices)}else{this.renderBar(context,vector,start,end,clip,this.isColumns?fullAvailableSpace-offset-barSize:offset,barSize)}}offset+=barSize+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT))){context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;this.renderText(context,vector,this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR),this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT),start,end,clip,this.isColumns?fullAvailableSpace-offset:offset);offset+=this.settings.maxTextWidth+2;availableSpace-=offset}if(!this.settings.squished&&this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)&&!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)&&!this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;var dataType=morpheus.VectorUtil.getDataType(vector);if(dataType==="url"){context.fillStyle="blue";this.canvas.style.cursor="pointer"}this.renderText(context,vector,false,false,start,end,clip,this.isColumns?fullAvailableSpace-offset:offset)}},showPopup:function(e,isHeader){var _this=this;var project=this.project;var isColumns=this.isColumns;var hasSelection=isColumns?project.getColumnSelectionModel().count()>0:project.getRowSelectionModel().count()>0;var ANNOTATE_SELECTION="Annotate Selection";var INVERT_SELECTION="Invert Selection";var SELECT_ALL="Select All";var SHOW_SELECTION_ONLY="Show Selection Only";var CLEAR_SELECTION="Clear Selection";var HIGHLIGHT_MATCHING_VALUES="Highlight Matching Values";var FIELDS="Choose Fields...";var DELETE="Delete...";var TOOLTIP="Show In Tooltip";var HIDE="Hide";var HIDE_OTHERS="Hide Others";var REMOVE_SHOW_SELECTION_ONLY="Show All";var SORT_ASC="Sort Ascending";var SORT_DESC="Sort Descending";var MOVE_TO_TOP="Move To Top";var SORT_SEL_ASC="Sort Heat Map Ascending ↑";var SORT_SEL_DESC="Sort Heat Map Descending ↓";var SORT_SEL_TOP_N="Sort Heat Map Descending/Ascending";var DISPLAY_BAR="Show Bar Chart";var NUMBER_FORMAT="Format";var DISPLAY_STACKED_BAR="Show Stacked Bar Chart";var DISPLAY_BOX_PLOT="Show Box Plot";var DISPLAY_COLOR="Show Color";var COLOR_BAR_SIZE="Color Bar Size...";var DISPLAY_TEXT="Show Text";var DISPLAY_SHAPE="Show Shape";var DISPLAY_ARC="Show Arc";var DISPLAY_TEXT_AND_COLOR="Encode Text Using Color";var DISPLAY_TEXT_AND_FONT="Encode Text Using Font";var DISPLAY_STRUCTURE="Show Chemical Structure";var DISPLAY_CONTINUOUS="Continuous";var positions=this.positions;var heatmap=this.heatmap;var sectionToItems={Sort:[],Selection:[],Display:[]};var customItems=this.heatmap.getPopupItems();if(customItems&&customItems.length>0){customItems.forEach(function(item){if(item.columns===isColumns){sectionToItems[item.section].push(item)}})}if(sectionToItems.Selection.length>0){sectionToItems.Selection.push({separator:true})}sectionToItems.Selection.push({name:MOVE_TO_TOP});if(this.heatmap.options.menu.Edit&&this.heatmap.options.menu.Edit.indexOf("Annotate"+" Selected Rows")!==-1){sectionToItems.Selection.push({name:ANNOTATE_SELECTION})}sectionToItems.Selection.push({name:"Copy",class:"copy"});sectionToItems.Selection.push({name:INVERT_SELECTION});sectionToItems.Selection.push({name:SELECT_ALL});sectionToItems.Selection.push({name:CLEAR_SELECTION});var combinedFilter=isColumns?project.getColumnFilter():project.getRowFilter();var showSelectionOnlyIndex=combinedFilter.indexOf(SHOW_SELECTION_ONLY);if(showSelectionOnlyIndex!==-1){sectionToItems.Selection.push({name:REMOVE_SHOW_SELECTION_ONLY})}if(!isHeader){sectionToItems["Sort"].push({name:SORT_SEL_ASC,disabled:!hasSelection});sectionToItems["Sort"].push({name:SORT_SEL_DESC,disabled:!hasSelection});sectionToItems["Sort"].push({name:SORT_SEL_TOP_N,disabled:!hasSelection})}var dataType=morpheus.VectorUtil.getDataType(this.getFullVector());var arrayFields=this.getFullVector().getProperties().get(morpheus.VectorKeys.FIELDS);var isArray=arrayFields!==undefined;var isNumber=dataType==="number"||dataType==="[number]";if(isNumber||isArray){sectionToItems.Display.push({name:NUMBER_FORMAT});sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:DISPLAY_BAR,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)})}if(isArray){sectionToItems.Display.push({name:DISPLAY_STACKED_BAR,checked:this.settings.stackedBar});sectionToItems.Display.push({name:DISPLAY_BOX_PLOT,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)});sectionToItems.Display.push({name:FIELDS})}if(dataType!=="url"){sectionToItems.Display.push({name:DISPLAY_TEXT,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)});if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT)){sectionToItems.Display.push({name:DISPLAY_TEXT_AND_COLOR,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)});sectionToItems.Display.push({name:DISPLAY_TEXT_AND_FONT,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)})}sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:DISPLAY_COLOR,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)});if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)){sectionToItems.Display.push({name:COLOR_BAR_SIZE})}}if(!isArray&&dataType!=="url"){sectionToItems.Display.push({name:DISPLAY_SHAPE,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)})}if(!isArray&&!isNumber&&!this.isColumns&&name.toLowerCase().indexOf("smile")!==-1){sectionToItems.Display.push({name:DISPLAY_STRUCTURE,checked:this.isRenderAs(morpheus.VectorTrack.RENDER.MOLECULE)})}sectionToItems.Display.push({name:TOOLTIP,checked:this.settings.inlineTooltip});if(!isArray&&dataType!=="url"){sectionToItems.Display.push({name:HIGHLIGHT_MATCHING_VALUES,checked:this.settings.highlightMatchingValues})}if(dataType!=="url"){}if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BOX_PLOT)){sectionToItems.Display.push({separator:true});if(this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)){sectionToItems.Display.push({name:"Edit Bar Color..."})}sectionToItems.Display.push({name:"Auto Range"});sectionToItems.Display.push({name:"Custom Range..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)||this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){sectionToItems.Display.push({separator:true});if(isNumber){sectionToItems.Display.push({name:DISPLAY_CONTINUOUS,checked:!this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)&&isArray){sectionToItems.Display.push({name:"Edit Colors..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){sectionToItems.Display.push({name:"Edit Shapes..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){sectionToItems.Display.push({name:"Edit Fonts..."})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_COLOR)||this.isRenderAs(morpheus.VectorTrack.RENDER.BAR)&&isArray){sectionToItems.Display.push({name:"Color Key",icon:"fa fa-key"})}}if(this.isRenderAs(morpheus.VectorTrack.RENDER.SHAPE)){sectionToItems.Display.push({name:"Shape Key",icon:"fa fa-key"})}if(this.isRenderAs(morpheus.VectorTrack.RENDER.TEXT_AND_FONT)){sectionToItems.Display.push({name:"Font Key",icon:"fa fa-key"})}sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:HIDE});sectionToItems.Display.push({name:HIDE_OTHERS,disabled:heatmap.getVisibleTrackNames(this.isColumns).length<=1});sectionToItems.Display.push({separator:true});sectionToItems.Display.push({name:DELETE});var items=[];function addSection(name){if(items.length>0){items.push({separator:true})}items=items.concat(sectionToItems[name])}addSection("Sort");_.each(sectionToItems.Selection,function(item){if(item.name!==REMOVE_SHOW_SELECTION_ONLY&&item.name!==SELECT_ALL){item.disabled=!hasSelection}});if(!isHeader){addSection("Selection")}else if(this.heatmap.options.toolbar.options){addSection("Display")}if(e.preventDefault){e.preventDefault()}if(items.length===0){return}morpheus.Popup.showPopup(items,{x:e.pageX,y:e.pageY},e.target,function(event,item){var customItem;if(item===NUMBER_FORMAT){var vector=_this.getFullVector();var formatter=vector.getProperties().get(morpheus.VectorKeys.FORMATTER);if(formatter!=null){if(typeof formatter==="object"){formatter=morpheus.Util.createNumberFormat(formatter.pattern);vector.getProperties().set(morpheus.VectorKeys.FORMATTER,formatter)}}var pattern=formatter!=null?formatter.toJSON().pattern:".2f";var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"number_of_fraction_digits",type:"number",value:morpheus.Util.getNumberFormatPatternFractionDigits(pattern),required:true,style:"max-width:60px;"});formBuilder.find("number_of_fraction_digits").on("keyup input",_.debounce(function(){var n=parseInt($(this).val());if(n>=0){vector.getProperties().set(morpheus.VectorKeys.FORMATTER,{pattern:"."+n+"f"});_this.setInvalid(true);_this.repaint()}},100));morpheus.FormBuilder.showInModal({title:"Format",close:"Close",html:formBuilder.$form,focus:heatmap.getFocusEl()})}else if(item==="Copy"){heatmap.getActionManager().execute(isColumns?"Copy Selected Columns":"Copy"+" Selected Rows")}else if(item===FIELDS){var visibleFieldIndices=_this.getFullVector().getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);var visibleFields;if(visibleFieldIndices==null){visibleFields=arrayFields.slice(0)}else{visibleFields=[];for(var i=0;i<visibleFieldIndices.length;i++){visibleFields.push(arrayFields[visibleFieldIndices[i]])}}var availableFields=[];for(var i=0;i<arrayFields.length;i++){if(visibleFields.indexOf(arrayFields[i])===-1){availableFields.push(arrayFields[i])}}var leftOptions=[];var rightOptions=[];for(var i=0;i<availableFields.length;i++){leftOptions.push(new Option(availableFields[i],availableFields[i]))}for(var i=0;i<visibleFields.length;i++){rightOptions.push(new Option(visibleFields[i],visibleFields[i]))}var list=new morpheus.DualList(leftOptions,rightOptions);morpheus.FormBuilder.showOkCancel({title:"Fields",okCallback:function(){var visibleFields=list.getOptions(false);var visibleFieldIndices=[];for(var i=0;i<visibleFields.length;i++){visibleFieldIndices.push(arrayFields.indexOf(visibleFields[i]))}var fullVector=_this.getFullVector();fullVector.getProperties().set(morpheus.VectorKeys.VISIBLE_FIELDS,visibleFieldIndices);var summaryFunction=fullVector.getProperties().get(morpheus.VectorKeys.ARRAY_SUMMARY_FUNCTION);if(summaryFunction){summaryFunction.indices=visibleFieldIndices}var updatedVector=_this.isColumns?_this.project.getFullDataset().getColumnMetadata().add(_this.name):_this.project.getFullDataset().getRowMetadata().add(_this.name);for(var i=0;i<updatedVector.size();i++){var array=fullVector.getValue(i);if(array!=null){array.summary=undefined}}_this.setInvalid(true);_this.repaint()},content:list.$el})}else if(item==="Edit Bar Color..."){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"bar_color",type:"color",value:_this.settings.barColor,required:true,style:"max-width:50px;"});formBuilder.find("bar_color").on("change",function(){_this.settings.barColor=$(this).val();_this.setInvalid(true);_this.repaint()});morpheus.FormBuilder.showInModal({title:"Bar Color",close:"Close",html:formBuilder.$form,focus:heatmap.getFocusEl()})}else if(item===COLOR_BAR_SIZE){var formBuilder=new morpheus.FormBuilder;formBuilder.append({name:"size",type:"text",value:_this.settings.colorBarSize,required:true,style:"max-width:50px;"});formBuilder.find("size").on("change",function(){var val=parseFloat($(this).val());if(val>0){_this.settings.colorBarSize=val;_this.setInvalid(true);_this.repaint()}});morpheus.FormBuilder.showInModal({title:"Color Bar Size",close:"Close",html:formBuilder.$form,focus:heatmap.getFocusEl()})}else if(item===ANNOTATE_SELECTION){heatmap.getActionManager().execute(isColumns?"Annotate Selected Columns":"Annotate"+" Selected Rows")}else if(item===DELETE){morpheus.FormBuilder.showOkCancel({title:"Delete",content:"Are you sure you want to delete "+_this.name+"?",okCallback:function(){var metadata=isColumns?project.getFullDataset().getColumnMetadata():project.getFullDataset().getRowMetadata();metadata.remove(morpheus.MetadataUtil.indexOf(metadata,_this.name));var sortKeys=isColumns?project.getColumnSortKeys():project.getRowSortKeys();var sortKeyIndex=_.indexOf(sortKeys.map(function(key){return key.field}),_this.name);if(sortKeyIndex!==-1){sortKeys.splice(sortKeyIndex,1);if(isColumns){project.setColumnSortKeys(sortKeys,true)}else{project.setRowSortKeys(sortKeys,true)}}var groupByKeys=isColumns?project.getGroupColumns():project.getGroupRows();var groupByKeyIndex=_.indexOf(groupByKeys.map(function(key){return key.field}),_this.name);if(groupByKeyIndex!==-1){groupByKeys.splice(groupByKeyIndex,1);if(isColumns){project.setGroupColumns(groupByKeys,true)}else{project.setGroupRows(groupByKeys,true)}}if(!isColumns){project.trigger("rowTrackRemoved",{vector:_this.getFullVector()})}else{project.trigger("columnTrackRemoved",{vector:_this.getFullVector()})}}})}else if(item===CLEAR_SELECTION){heatmap.getActionManager().execute(isColumns?"Clear Selected Columns":"Clear"+" Selected Rows")}else if(item===INVERT_SELECTION){heatmap.getActionManager().execute(isColumns?"Invert Selected Columns":"Invert"+" Selected Rows")}else if(item===MOVE_TO_TOP){heatmap.getActionManager().execute(isColumns?"Move Selected Columns To Top":"Move"+" Selected Rows To Top")}else if(item===SORT_ASC||item===SORT_DESC){var sortKey=new morpheus.SortKey(_this.name,item===SORT_ASC?morpheus.SortKey.SortOrder.ASCENDING:morpheus.SortKey.SortOrder.DESCENDING);if(_this.isColumns){_this.project.setColumnSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getColumnSortKeys()),true)}else{_this.project.setRowSortKeys(morpheus.SortKey.keepExistingSortKeys([sortKey],project.getRowSortKeys()),true)}}else if(item==SORT_SEL_ASC||item==SORT_SEL_DESC||item===SORT_SEL_TOP_N){var sortOrder;if(item===SORT_SEL_ASC){sortOrder=morpheus.SortKey.SortOrder.ASCENDING}else if(item===SORT_SEL_DESC){sortOrder=morpheus.SortKey.SortOrder.DESCENDING}else{sortOrder=morpheus.SortKey.SortOrder.TOP_N}heatmap.sortBasedOnSelection(sortOrder,isColumns,e&&e.shiftKey)}else if(item===SELECT_ALL){heatmap.getActionManager().execute(isColumns?"Select All Columns":"Select All Rows")}else if(item==="Auto Range"){delete _this.settings.min;delete _this.settings.max;delete _this.settings.mid;_this._update();heatmap.revalidate()}else if(item==="Custom Range..."){var formBuilder=new morpheus.FormBuilder;var items=[{name:"min",required:true,type:"number",value:_this.settings.min},{name:"mid",required:true,type:"number",value:_this.settings.mid},{name:"max",required:true,type:"number",value:_this.settings.max}];_.each(items,function(item){formBuilder.append(item)});morpheus.FormBuilder.showOkCancel({title:"Range",content:formBuilder.$form,okCallback:function(){_this.settings.min=parseFloat(formBuilder.getValue("min"));_this.settings.mid=parseFloat(formBuilder.getValue("mid"));_this.settings.max=parseFloat(formBuilder.getValue("max"));_this._update();heatmap.revalidate()}})}else if(item==="Squished"){_this.settings.squished=!_this.settings.squished;heatmap.revalidate()}else if(item==="Color Key"){var legend=new morpheus.HeatMapTrackColorLegend([_this],isColumns?_this.project.getColumnColorModel():_this.project.getRowColorModel());var size=legend.getPreferredSize();legend.setBounds(size);legend.repaint();morpheus.FormBuilder.showInModal({title:"Color Key",html:legend.canvas,focus:heatmap.getFocusEl()})}else if(item==="Shape Key"){var legend=new morpheus.HeatMapTrackShapeLegend([_this],isColumns?_this.project.getColumnShapeModel():_this.project.getRowShapeModel());var size=legend.getPreferredSize();legend.setBounds(size);legend.repaint();morpheus.FormBuilder.showInModal({title:"Shape Key",html:legend.canvas,focus:heatmap.getFocusEl()})}else if(item==="Font Key"){var legend=new morpheus.HeatMapTrackFontLegend([_this],isColumns?_this.project.getColumnFontModel():_this.project.getRowFontModel());var size=legend.getPreferredSize();legend.setBounds(size);legend.repaint();morpheus.FormBuilder.showInModal({title:"Font Key",html:legend.canvas,focus:heatmap.getFocusEl()})}else if(item==="Edit Fonts..."){heatmap.getActionManager().execute("Edit Fonts")}else if(item==="Edit Shapes..."){var shapeFormBuilder=new morpheus.FormBuilder;var shapeModel=isColumns?_this.project.getColumnShapeModel():_this.project.getRowShapeModel();var chooser=new morpheus.ShapeChooser({map:shapeModel.getMap(_this.name)});chooser.on("change",function(event){shapeModel.setMappedValue(_this.getFullVector(),event.value,event.shape);_this.setInvalid(true);_this.repaint()});morpheus.FormBuilder.showInModal({title:"Edit Shapes",html:chooser.$div,close:"Close",focus:heatmap.getFocusEl()})}else if(item==="Edit Colors..."){var colorModel=isColumns?_this.project.getColumnColorModel():_this.project.getRowColorModel();var colorSchemeChooser=new morpheus.ColorSchemeChooser({track:_this,heatMap:_this.heatmap,colorModel:colorModel});morpheus.FormBuilder.showInModal({title:"Edit Colors",html:colorSchemeChooser.$div,close:"Close",focus:heatmap.getFocusEl()})}else if(item===TOOLTIP){_this.settings.inlineTooltip=!_this.settings.inlineTooltip}else if(item===HIGHLIGHT_MATCHING_VALUES){_this.settings.highlightMatchingValues=!_this.settings.highlightMatchingValues}else if(customItem=_.find(customItems,function(customItem){return customItem.name===item&&customItem.columns===isColumns})){if(customItem.task){var task={tabId:_this.heatmap.getTabManager().getActiveTabId()};_this.heatmap.getTabManager().addTask(task);setTimeout(function(){customItem.callback(heatmap);_this.heatmap.getTabManager().removeTask(task)},1)}else{customItem.callback(heatmap)}}else if(item===DISPLAY_CONTINUOUS){var discrete=_this.getFullVector().getProperties().get(morpheus.VectorKeys.DISCRETE)||false;_this.getFullVector().getProperties().set(morpheus.VectorKeys.DISCRETE,!discrete);_this._setChartMinMax();_this.setInvalid(true);_this.repaint()}else if(item===HIDE){heatmap.setTrackVisible(_this.name,false,_this.isColumns);heatmap.revalidate()}else if(item===HIDE_OTHERS){var names=heatmap.getVisibleTrackNames(_this.isColumns);for(var i=0;i<names.length;i++){if(names[i]!==_this.name){heatmap.setTrackVisible(names[i],false,_this.isColumns)}}heatmap.revalidate()}else if(item===DISPLAY_STACKED_BAR){_this.settings.stackedBar=!_this.settings.stackedBar;_this._update();heatmap.revalidate()}else{if(item===DISPLAY_BAR){item=morpheus.VectorTrack.RENDER.BAR}else if(item===DISPLAY_COLOR){item=morpheus.VectorTrack.RENDER.COLOR}else if(item===DISPLAY_TEXT){item=morpheus.VectorTrack.RENDER.TEXT}else if(item===DISPLAY_TEXT_AND_COLOR){item=morpheus.VectorTrack.RENDER.TEXT_AND_COLOR}else if(item===DISPLAY_TEXT_AND_FONT){item=morpheus.VectorTrack.RENDER.TEXT_AND_FONT}else if(item===DISPLAY_STRUCTURE){item=morpheus.VectorTrack.RENDER.MOLECULE}else if(item===DISPLAY_SHAPE){item=morpheus.VectorTrack.RENDER.SHAPE}else if(item===DISPLAY_ARC){item=morpheus.VectorTrack.RENDER.ARC}else if(item===DISPLAY_BOX_PLOT){item=morpheus.VectorTrack.RENDER.BOX_PLOT}else{console.log("Unknown item "+item)}var show=!_this.isRenderAs(item);var remove;if(!show){_this.settings.display.splice(_this.settings.display.indexOf(item),1);if(item===morpheus.VectorTrack.RENDER.TEXT){remove=[morpheus.VectorTrack.RENDER.TEXT_AND_FONT,morpheus.VectorTrack.RENDER.TEXT_AND_COLOR]}}else{if(item===morpheus.VectorTrack.RENDER.COLOR){remove=[morpheus.VectorTrack.RENDER.TEXT_AND_COLOR]}else if(item===morpheus.VectorTrack.RENDER.TEXT_AND_COLOR){remove=[morpheus.VectorTrack.RENDER.COLOR]}_this.settings.display.push(item)}if(remove){remove.forEach(function(key){var index=_this.settings.display.indexOf(key);if(index!==-1){_this.settings.display.splice(index,1)}})}_this._update();heatmap.revalidate();if(show&&item===morpheus.VectorTrack.RENDER.TEXT_AND_FONT){heatmap.getActionManager().execute("Edit Fonts")}}})},renderColor:function(context,vector,start,end,clip,offset,continuous){var isColumns=this.isColumns;var positions=this.positions;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();var settings=this.settings;var canvasSize=isColumns?this.getUnscaledHeight():this.getUnscaledWidth();var colorBarSize=settings.colorBarSize;if(colorBarSize>canvasSize){colorBarSize=canvasSize>=5?canvasSize-1:canvasSize}var getColor;if(!continuous){getColor=_.bind(colorModel.getMappedValue,colorModel)}else{getColor=_.bind(colorModel.getContinuousMappedValue,colorModel)}if(vector.getProperties().get(morpheus.VectorKeys.FIELDS)!=null){var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);if(visibleFieldIndices==null){visibleFieldIndices=morpheus.Util.seq(vector.getProperties().get(morpheus.VectorKeys.FIELDS).length)}colorBarSize/=visibleFieldIndices.length;var nvisibleFieldIndices=visibleFieldIndices.length;for(var i=start;i<end;i++){var array=vector.getValue(i);var position=positions.getPosition(i);var size=positions.getItemSize(i);var _offset=offset;if(array!=null){for(var j=0;j<nvisibleFieldIndices;j++){var value=array[visibleFieldIndices[j]];var color=getColor(vector,value);context.fillStyle=color;if(isColumns){context.beginPath();context.rect(position,_offset-colorBarSize,size,colorBarSize);context.fill()}else{context.beginPath();context.rect(_offset,position,colorBarSize,size);context.fill()}_offset+=colorBarSize}}}}else{for(var i=start;i<end;i++){var value=vector.getValue(i);var position=positions.getPosition(i);var size=positions.getItemSize(i);var color=getColor(vector,value);context.fillStyle=color;if(isColumns){context.beginPath();context.rect(position,offset-colorBarSize,size,settings.colorBarSize);context.fill()}else{context.beginPath();context.rect(offset,position,colorBarSize,size);context.fill()}}}},renderShape:function(context,vector,start,end,clip,offset){var isColumns=this.isColumns;var positions=this.positions;var shapeModel=isColumns?this.project.getColumnShapeModel():this.project.getRowShapeModel();var settings=this.settings;var canvasSize=isColumns?this.getUnscaledHeight():this.getUnscaledWidth();var colorBarSize=settings.colorBarSize;if(colorBarSize>canvasSize){colorBarSize=canvasSize>=5?canvasSize-1:canvasSize}context.fillStyle="black";context.strokeStyle="black";var lineWidth=context.lineWidth;context.lineWidth=1;for(var i=start;i<end;i++){var value=vector.getValue(i);var position=positions.getPosition(i);var itemSize=positions.getItemSize(i);var minSize=Math.min(colorBarSize,itemSize);var size2=minSize/2;var shape=shapeModel.getMappedValue(vector,value);var x=isColumns?position+itemSize/2:offset+size2;var y=isColumns?offset-size2:position+itemSize/2;size2-=.5;morpheus.CanvasUtil.drawShape(context,shape,x,y,size2)}context.lineWidth=lineWidth},renderHeatMap:function(context,vector,start,end,clip,size){var isColumns=this.isColumns;var positions=this.positions;var project=this.project;context.save();context.lineWidth=1;var width=clip.width;var height=clip.height;var colorScheme=this.heatmap.getHeatMapElementComponent().getColorScheme();var drawGrid=this.heatmap.getHeatMapElementComponent().isDrawGrid();var gridColor=this.heatmap.getHeatMapElementComponent().getGridColor();var gridThickness=this.heatmap.getHeatMapElementComponent().getGridThickness();for(var i=start;i<end;i++){var value=vector.getValue(i);if(value!=null){var pix=positions.getPosition(i);var itemSize=positions.getItemSize(i);var currentPix=0;var nvalues=value.length;var pixPer=size/nvalues;for(var j=0;j<nvalues;j++){var val=value[j];context.fillStyle=colorScheme.getColor(i,-1,val);context.fillRect(j*pixPer,pix,pixPer,itemSize)}if(drawGrid&&itemSize>10){context.strokeStyle=gridColor;context.lineWidth=gridThickness;context.beginPath();for(var j=0;j<nvalues;j++){var val=value[j];context.rect(j*pixPer,pix,pixPer,itemSize)}context.stroke()}}}context.restore()},renderArc:function(context,vector,start,end,clip,size){var isColumns=this.isColumns;var positions=this.positions;var project=this.project;context.save();context.lineWidth=1;var total=positions.getPosition(positions.getLength()-1)+positions.getItemSize(positions.getLength()-1);context.translate(clip.x,clip.y);var width=clip.width;var height=clip.height;for(var i=start;i<end;i++){var value=vector.getValue(i);if(value!=null){var startPix=positions.getPosition(i)+positions.getItemSize(i)/2;for(var j=0,nindices=value.length;j<nindices;j++){var viewIndex=value[j];var endPix=positions.getPosition(viewIndex)+positions.getItemSize(viewIndex)/2;var midPix=(endPix+startPix)/2;var distance=Math.abs(i-viewIndex);var arcRadius=size;if(isColumns){context.beginPath();context.moveTo(startPix,arcRadius);context.quadraticCurveTo(midPix,1,endPix,arcRadius)}else{console.log(i,viewIndex,startPix,endPix);context.beginPath();context.moveTo(1,startPix);context.quadraticCurveTo(arcRadius,midPix,1,endPix)}context.stroke()}}}context.restore()},sdfToSvg:function(sdf,width,height){if(!this.jsme&&typeof JSApplet!=="undefined"){this.jsmeId=_.uniqueId("m");this.$jsmeDiv=$('<div id="'+this.jsmeId+'" style="position:absolute;left:-10000px;top:-10000px;"></div>').appendTo($(document.body));this.jsme=new JSApplet.JSME(this.jsmeId,"380px","340px",{})}this.jsme.readMolFile(sdf);var svg=$("#"+this.jsmeId+" > div > div > div:nth-child(2) > svg");var svgWidth=svg.width.baseVal.value;var svgHeight=svg.height.baseVal.value;var scale=Math.min(width/svgWidth,height/svgHeight);var text='<svg><g transform="scale('+scale+')">'+svg.innerHTML+"</g></svg>";return text},renderMolecule:function(context,vector,start,end,clip,offset){var isColumns=this.isColumns;var positions=this.positions;context.fillStyle=morpheus.CanvasUtil.FONT_COLOR;context.strokeStyle="black";var width=this.getUnscaledWidth();var customUrlProvider=this.heatmap.options.structureUrlProvider!==undefined;var dummyTarget={childNodes:[],getContext:function(){return context}};for(var i=start;i<end;i++){var spanEnd=this.spanMap.get(i);if(spanEnd!==undefined){var startPix=positions.getPosition(i);var endPix=positions.getPosition(spanEnd-1)+positions.getSize();var size=endPix-startPix;var value=vector.getValue(i);var cache=this.moleculeCache[value];if(cache){if(customUrlProvider){if(cache.complete){var scaleFactor=Math.min(size/cache.height,width/cache.width);var scaledWidth=cache.width*scaleFactor;var scaledHeight=cache.height*scaleFactor;var diff=cache.height-scaledHeight;startPix+=diff/2;try{context.drawImage(cache,offset,startPix,scaledWidth,scaledHeight)}catch(x){}}}else{var text=this.sdfToSvg(cache,width,size);canvg(dummyTarget,text,{ignoreMouse:true,ignoreAnimation:true,offsetY:startPix,ignoreClear:true,ignoreDimensions:true})}}}}},createChartScale:function(availableSpace){var domain;var range;if(this.settings.mid!==this.settings.min&&this.settings.mid!==this.settings.max){domain=[this.settings.min,this.settings.mid,this.settings.max];range=this.isColumns?[availableSpace,availableSpace/2,0]:[0,availableSpace/2,availableSpace]}else{domain=[this.settings.min,this.settings.max];range=this.isColumns?[availableSpace,0]:[0,availableSpace]}var scale=d3.scale.linear().domain(domain).range(range).clamp(true);return scale},renderBar:function(context,vector,start,end,clip,offset,availableSpace){var isColumns=this.isColumns;var positions=this.positions;context.fillStyle=this.settings.barColor;var scale=this.createChartScale(availableSpace);var midPix=scale(this.settings.mid);var settings=this.settings;var discrete=vector.getProperties().get(morpheus.VectorKeys.DISCRETE)&&this.discreteValueMap!=null;var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):null;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();for(var i=start;i<end;i++){var value=vector.getValue(i);if(discrete){value=this.discreteValueMap.get(value)}var position=positions.getPosition(i);var size=positions.getItemSize(i);var scaledValue=scale(value);if(colorByVector!==null){context.fillStyle=colorModel.getMappedValue(colorByVector,colorByVector.getValue(i))}if(isColumns){context.beginPath();context.rect(position,Math.min(midPix,scaledValue)+offset,size,Math.abs(midPix-scaledValue));context.fill()}else{context.beginPath();context.rect(offset+Math.min(midPix,scaledValue),position,Math.abs(midPix-scaledValue),size);context.fill()}}},renderBoxPlot:function(context,vector,start,end,clip,offset,availableSpace){var isColumns=this.isColumns;var positions=this.positions;context.strokeStyle="black";context.save();context.translate(offset,0);var scale=this.createChartScale(availableSpace);var visibleFieldIndices=vector.getProperties().get(morpheus.VectorKeys.VISIBLE_FIELDS);var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):null;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();for(var i=start;i<end;i++){var array=vector.getValue(i);if(array!=null){var itemSize=positions.getItemSize(i);if(itemSize<=3){continue}var radius=2;var pix=positions.getPosition(i);var start=pix+1;var end=pix+itemSize-1;var center=(start+end)/2;var _itemSize=itemSize-2;var lineHeight=Math.max(2,_itemSize-8);var box=array.summary;if(box==null){var v=morpheus.VectorUtil.arrayAsVector(array);box=morpheus.BoxPlotItem(visibleFieldIndices!=null?new morpheus.SlicedVector(v,visibleFieldIndices):v);array.summary=box}context.fillStyle="#bdbdbd";if(!isColumns){context.fillRect(Math.min(scale(box.q1),scale(box.q3)),start,Math.abs(scale(box.q1)-scale(box.q3)),_itemSize);context.fillRect(Math.min(scale(box.q1),scale(box.lowerAdjacentValue)),center-lineHeight/2,Math.abs(scale(box.q1)-scale(box.lowerAdjacentValue)),lineHeight);context.fillRect(Math.min(scale(box.q3),scale(box.upperAdjacentValue)),center-lineHeight/2,Math.abs(scale(box.q3)-scale(box.upperAdjacentValue)),lineHeight);context.fillStyle="#31a354";context.fillRect(scale(box.median)-3,start,3,end-start);context.fillStyle="#636363"}else{}}}context.restore()},renderStackedBar:function(context,vector,start,end,clip,offset,availableSpace){var isColumns=this.isColumns;var positions=this.positions;var scale=this.createChartScale(availableSpace);var midPix=scale(this.settings.mid);var settings=this.settings;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();context.strokeStyle="black";context.lineWidth=2;for(var i=start;i<end;i++){var array=vector.getValue(i);if(array!=null){var position=positions.getPosition(i);var size=positions.getItemSize(i);var positivePairs=[];var negativePairs=[];for(var j=0,length=array.length;j<length;j++){var value=array[j];if(value>=this.settings.mid){positivePairs.push({value:value,index:j})}else if(value<0){negativePairs.push({value:value,index:j})}}var positiveIndices=morpheus.Util.indexSortPairs(positivePairs,false);for(var j=0,length=positiveIndices.length;j<length;j++){var index=positiveIndices[j];var value=array[index];var color=colorModel.getMappedValue(vector,index);context.fillStyle=color;var scaledValue=scale(value);var nextScaledValue=j===length-1?midPix:scale(array[positiveIndices[j+1]]);if(isColumns){context.beginPath();context.rect(position,Math.min(nextScaledValue,scaledValue),size,Math.abs(nextScaledValue-scaledValue));context.fill()}else{context.beginPath();context.rect(offset+Math.min(nextScaledValue,scaledValue),position,Math.abs(nextScaledValue-scaledValue),size);context.fill()}}var negativeIndices=morpheus.Util.indexSortPairs(negativePairs,true);for(var j=0,length=negativeIndices.length;j<length;j++){var index=negativeIndices[j];var value=array[index];var color=colorModel.getMappedValue(vector,index);context.fillStyle=color;var scaledValue=scale(value);var nextScaledValue=j===length-1?midPix:scale(array[negativeIndices[j+1]]);if(isColumns){context.beginPath();context.rect(position,Math.min(nextScaledValue,scaledValue),size,Math.abs(nextScaledValue-scaledValue));context.fill()}else{context.beginPath();context.rect(offset+Math.min(nextScaledValue,scaledValue),position,Math.abs(nextScaledValue-scaledValue),size);context.fill()}}}}context.lineWidth=1},renderUnstackedBar:function(context,vector,start,end,clip,offset,availableSpace,fieldIndices){var isColumns=this.isColumns;var positions=this.positions;var nvalues=fieldIndices.length;var settings=this.settings;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();context.fillStyle=this.settings.barColor;var barSpacer=0;var barWidth=(availableSpace-(nvalues-1)*barSpacer)/nvalues;var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):null;context.strokeStyle="white";for(var i=start;i<end;i++){var array=vector.getValue(i);if(array!=null){var position=positions.getPosition(i);var itemSize=positions.getItemSize(i);var scale=this.createChartScale(itemSize-1);var midPix=scale(this.settings.mid);var xpix=0;for(var j=0;j<nvalues;j++){var value=array[fieldIndices[j]];if(colorByVector!=null){var colorByArray=colorByVector.getValue(i);var color=colorModel.getMappedValue(colorByVector,colorByArray!=null?colorByArray[fieldIndices[j]]:null);context.fillStyle=color}var scaledValue=scale(value);if(isColumns){context.beginPath();context.rect(Math.min(midPix,scaledValue),offset+xpix,Math.abs(midPix-scaledValue),barWidth);context.fill()}else{context.beginPath();var barHeight=Math.abs(midPix-scaledValue);var ypix=position+itemSize-Math.max(midPix,scaledValue);context.rect(offset+xpix,ypix,barWidth,barHeight);context.fill()}xpix+=barWidth+barSpacer}}}},renderText:function(context,vector,isColor,isFont,start,end,clip,offset,canvasSize){context.textBaseline="middle";if(typeof C2S!=="undefined"&&context instanceof C2S){context.translate(this.isColumns?2:0,this.isColumns?0:2)}var positions=this.positions;var isColumns=this.isColumns;var colorModel=isColumns?this.project.getColumnColorModel():this.project.getRowColorModel();var fontModel=isColumns?this.project.getColumnFontModel():this.project.getRowFontModel();if(isColumns){context.translate(clip.x,clip.y)}var colorByVector=this.settings.colorByField!=null?this.getVector(this.settings.colorByField):vector;var getColor;if(colorByVector.getProperties().get(morpheus.VectorKeys.DISCRETE)){getColor=_.bind(colorModel.getMappedValue,colorModel)}else{getColor=_.bind(colorModel.getContinuousMappedValue,colorModel)}var fontVector=this.settings.fontField!=null?this.getVector(this.settings.fontField):vector;var toStringFunction=morpheus.VectorTrack.vectorToString(vector);var font=context.font;for(var i=start;i<end;i++){var size=this.positions.getItemSize(i);if(size<6){continue}var value=vector.getValue(i);if(value!=null){var stringValue=toStringFunction(value);var position=positions.getPosition(i);if(isColor){context.fillStyle=getColor(colorByVector,colorByVector.getValue(i))}if(isFont){context.font=fontModel.getMappedValue(fontVector,fontVector.getValue(i)).weight+" "+font}if(isColumns){context.save();context.translate(position+size/2-clip.x,offset-clip.y);context.rotate(-Math.PI/2);context.fillText(stringValue,0,0);context.restore()}else{context.fillText(stringValue,offset,position+size/2)}}}context.font=font}};morpheus.Util.extend(morpheus.VectorTrack,morpheus.AbstractCanvas);morpheus.VectorTrack.MAX_FONT_SIZE=18;morpheus.AverageLinkage=function(nelements,distmatrix){var j;var n;var clusterid;var number;var result;clusterid=[];number=[];result=[];for(var i=0;i<nelements-1;i++){result[i]={left:0,right:0,distance:0}}for(j=0;j<nelements;j++){number[j]=1;clusterid[j]=j}var r={};for(n=nelements;n>1;n--){morpheus.HCluster.findClosestPair(n,distmatrix,r);result[nelements-n]={};result[nelements-n].distance=r.distance;var is=r.ip;var js=r.jp;result[nelements-n].left=clusterid[is];result[nelements-n].right=clusterid[js];var sum=number[is]+number[js];for(j=0;j<js;j++){distmatrix[js][j]=distmatrix[is][j]*number[is]+distmatrix[js][j]*number[js];distmatrix[js][j]/=sum}for(j=js+1;j<is;j++){distmatrix[j][js]=distmatrix[is][j]*number[is]+distmatrix[j][js]*number[js];distmatrix[j][js]/=sum}for(j=is+1;j<n;j++){distmatrix[j][js]=distmatrix[j][is]*number[is]+distmatrix[j][js]*number[js];distmatrix[j][js]/=sum}for(j=0;j<is;j++){distmatrix[is][j]=distmatrix[n-1][j]}for(j=is+1;j<n-1;j++){distmatrix[j][is]=distmatrix[n-1][j]}number[js]=sum;number[is]=number[n-1];clusterid[js]=n-nelements-1;clusterid[is]=clusterid[n-1]}return result};morpheus.CollapseDataset=function(dataset,collapseToFields,summarizeFunction,shallowCopy){var vectors=[];for(var i=0;i<collapseToFields.length;i++){var v=dataset.getRowMetadata().getByName(collapseToFields[i]);if(!v){throw collapseToFields[i]+" not found. Available fields are "+morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata())}vectors.push(v)}var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);var collapsedDataset=new morpheus.Dataset({name:dataset.getName(),rows:idToIndices.size(),columns:dataset.getColumnCount(),dataType:"Float32"});var nseries=dataset.getSeriesCount();for(var series=1;series<nseries;series++){collapsedDataset.addSeries({name:dataset.getName(i),dataType:"Float32"})}if(shallowCopy){collapsedDataset.setColumnMetadata(dataset.getColumnMetadata())}else{morpheus.MetadataUtil.copy(dataset.getColumnMetadata(),collapsedDataset.getColumnMetadata())}var nfields=collapseToFields.length;var collapseToVectors=[];for(var i=0;i<nfields;i++){collapseToVectors.push(collapsedDataset.getRowMetadata().add(collapseToFields[i]))}var counter=0;idToIndices.forEach(function(rowIndices,key){var slice=morpheus.DatasetUtil.slicedView(dataset,rowIndices,null);var view=new morpheus.DatasetColumnView(slice);for(var series=0;series<nseries;series++){view.setSeriesIndex(series);for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){view.setIndex(j);collapsedDataset.setValue(counter,j,summarizeFunction(view),series)}}for(var i=0;i<nfields;i++){var collapsedToVector=collapseToVectors[i];var vector=vectors[i];collapsedToVector.setValue(counter,vector.getValue(rowIndices[0]))}counter++});if(nfields===1){var newVector=collapseToVectors[0];vectors[0].getProperties().forEach(function(val,key){if(!morpheus.VectorKeys.COPY_IGNORE.has(key)){newVector.properties.set(key,val)}})}return collapsedDataset};morpheus.SelectRow=function(dataset,collapseToFields,summarizeFunction,shallowCopy){var vectors=[];var nfields=collapseToFields.length;for(var i=0;i<nfields;i++){var v=dataset.getRowMetadata().getByName(collapseToFields[i]);if(!v){throw collapseToFields[i]+" not found. Available fields are "+morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata())}vectors.push(v)}var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);var collapsedDataset=new morpheus.Dataset({name:dataset.getName(),rows:idToIndices.size(),columns:dataset.getColumnCount(),dataType:"Float32"});var nseries=dataset.getSeriesCount();for(var series=1;series<nseries;series++){collapsedDataset.addSeries({name:dataset.getName(i),dataType:"Float32"})}if(shallowCopy){collapsedDataset.setColumnMetadata(dataset.getColumnMetadata())}else{morpheus.MetadataUtil.copy(dataset.getColumnMetadata(),collapsedDataset.getColumnMetadata())}var names=morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata());var collapseToVectors=[];var allvectors=[];for(var i=0;i<names.length;i++){var v=dataset.getRowMetadata().getByName(names[i]);collapseToVectors.push(collapsedDataset.getRowMetadata().add(names[i]));allvectors.push(v)}var counter=0;idToIndices.forEach(function(rowIndices,key){var slice=morpheus.DatasetUtil.slicedView(dataset,rowIndices,null);var view=new morpheus.DatasetRowView(slice);var indexInDataset;for(var series=0;series<nseries;series++){view.setSeriesIndex(series);var chosenIndex=summarizeFunction(view).index;view.setIndex(chosenIndex);indexInDataset=view.dataset.rowIndices[chosenIndex];for(var j=0,ncols=dataset.getColumnCount();j<ncols;j++){collapsedDataset.setValue(counter,j,view.getValue(j),series)}}for(var i=0;i<names.length;i++){var collapsedToVector=collapseToVectors[i];var vector=allvectors[i];collapsedToVector.setValue(counter,vector.getValue(indexInDataset))}counter++});return collapsedDataset};morpheus.CompleteLinkage=function(nelements,distmatrix){var j;var n;var clusterid=[];var result=[];for(var i=0;i<nelements-1;i++){result[i]={left:0,right:0,distance:0}}for(j=0;j<nelements;j++){clusterid[j]=j}var r={};for(n=nelements;n>1;n--){morpheus.HCluster.findClosestPair(n,distmatrix,r);result[nelements-n].distance=r.distance;var is=r.ip;var js=r.jp;for(j=0;j<js;j++){distmatrix[js][j]=Math.max(distmatrix[is][j],distmatrix[js][j])}for(j=js+1;j<is;j++){distmatrix[j][js]=Math.max(distmatrix[is][j],distmatrix[j][js])}for(j=is+1;j<n;j++){distmatrix[j][js]=Math.max(distmatrix[j][is],distmatrix[j][js])}for(j=0;j<is;j++){distmatrix[is][j]=distmatrix[n-1][j]}for(j=is+1;j<n-1;j++){distmatrix[j][is]=distmatrix[n-1][j]}result[nelements-n].left=clusterid[is];result[nelements-n].right=clusterid[js];clusterid[js]=n-nelements-1;clusterid[is]=clusterid[n-1]}return result};morpheus.HClusterGroupBy=function(dataset,groupByFieldNames,distanceFunction,linkageMethod){var model=dataset.getRowMetadata();var vectors=morpheus.MetadataUtil.getVectors(dataset.getRowMetadata(),groupByFieldNames);var idToIndices=morpheus.VectorUtil.createValuesToIndicesMap(vectors);var reorderedIndices=[];var offset=0;var root={id:-1,children:[],height:0};var tree={maxHeight:0,rootNode:root,leafNodes:[],nLeafNodes:0};idToIndices.forEach(function(rowIndices,id){var originalIndicesForGroup=idToIndices.get(id);var subset=morpheus.DatasetUtil.slicedView(dataset,originalIndicesForGroup,null);var hcl;var distanceMatrix=morpheus.HCluster.computeDistanceMatrix(subset,distanceFunction);hcl=new morpheus.HCluster(distanceMatrix,linkageMethod);var reorderedGroupIndices=hcl.reorderedIndices;for(var i=0,rows=subset.getRowCount();i<rows;i++){var originalIndex=originalIndicesForGroup[reorderedGroupIndices[i]];reorderedIndices.push(originalIndex)}morpheus.DendrogramUtil.dfs(hcl.tree.rootNode,function(node){node.index+=offset;node.minIndex+=offset;node.maxIndex+=offset;node.id+=offset;return true});if(hcl.tree.leafNodes.length===0){tree.leafNodes=tree.leafNodes.concat([hcl.tree.rootNode])}else{tree.leafNodes=tree.leafNodes.concat(hcl.tree.leafNodes)}root.children.push(hcl.tree.rootNode);if(!isNaN(hcl.tree.maxHeight)){tree.maxHeight=Math.max(tree.maxHeight,hcl.tree.maxHeight)}offset+=subset.getRowCount()});tree.nLeafNodes=tree.leafNodes.length;tree.rootNode.height=tree.maxHeight;this.tree=tree;this.reorderedIndices=reorderedIndices};morpheus.HCluster=function(distmatrix,linkageAlgorithm){var nelements=distmatrix.length;var nNodes=nelements-1;if(nNodes===-1){var root={id:0,height:0,index:0,minIndex:0,maxIndex:0,depth:0};this.tree={maxHeight:0,rootNode:root,leafNodes:[],nLeafNodes:0};this.reorderedIndices=[0];return}var tree=linkageAlgorithm(nelements,distmatrix);var nodeorder=[];var nodecounts=[];var order=[];var nodeID=[];for(var i=0;i<nelements;i++){order[i]=i}var leftIds=[];var rightIds=[];for(var i=0;i<nNodes;i++){var min1=tree[i].left;var min2=tree[i].right;var order1;var order2;var counts1;var counts2;var ID1;var ID2;nodeID[i]=nNodes+(i+2);if(min1<0){var index1=-min1-1;order1=nodeorder[index1];counts1=nodecounts[index1];ID1=nodeID[index1];tree[i].distance=Math.max(tree[i].distance,tree[index1].distance)}else{order1=order[min1];counts1=1;ID1=min1}if(min2<0){var index2=-min2-1;order2=nodeorder[index2];counts2=nodecounts[index2];ID2=nodeID[index2];tree[i].distance=Math.max(tree[i].distance,tree[index2].distance)}else{order2=order[min2];counts2=1;ID2=min2}leftIds[i]=ID1;rightIds[i]=ID2;nodecounts[i]=counts1+counts2;nodeorder[i]=(counts1*order1+counts2*order2)/(counts1+counts2)}var reorderedIndices=morpheus.HCluster.treeSort(nNodes,order,nodeorder,nodecounts,tree);var idToIndex={};for(var i=0,length=reorderedIndices.length;i<length;i++){var index=reorderedIndices[i];idToIndex[index]=i}var nodeIdToNode={};var node;for(var i=0,length=nodeID.length;i<length;i++){var id=nodeID[i];var leftId=leftIds[i];var lnode=nodeIdToNode[leftId];if(lnode===undefined){lnode={id:leftId};var index=idToIndex[leftId];lnode.index=index;lnode.minIndex=index;lnode.maxIndex=index;nodeIdToNode[lnode.id]=lnode}var rightId=rightIds[i];var rnode=nodeIdToNode[rightId];if(rnode===undefined){rnode={id:rightId};var index=idToIndex[rightId];rnode.index=index;rnode.minIndex=index;rnode.maxIndex=index;nodeIdToNode[rnode.id]=rnode}node={id:id,children:lnode.index<rnode.index?[lnode,rnode]:[rnode,lnode],height:tree[i].distance,index:(rnode.index+lnode.index)/2};node.minIndex=Math.min(rnode.minIndex,lnode.minIndex);node.maxIndex=Math.max(rnode.maxIndex,lnode.maxIndex);lnode.parent=node;rnode.parent=node;nodeIdToNode[node.id]=node}this.reorderedIndices=reorderedIndices;var leafNodes=[];for(var i=0,length=reorderedIndices.length;i<length;i++){var leaf=nodeIdToNode[reorderedIndices[i]];leaf.height=0;leafNodes.push(leaf)}morpheus.DendrogramUtil.setNodeDepths(node);this.tree={maxHeight:node.height,rootNode:node,leafNodes:leafNodes,nLeafNodes:leafNodes.length}};morpheus.HCluster.findClosestPair=function(n,distmatrix,r){var i,j;var temp;var distance=distmatrix[1][0];var ip=1;var jp=0;for(i=1;i<n;i++){for(j=0;j<i;j++){temp=distmatrix[i][j];if(temp<distance){distance=temp;ip=i;jp=j}}}r.distance=distance;r.ip=ip;r.jp=jp};morpheus.HCluster.computeDistanceMatrix=function(dataset,distanceFunction){var matrix=[];var n=dataset.getRowCount();for(var i=1;i<n;i++){matrix[i]=new Float32Array(i)}if(distanceFunction===0){for(var i=1;i<n;i++){for(var j=0;j<i;j++){matrix[i][j]=dataset.getValue(i,j)}}}else if(distanceFunction===1){var max=-Number.MAX_VALUE;for(var i=1;i<n;i++){for(var j=0;j<i;j++){var value=dataset.getValue(i,j);if(!isNaN(value)){max=Math.max(value,max)}}}for(var i=1;i<n;i++){for(var j=0;j<i;j++){matrix[i][j]=max-dataset.getValue(i,j)}}}else{var list1=new morpheus.DatasetRowView(dataset);var list2=new morpheus.DatasetRowView(dataset);for(var i=1;i<n;i++){list1.setIndex(i);for(var j=0;j<i;j++){matrix[i][j]=distanceFunction(list1,list2.setIndex(j))}}}return matrix};morpheus.HCluster.treeSort=function(nNodes,order,nodeorder,nodecounts,tree){var nElements=nNodes+1;var i;var neworder=[];var clusterids=[];for(i=0;i<nElements;i++){clusterids[i]=i;neworder[i]=0}for(i=0;i<nNodes;i++){var i1=tree[i].left;var i2=tree[i].right;var order1=i1<0?nodeorder[-i1-1]:order[i1];var order2=i2<0?nodeorder[-i2-1]:order[i2];var count1=i1<0?nodecounts[-i1-1]:1;var count2=i2<0?nodecounts[-i2-1]:1;if(i1<i2){var increase=order1<order2?count1:count2;var j;for(j=0;j<nElements;j++){var clusterid=clusterids[j];if(clusterid==i1&&order1>=order2){neworder[j]+=increase}if(clusterid==i2&&order1<order2){neworder[j]+=increase}if(clusterid==i1||clusterid==i2){clusterids[j]=-i-1}}}else{var increase=order1<=order2?count1:count2;var j;for(j=0;j<nElements;j++){var clusterid=clusterids[j];if(clusterid==i1&&order1>order2){neworder[j]+=increase}if(clusterid==i2&&order1<=order2){neworder[j]+=increase}if(clusterid==i1||clusterid==i2){clusterids[j]=-i-1}}}}return morpheus.Util.indexSort(neworder,true)};morpheus.KMeansPlusPlusClusterer=function(k,maxIterations,distanceFunction){var distance=function(points1,points2){return distanceFunction(points1.getPoint(),points2.getPoint())};function nextInt(upperBound){return Math.floor(Math.random()*upperBound)|0}function nextDouble(){return Math.random()}function PointWrapper(point){this.getPoint=function(){return point}}function CentroidCluster(center){var centroidPoints=[];this.addPoint=function(p){centroidPoints.push(p)};this.getPoints=function(){return centroidPoints};this.getCenter=function(){return center}}function cluster(points){if(points.length<k){throw"Too many clusters"}var clusters=chooseInitialCenters(points);var assignments=new Int32Array(points.length);assignPointsToClusters(clusters,points,assignments);var max=maxIterations<0?Number.MAX_VALUE:maxIterations;for(var count=0;count<max;count++){var emptyCluster=false;var newClusters=[];for(var clusterIndex=0;clusterIndex<clusters.length;clusterIndex++){var cluster=clusters[clusterIndex];var newCenter;if(cluster.getPoints().length===0){newCenter=getPointFromLargestVarianceCluster(clusters);emptyCluster=true}else{newCenter=centroidOf(cluster.getPoints(),cluster.getCenter().getPoint().size())}newClusters.push(new CentroidCluster(newCenter))}var changes=assignPointsToClusters(newClusters,points,assignments);clusters=newClusters;if(changes===0&&!emptyCluster){return clusters}}return clusters}function assignPointsToClusters(clusters,points,assignments){var assignedDifferently=0;var pointIndex=0;for(var i=0;i<points.length;i++){var p=points[i];var clusterIndex=getNearestCluster(clusters,p);if(clusterIndex!=assignments[pointIndex]){assignedDifferently++}var cluster=clusters[clusterIndex];cluster.addPoint(p);assignments[pointIndex++]=clusterIndex}return assignedDifferently}function chooseInitialCenters(points){var pointList=points;var numPoints=pointList.length;var taken=new Array(numPoints);for(var i=0;i<taken.length;i++){taken[i]=false}var resultSet=[];var firstPointIndex=nextInt(numPoints);var firstPoint=pointList[firstPointIndex];resultSet.push(new CentroidCluster(firstPoint));taken[firstPointIndex]=true;var minDistSquared=new Float32Array(numPoints);for(var i=0;i<numPoints;i++){if(i!==firstPointIndex){var d=distance(firstPoint,pointList[i]);minDistSquared[i]=d*d}}while(resultSet.length<k){var distSqSum=0;for(var i=0;i<numPoints;i++){if(!taken[i]){distSqSum+=minDistSquared[i]}}var r=nextDouble()*distSqSum;var nextPointIndex=-1;var sum=0;for(var i=0;i<numPoints;i++){if(!taken[i]){sum+=minDistSquared[i];if(sum>=r){nextPointIndex=i;break}}}if(nextPointIndex===-1){for(var i=numPoints-1;i>=0;i--){if(!taken[i]){nextPointIndex=i;break}}}if(nextPointIndex>=0){var p=pointList[nextPointIndex];resultSet.push(new CentroidCluster(p));taken[nextPointIndex]=true;if(resultSet.length<k){for(var j=0;j<numPoints;j++){if(!taken[j]){var d=distance(p,pointList[j]);var d2=d*d;if(d2<minDistSquared[j]){minDistSquared[j]=d2}}}}}else{break}}return resultSet}function getPointFromLargestVarianceCluster(clusters){var maxVariance=-Number.MAX_VALUE;var selected=null;for(var clusterIndex=0;clusterIndex<clusters.length;clusterIndex++){var cluster=clusters[clusterIndex];if(cluster.getPoints().length>0){var center=cluster.getCenter();var points=cluster.getPoints();var distances=new Float32Array(points.length);for(var i=0;i<points.length;i++){distances[i]=distance(points[i],center)}var variance=morpheus.Variance(morpheus.VectorUtil.arrayAsVector(distances));if(variance>maxVariance){maxVariance=variance;selected=cluster}}}if(selected==null){throw"All clusters are empty"}var selectedPoints=selected.getPoints();return selectedPoints.splice(nextInt(selectedPoints.length),1)}function getNearestCluster(clusters,point){var minDistance=Number.MAX_VALUE;var clusterIndex=0;var minCluster=0;for(var i=0;i<clusters.length;i++){var c=clusters[i];var d=distance(point,c.getCenter());if(d<minDistance){minDistance=d;minCluster=clusterIndex}clusterIndex++}return minCluster}function centroidOf(points,dimension){var centroid=new Float32Array(dimension);for(var i=0;i<centroid.length;i++){var sum=0;var count=0;for(var pointIndex=0;pointIndex<points.length;pointIndex++){var p=points[pointIndex];var point=p.getPoint();var val=point.getValue(i);if(!isNaN(val)){sum+=val;count++}}centroid[i]=sum/count}return new PointWrapper(morpheus.VectorUtil.arrayAsVector(centroid))}this.execute=function(vectors){var points=[];var npoints=vectors.length;for(var i=0;i<npoints;i++){var p=new PointWrapper(vectors[i]);p.i=i;points.push(p)}return cluster(points)};this.cluster=cluster};morpheus.PermutationPValues=function(dataset,aIndices,bIndices,numPermutations,f,continuousList){var numRows=dataset.getRowCount();var scores=new Float32Array(numRows);var smoothPValues=true;var permuter;var permutationScore;if(aIndices!=null){var list1=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,aIndices));var list2=new morpheus.DatasetRowView(new morpheus.SlicedDatasetView(dataset,null,bIndices));dataset=new morpheus.SlicedDatasetView(dataset,null,aIndices.concat(bIndices));permuter=new morpheus.UnbalancedPermuter(aIndices.length,bIndices.length);permutationScore=new morpheus.TwoClassPermutationScore;permutationScore.init(dataset,f);for(var i=0;i<numRows;i++){scores[i]=f(list1.setIndex(i),list2.setIndex(i))}}else{permuter=new morpheus.UnbalancedContinuousPermuter(continuousList.size());permutationScore=new morpheus.ContinuousPermutationScore(continuousList);permutationScore.init(dataset,f);var list=new morpheus.DatasetRowView(dataset);for(var i=0;i<numRows;i++){scores[i]=f(continuousList,list.setIndex(i))}}var rowSpecificPValues=new Float32Array(numRows);for(var permutationIndex=0;permutationIndex<numPermutations;permutationIndex++){permutationScore.setPermutation(permuter.next());for(var i=0;i<numRows;i++){var permutedScore=permutationScore.getScore(i);var score=scores[i];if(permutedScore>=score){rowSpecificPValues[i]++}}}var N=numPermutations;var kArray=new Uint32Array(numRows);for(var i=0;i<numRows;i++){var k=rowSpecificPValues[i];kArray[i]=k;var p;if(smoothPValues){p=(k+1)/(N+2)}else{p=k/N}var oneMinusP=1-p;if(oneMinusP<p){p=oneMinusP}p*=2;if(p===0){var val=dataset.getValue(i,0);var flat=true;for(var j=1,cols=dataset.getColumnCount();j<cols&&flat;j++){if(dataset.getValue(i,j)!=val){flat=false}}if(flat){p=1}}rowSpecificPValues[i]=p}this.rowSpecificPValues=rowSpecificPValues;this.k=kArray;this.fdr=morpheus.FDR_BH(rowSpecificPValues);this.scores=scores};morpheus.PermutationPValues.prototype={getBonferroni:function(index){return Math.min(this.rowSpecificPValues[index]*this.numRows,1)}};morpheus.UnbalancedContinuousPermuter=function(size){var indices=new Uint32Array(size);for(var i=0;i<indices.length;i++){indices[i]=i}var n=indices.length;function getRandomIntInclusive(min,max){return Math.floor(Math.random()*(max-min+1))+min}this.next=function(){for(var i=n-1;i>=1;i--){var j=getRandomIntInclusive(0,i);var tmp=indices[j];indices[j]=indices[i];indices[i]=tmp}return indices}};morpheus.UnbalancedPermuter=function(numClassZero,numClassOne){var assignments=new Uint32Array(numClassZero+numClassOne);var indices=new Uint32Array(numClassZero+numClassOne);for(var i=0;i<indices.length;i++){indices[i]=i}var n=indices.length;function getRandomIntInclusive(min,max){return Math.floor(Math.random()*(max-min+1))+min}this.next=function(){for(var i=n-1;i>=1;i--){var j=getRandomIntInclusive(0,i);var tmp=indices[j];indices[j]=indices[i];indices[i]=tmp}for(var i=0;i<n;i++){assignments[i]=0}for(var i=0;i<numClassOne;i++){assignments[indices[i]]=1}return assignments}};morpheus.TwoClassPermutationScore=function(){this.classZeroView=null;this.classOneView=null};morpheus.TwoClassPermutationScore.prototype={getScore:function(index){this.classZeroView.setIndex(index);this.classOneView.setIndex(index);return this.f(this.classZeroView,this.classOneView)},init:function(dataset,f){this.dataset=dataset;this.classZeroView=new morpheus.DatasetRowView(dataset);this.classOneView=new morpheus.DatasetRowView(dataset);this.f=f},setPermutation:function(permutedAssignments){var zeroIndices=[];var oneIndices=[];for(var i=0,length=permutedAssignments.length;i<length;i++){if(permutedAssignments[i]===0){zeroIndices.push(i)}else{oneIndices.push(i)}}this.classZeroView.setDataset(new morpheus.SlicedDatasetView(this.dataset,null,zeroIndices));this.classOneView.setDataset(new morpheus.SlicedDatasetView(this.dataset,null,oneIndices))}};morpheus.ContinuousPermutationScore=function(referenceList){this.referenceList=referenceList};morpheus.ContinuousPermutationScore.prototype={getScore:function(index){this.datasetRowView.setIndex(index);return this.f(this.referenceListView,this.datasetRowView)},init:function(dataset,f){this.dataset=dataset;this.referenceListView=null;this.datasetRowView=new morpheus.DatasetRowView(dataset);this.f=f},setPermutation:function(indices){this.referenceListView=new morpheus.SlicedVector(this.referenceList,indices)}};morpheus.Ranking=function(values){var ranks=[];for(var i=0,length=values.length;i<length;i++){ranks.push({value:values[i],position:i})}if(ranks.length===0){return[]}ranks.sort(function(a,b){return a.value<b.value?-1:a.value===b.value?0:1});var out=[];var pos=1;out[ranks[0].position]=pos;var tiesTrace=[];tiesTrace.push(ranks[0].position);for(var i=1;i<ranks.length;i++){if(ranks[i].value>ranks[i-1].value){pos=i+1;if(tiesTrace.length>1){morpheus.Ranking.fillAverage(out,tiesTrace)}tiesTrace=[];tiesTrace.push(ranks[i].position)}else{tiesTrace.push(ranks[i].position)}out[ranks[i].position]=pos}if(tiesTrace.length>1){morpheus.Ranking.fillAverage(out,tiesTrace)}return out};morpheus.Ranking.fill=function(data,tiesTrace,value){for(var i=0,length=tiesTrace.length;i<length;i++){data[tiesTrace[i]]=value}};morpheus.Ranking.fillAverage=function(ranks,tiesTrace){var c=ranks[tiesTrace[0]];var length=tiesTrace.length;morpheus.Ranking.fill(ranks,tiesTrace,(2*c+length-1)/2)};morpheus.SingleLinkage=function(nelements,distmatrix){var i,j,k;var nnodes=nelements-1;var temp=[];var index=[];var vector=[];var result=[];for(i=0;i<nelements;i++){result[i]={left:0,right:0,distance:0}}for(i=0;i<nnodes;i++){vector[i]=i}for(i=0;i<nelements;i++){result[i].distance=Number.MAX_VALUE;for(j=0;j<i;j++){temp[j]=distmatrix[i][j]}for(j=0;j<i;j++){k=vector[j];if(result[j].distance>=temp[j]){if(result[j].distance<temp[k]){temp[k]=result[j].distance}result[j].distance=temp[j];vector[j]=i}else if(temp[j]<temp[k]){temp[k]=temp[j]}}for(j=0;j<i;j++){if(result[j].distance>=result[vector[j]].distance){vector[j]=i}}}for(i=0;i<nnodes;i++){result[i].left=i}result.sort(function(node1,node2){var term1=node1.distance;var term2=node2.distance;if(term1<term2)return-1;if(term1>term2)return+1;return 0});for(i=0;i<nelements;i++){index[i]=i}for(i=0;i<nnodes;i++){j=result[i].left;k=vector[j];result[i].left=index[j];result[i].right=index[k];index[k]=-i-1}var result2=[];for(i=0;i<nelements-1;i++){result2[i]=result[i]}return result2}})(typeof window!=="undefined"?window:this);
\ No newline at end of file
diff --git a/js/morpheus.js b/js/morpheus.js
index d999a42e..40a1ef80 100644
--- a/js/morpheus.js
+++ b/js/morpheus.js
@@ -8591,6 +8591,43 @@ morpheus.MolarConcentration.CONCENTRATIONS = [
 
 
 
+morpheus.MaximumMeanProbe = function(probes) {
+  return morpheus.MaximumUnivariateFunction(probes, morpheus.Mean);
+};
+
+morpheus.MaximumMeanProbe.toString = function() {
+  return "Maximum Mean Probe";
+};
+
+morpheus.MaximumMeanProbe.selectOne = true;
+
+morpheus.MaximumMedianProbe = function(probes) {
+  return morpheus.MaximumUnivariateFunction(probes, morpheus.Median);
+};
+
+morpheus.MaximumMedianProbe.toString = function() {
+  return "Maximum Median Probe";
+};
+
+morpheus.MaximumMedianProbe.selectOne = true;
+
+morpheus.MaximumUnivariateFunction = function(rowView, fun) {
+  var curMax = Number.NEGATIVE_INFINITY;
+  var curIndex = -1;
+  for (var i = 0; i < rowView.dataset.getRowCount(); i++) {
+    rowView.setIndex(i);
+    var mean = fun(rowView);
+    if (mean > curMax) {
+      curMax = mean;
+      curIndex = i;
+    }
+  }
+  return {
+    value : curMax,
+    index : curIndex
+  }
+};
+
 morpheus.Positions = function () {
   this.spaces = undefined;
   this.defaultPositionFunction = function (index) {
@@ -13317,7 +13354,8 @@ morpheus.ChartTool.getTooltip = function (options) {
 morpheus.CollapseDatasetTool = function () {
 };
 morpheus.CollapseDatasetTool.Functions = [morpheus.Mean, morpheus.Median,
-  new morpheus.MaxPercentiles([25, 75]), morpheus.Min, morpheus.Max, morpheus.Percentile, morpheus.Sum];
+  new morpheus.MaxPercentiles([25, 75]), morpheus.Min, morpheus.Max, morpheus.Percentile, morpheus.Sum,
+  morpheus.MaximumMeanProbe, morpheus.MaximumMedianProbe];
 morpheus.CollapseDatasetTool.Functions.fromString = function (s) {
   for (var i = 0; i < morpheus.CollapseDatasetTool.Functions.length; i++) {
     if (morpheus.CollapseDatasetTool.Functions[i].toString() === s) {
@@ -13344,6 +13382,7 @@ morpheus.CollapseDatasetTool.prototype = {
     form.setVisible('percentile', false);
     form.$form.find('[name=collapse_method]').on('change', function (e) {
       form.setVisible('percentile', $(this).val() === morpheus.Percentile.toString());
+      form.setVisible('collapse', !morpheus.CollapseDatasetTool.Functions.fromString($(this).val()).selectOne);
     });
 
     setValue('Rows');
@@ -13392,7 +13431,8 @@ morpheus.CollapseDatasetTool.prototype = {
     }
     var allFields = morpheus.MetadataUtil.getMetadataNames(dataset
     .getRowMetadata());
-    dataset = morpheus.CollapseDataset(dataset, collapseToFields, f, true);
+    var collapseMethod = f.selectOne ? morpheus.SelectRow : morpheus.CollapseDataset;
+    dataset = collapseMethod(dataset, collapseToFields, f, true);
     if (!rows) {
       dataset = new morpheus.TransposedDatasetView(dataset);
     }
@@ -13404,9 +13444,9 @@ morpheus.CollapseDatasetTool.prototype = {
       set.remove(field);
     });
     // hide fields that were not part of collapse to
-    set.forEach(function (val, name) {
-      heatMap.setTrackVisible(name, false, !rows);
-    });
+    // set.forEach(function (val, name) {
+    //   heatMap.setTrackVisible(name, false, !rows);
+    // });
     return new morpheus.HeatMap({
       name: heatMap.getName(),
       dataset: dataset,
@@ -38056,6 +38096,86 @@ morpheus.CollapseDataset = function (dataset, collapseToFields,
   return collapsedDataset;
 };
 
+
+morpheus.SelectRow = function (dataset, collapseToFields,
+                                summarizeFunction, shallowCopy) {
+  var vectors = [];
+  var nfields = collapseToFields.length;
+
+  for (var i = 0; i < nfields; i++) {
+    var v = dataset.getRowMetadata().getByName(collapseToFields[i]);
+    if (!v) {
+      throw collapseToFields[i]
+      + ' not found. Available fields are '
+      + morpheus.MetadataUtil.getMetadataNames(dataset
+        .getRowMetadata());
+    }
+    vectors.push(v);
+  }
+
+  var idToIndices = morpheus.VectorUtil.createValuesToIndicesMap(vectors);
+
+  var collapsedDataset = new morpheus.Dataset({
+    name: dataset.getName(),
+    rows: idToIndices.size(),
+    columns: dataset.getColumnCount(),
+    dataType: 'Float32'
+  });
+
+
+  var nseries = dataset.getSeriesCount();
+  for (var series = 1; series < nseries; series++) {
+    collapsedDataset.addSeries({
+      name: dataset.getName(i),
+      dataType: 'Float32'
+    });
+  }
+  if (shallowCopy) {
+    collapsedDataset.setColumnMetadata(dataset.getColumnMetadata());
+  } else {
+    morpheus.MetadataUtil.copy(dataset.getColumnMetadata(),
+      collapsedDataset.getColumnMetadata());
+  }
+
+  var names = morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata());
+  var collapseToVectors = [];
+  var allvectors = [];
+  for (var i = 0; i < names.length; i++) {
+    var v = dataset.getRowMetadata().getByName(names[i]);
+    collapseToVectors.push(collapsedDataset.getRowMetadata().add(names[i]));
+    allvectors.push(v);
+  }
+
+  var counter = 0;
+
+  idToIndices
+    .forEach(function (rowIndices, key) {
+      var slice = morpheus.DatasetUtil.slicedView(dataset,
+        rowIndices, null);
+      var view = new morpheus.DatasetRowView(slice);
+      var indexInDataset;
+      for (var series = 0; series < nseries; series++) {
+        view.setSeriesIndex(series);
+        var chosenIndex = summarizeFunction(view).index;
+        view.setIndex(chosenIndex);
+        indexInDataset = view.dataset.rowIndices[chosenIndex];
+
+        for (var j = 0, ncols = dataset.getColumnCount(); j < ncols; j++) {
+          collapsedDataset.setValue(counter, j,
+            view.getValue(j), series);
+        }
+      }
+      for (var i = 0; i < names.length; i++) {
+        var collapsedToVector = collapseToVectors[i];
+        var vector = allvectors[i];
+        collapsedToVector.setValue(counter, vector
+          .getValue(indexInDataset));
+      }
+      counter++;
+    });
+  return collapsedDataset;
+};
+
 morpheus.CompleteLinkage = function (nelements, distmatrix) {
   var j;
   var n;
diff --git a/src/algorithm/collapse_dataset.js b/src/algorithm/collapse_dataset.js
index e488a025..ce0d1658 100644
--- a/src/algorithm/collapse_dataset.js
+++ b/src/algorithm/collapse_dataset.js
@@ -70,3 +70,83 @@ morpheus.CollapseDataset = function (dataset, collapseToFields,
   }
   return collapsedDataset;
 };
+
+
+morpheus.SelectRow = function (dataset, collapseToFields,
+                                summarizeFunction, shallowCopy) {
+  var vectors = [];
+  var nfields = collapseToFields.length;
+
+  for (var i = 0; i < nfields; i++) {
+    var v = dataset.getRowMetadata().getByName(collapseToFields[i]);
+    if (!v) {
+      throw collapseToFields[i]
+      + ' not found. Available fields are '
+      + morpheus.MetadataUtil.getMetadataNames(dataset
+        .getRowMetadata());
+    }
+    vectors.push(v);
+  }
+
+  var idToIndices = morpheus.VectorUtil.createValuesToIndicesMap(vectors);
+
+  var collapsedDataset = new morpheus.Dataset({
+    name: dataset.getName(),
+    rows: idToIndices.size(),
+    columns: dataset.getColumnCount(),
+    dataType: 'Float32'
+  });
+
+
+  var nseries = dataset.getSeriesCount();
+  for (var series = 1; series < nseries; series++) {
+    collapsedDataset.addSeries({
+      name: dataset.getName(i),
+      dataType: 'Float32'
+    });
+  }
+  if (shallowCopy) {
+    collapsedDataset.setColumnMetadata(dataset.getColumnMetadata());
+  } else {
+    morpheus.MetadataUtil.copy(dataset.getColumnMetadata(),
+      collapsedDataset.getColumnMetadata());
+  }
+
+  var names = morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata());
+  var collapseToVectors = [];
+  var allvectors = [];
+  for (var i = 0; i < names.length; i++) {
+    var v = dataset.getRowMetadata().getByName(names[i]);
+    collapseToVectors.push(collapsedDataset.getRowMetadata().add(names[i]));
+    allvectors.push(v);
+  }
+
+  var counter = 0;
+
+  idToIndices
+    .forEach(function (rowIndices, key) {
+      var slice = morpheus.DatasetUtil.slicedView(dataset,
+        rowIndices, null);
+      var view = new morpheus.DatasetRowView(slice);
+      var indexInDataset;
+      for (var series = 0; series < nseries; series++) {
+        view.setSeriesIndex(series);
+        var chosenIndex = summarizeFunction(view).index;
+        view.setIndex(chosenIndex);
+        indexInDataset = view.dataset.rowIndices[chosenIndex];
+
+        for (var j = 0, ncols = dataset.getColumnCount(); j < ncols; j++) {
+          collapsedDataset.setValue(counter, j,
+            view.getValue(j), series);
+        }
+      }
+      for (var i = 0; i < names.length; i++) {
+        var collapsedToVector = collapseToVectors[i];
+        var vector = allvectors[i];
+        collapsedToVector.setValue(counter, vector
+          .getValue(indexInDataset));
+      }
+      counter++;
+    });
+  return collapsedDataset;
+};
diff --git a/src/matrix/multivariate_functions.js b/src/matrix/multivariate_functions.js
new file mode 100644
index 00000000..5bf44aa7
--- /dev/null
+++ b/src/matrix/multivariate_functions.js
@@ -0,0 +1,36 @@
+morpheus.MaximumMeanProbe = function(probes) {
+  return morpheus.MaximumUnivariateFunction(probes, morpheus.Mean);
+};
+
+morpheus.MaximumMeanProbe.toString = function() {
+  return "Maximum Mean Probe";
+};
+
+morpheus.MaximumMeanProbe.selectOne = true;
+
+morpheus.MaximumMedianProbe = function(probes) {
+  return morpheus.MaximumUnivariateFunction(probes, morpheus.Median);
+};
+
+morpheus.MaximumMedianProbe.toString = function() {
+  return "Maximum Median Probe";
+};
+
+morpheus.MaximumMedianProbe.selectOne = true;
+
+morpheus.MaximumUnivariateFunction = function(rowView, fun) {
+  var curMax = Number.NEGATIVE_INFINITY;
+  var curIndex = -1;
+  for (var i = 0; i < rowView.dataset.getRowCount(); i++) {
+    rowView.setIndex(i);
+    var mean = fun(rowView);
+    if (mean > curMax) {
+      curMax = mean;
+      curIndex = i;
+    }
+  }
+  return {
+    value : curMax,
+    index : curIndex
+  }
+};
diff --git a/src/tools/collapse_dataset_tool.js b/src/tools/collapse_dataset_tool.js
index a0aaf557..b84178f2 100644
--- a/src/tools/collapse_dataset_tool.js
+++ b/src/tools/collapse_dataset_tool.js
@@ -1,7 +1,8 @@
 morpheus.CollapseDatasetTool = function () {
 };
 morpheus.CollapseDatasetTool.Functions = [morpheus.Mean, morpheus.Median,
-  new morpheus.MaxPercentiles([25, 75]), morpheus.Min, morpheus.Max, morpheus.Percentile, morpheus.Sum];
+  new morpheus.MaxPercentiles([25, 75]), morpheus.Min, morpheus.Max, morpheus.Percentile, morpheus.Sum,
+  morpheus.MaximumMeanProbe, morpheus.MaximumMedianProbe];
 morpheus.CollapseDatasetTool.Functions.fromString = function (s) {
   for (var i = 0; i < morpheus.CollapseDatasetTool.Functions.length; i++) {
     if (morpheus.CollapseDatasetTool.Functions[i].toString() === s) {
@@ -28,6 +29,7 @@ morpheus.CollapseDatasetTool.prototype = {
     form.setVisible('percentile', false);
     form.$form.find('[name=collapse_method]').on('change', function (e) {
       form.setVisible('percentile', $(this).val() === morpheus.Percentile.toString());
+      form.setVisible('collapse', !morpheus.CollapseDatasetTool.Functions.fromString($(this).val()).selectOne);
     });
 
     setValue('Rows');
@@ -76,7 +78,8 @@ morpheus.CollapseDatasetTool.prototype = {
     }
     var allFields = morpheus.MetadataUtil.getMetadataNames(dataset
     .getRowMetadata());
-    dataset = morpheus.CollapseDataset(dataset, collapseToFields, f, true);
+    var collapseMethod = f.selectOne ? morpheus.SelectRow : morpheus.CollapseDataset;
+    dataset = collapseMethod(dataset, collapseToFields, f, true);
     if (!rows) {
       dataset = new morpheus.TransposedDatasetView(dataset);
     }
@@ -88,9 +91,9 @@ morpheus.CollapseDatasetTool.prototype = {
       set.remove(field);
     });
     // hide fields that were not part of collapse to
-    set.forEach(function (val, name) {
-      heatMap.setTrackVisible(name, false, !rows);
-    });
+    // set.forEach(function (val, name) {
+    //   heatMap.setTrackVisible(name, false, !rows);
+    // });
     return new morpheus.HeatMap({
       name: heatMap.getName(),
       dataset: dataset,