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[Treebase-guts] SF.net SVN: treebase:[869] trunk/treebase-web/src/main/webapp/scripts/ jsphylosvg-min.js
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From: <rv...@us...> - 2011-05-17 19:20:07
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Revision: 869
http://treebase.svn.sourceforge.net/treebase/?rev=869&view=rev
Author: rvos
Date: 2011-05-17 19:19:58 +0000 (Tue, 17 May 2011)
Log Message:
-----------
Using the uncompressed version for debugging purposes.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-16 16:38:51 UTC (rev 868)
+++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-17 19:19:58 UTC (rev 869)
@@ -1,73 +1,2491 @@
-Smits={};
-Smits.Common={nodeIdIncrement:0,activeNode:0,roundFloat:function(a,c){for(var b=0,f=1;b<c;)f*=10,b++;return Math.round(a*f)/f},apply:function(a,c){if(a&&typeof c=="object")for(var b in c)a[b]=c[b];return a},addEventHandler:function(a,c,b,f){try{a.addEventListener(c,function(a){return function(c){f.e=c;a(f)}}(b,f),!1)}catch(l){}},isInteger:function(a){return!isNaN(parseInt(a))},isXMLSerializerAvailable:function(){return typeof XMLSerializer=="function"?!0:!1},createSvgEl:function(a,c){a=document.createElementNS("http://www.w3.org/2000/svg",a);
-if(c)for(var b in c)c.hasOwnProperty(b)&&a.setAttribute(b,String(c[b]));return a},createGradientEl:function(a,c,b){if(c.type!="radialGradient")return!1;a=Smits.Common.createSvgEl("radialGradient",{id:a,gradientUnits:"userSpaceOnUse",cx:b[0],cy:b[1],r:b[2],fx:b[0],fy:b[1]});if(c.stop){c=c.stop;for(b=0;b<c.length;b++){var f=c[b];f["@attributes"]?a.appendChild(Smits.Common.createSvgEl("stop",f["@attributes"])):(f._attributes&&delete f._attributes,f._children&&delete f._children,f.__proto__&&delete f.__proto__,
-a.appendChild(Smits.Common.createSvgEl("stop",f)))}}return a},setCssStyle:function(a,c){var b=document.styleSheets[0];b.addRule?b.addRule(a,c):b.insertRule&&b.insertRule(a+" { "+c+" }",b.cssRules.length)}};
-Smits.PhyloCanvas=function(){var a,c,b,f;return function(l,m,q,g,n){this.getNewickObject=function(){};this.clear=function(){};this.scale=function(d){b.svg.scale(d)};this.getSvg=function(){return b};this.getPhylogram=function(){return a};this.getSvgSource=function(){return Raphael.svg&&Smits.Common.isXMLSerializerAvailable()?(new XMLSerializer).serializeToString(b.svg.canvas):!1};if(typeof l==="object")if(l.xml){var d=l.fileSource?l.xml:XMLObjectifier.textToXML(l.xml),d=XMLObjectifier.xmlToJSON(d);
-f=new Smits.PhyloCanvas.PhyloxmlParse(d)}else l.phyloxml?(d=l.fileSource?l.phyloxml:XMLObjectifier.textToXML(l.phyloxml),d=XMLObjectifier.xmlToJSON(d),f=new Smits.PhyloCanvas.PhyloxmlParse(d)):l.nexml?(d=l.fileSource?l.nexml:XMLObjectifier.textToXML(l.nexml),d=XMLObjectifier.xmlToJSON(d),f=new Smits.PhyloCanvas.NexmlParse(d,l)):l.json?f=new Smits.PhyloCanvas.PhyloxmlParse(l.json):l.newick?f=new Smits.PhyloCanvas.NewickParse(l.newick):l.nexmlJson?f=new Smits.PhyloCanvas.NexmlJsonParse(l):alert("Please set the format of input data");
-else f=new Smits.PhyloCanvas.NewickParse(l);c=m;b=new Smits.PhyloCanvas.Render.SVG(c,q,g);a=n=="circular"?new Smits.PhyloCanvas.Render.CircularPhylogram(b,f):new Smits.PhyloCanvas.Render.Phylogram(b,f)}}();Smits.PhyloCanvas.prototype={};Smits.PhyloCanvas.Node=function(){return function(a,c){this.id=Smits.Common.nodeIdIncrement+=1;this.newickLen=this.len=this.level=0;this.type=this.name="";this.chart={};this.img=[];a&&Smits.Common.apply(this,a);this.children=[];c&&c.children.push(this)}}();
-Smits.PhyloCanvas.Node.prototype={getCountAllChildren:function(){var a=0,c;for(c in this.children)if(Smits.Common.isInteger(c)){var b=this.children[c];b.children&&b.children.length>0?a+=b.getCountAllChildren():a++}return a},getCountImmediateChildren:function(){var a=0,c;for(c in this.children)a+=this.children[c].length;return a},getMidbranchPosition:function(){for(var a=[0,0],c=0;c<this.children.length;c++){var b=this.children[c];b.children&&b.children.length>0?c==0?(a[0]=b.getMidbranchPosition(),
-a[1]+=b.getCountAllChildren()):a[1]+=c==this.children.length-1?b.getMidbranchPosition():b.getCountAllChildren():(c==0&&(a[0]=1),a[1]+=1)}return a[1]>=a[0]?(a[1]-a[0])/2+a[0]:a[0]}};
-Smits.PhyloCanvas.NewickParse=function(){var a,c,b,f=0,l=0,m,q=function(a){for(var e=new Smits.PhyloCanvas.Node;c!==")"&&c!==",";)if(c===":"){if(d(),e.len=Smits.Common.roundFloat(n(),4),e.len==0)e.len=1.0E-4}else if(c==="'"||c==='"'){e.type="label";for(var g=e,k=c,b="";c!==k;)b+=c,d();g.name=b}else e.type="label",e.name=n();e.level=a.level+1;return e},g=function(a){var e=new Smits.PhyloCanvas.Node;if(a)e.level=a.level+1;for(;c!==")";)d(),c==="("?e.children.push(g(e)):e.children.push(q(e));d();if(c!==
-":"&&c!==")"&&c!==","&&c!==";")e.type="label",e.name=n();if(c===":"){d();e.len=Smits.Common.roundFloat(n(),4);if(e.len==0)e.len=1.0E-4;e.type="stem"}return e},n=function(){for(var a="";c!==":"&&c!==")"&&c!==","&&c!==";";)a+=c,d();return a},d=function(){c=a.charAt(b);b+=1;return c},k=function(d){if(d.children&&d.children.length)for(var a=0;a<d.children.length;a++){var c=d.children[a];if(c.len===0)c.len=1;c.newickLen=Smits.Common.roundFloat(c.len+d.newickLen,4);if(c.level>f)f=c.level;if(c.newickLen>
-l)l=c.newickLen;c.children.length>0&&k(c,d)}return d};return function(c){this.getRoot=function(){return m};this.getLevels=function(){return f};this.getNewickLen=function(){return l};this.getValidate=function(){};a=c;b=0;d();m=g();m=k(m)}}();Smits.PhyloCanvas.NewickParse.prototype={};
-Smits.PhyloCanvas.PhyloxmlParse=function(){var a=0,c=0,b,f,l=function(a,c){var d=new Smits.PhyloCanvas.Node;if(c)d.level=c.level+1;if(a.clade&&a.clade.length)for(var k=0;k<a.clade.length;k++)d.children.push(l(a.clade[k],d));if(a.branch_length){if(typeof a.branch_length==="object")a.branch_length=a.branch_length[0].Text;d.len=Smits.Common.roundFloat(a.branch_length,4);if(d.len==0)d.len=1.0E-4}if(a.name){d.type="label";d.name=a.name[0].Text;if(a.name[0]&&a.name[0].style)d.style=a.name[0].style;if(a.name[0]&&
-a.name[0].bgStyle)d.bgStyle=a.name[0].bgStyle}else if(a.confidence)d.name=a.confidence[0].Text;if(a.sequence&&a.sequence[0]&&a.sequence[0].name&&a.sequence[0].name[0]&&a.sequence[0].name[0].Text)d.sequenceName=a.sequence[0].name[0].Text;if(a.taxonomy&&a.taxonomy[0]){if(a.taxonomy[0].scientific_name&&a.taxonomy[0].scientific_name[0]&&a.taxonomy[0].scientific_name[0].Text)d.taxonomyScientificName=a.taxonomy[0].scientific_name[0].Text;if(a.taxonomy[0].common_name&&a.taxonomy[0].common_name[0]&&a.taxonomy[0].common_name[0].Text)d.taxonomyCommonName=
-a.taxonomy[0].common_name[0].Text}if(a.sequence&&a.sequence[0]&&a.sequence[0].accession&&a.sequence[0].accession[0]&&a.sequence[0].accession[0].Text)d.sequenceAccession=a.sequence[0].accession[0].Text;if(a.point)d.LatLong=[a.point[0].lat[0].Text,a.point[0]["long"][0].Text];if(!d.name){if(d.sequenceName)d.name=d.sequenceName;else if(d.taxonomyScientificName)d.name=d.taxonomyScientificName;else if(d.taxonomyCommonName)d.name=d.taxonomyCommonName;else if(d.sequenceAccession)d.name=d.sequenceAccession;
-if(d.name)d.type="label"}if(a.annotation){if(a.annotation[0]&&a.annotation[0].desc&&a.annotation[0].desc[0]&&a.annotation[0].desc[0].Text)d.description=a.annotation[0].desc[0].Text;if(a.annotation[0]&&a.annotation[0].uri&&a.annotation[0].uri[0]&&a.annotation[0].uri[0].Text)d.uri=a.annotation[0].uri[0].Text;if(a.annotation[0]&&a.annotation[0].img)for(k in a.annotation[0].img)if(Smits.Common.isInteger(k))d.img[k]=a.annotation[0].img[k].Text}if(a.chart&&a.chart[0])for(k in a.chart[0])if(k!="Text"&&k!=
-"_children")d.chart[k]=a.chart[0][k][0].Text;d&&d.level>1&&(d.len||(f="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees."));return d},m=function(b){if(b.children&&b.children.length)for(var f=0;f<b.children.length;f++){var d=b.children[f];d.newickLen=Math.round((d.len+b.newickLen)*1E4)/1E4;if(d.level>a)a=d.level;if(d.newickLen>c)c=d.newickLen;d.children.length>0&&m(d,b)}return b},q=function(a,c){for(var d in a)d!="_children"&&d!="Text"&&(d=="rectangular"||d=="circular"?
-q(a[d][0],d):(Smits.PhyloCanvas.Render.Parameters[d]||(Smits.PhyloCanvas.Render.Parameters[d]={}),Smits.PhyloCanvas.Render.Parameters.set(d,a[d][0].Text,c)))};return function(g){this.getRoot=function(){return b};this.getLevels=function(){return a};this.getNewickLen=function(){return c};this.getValidate=function(){return f};g.phylogeny&&g.phylogeny[0]&&g.phylogeny[0].clade&&(b=l(g.phylogeny[0].clade[0]));if(g.phylogeny&&g.phylogeny[0]&&g.phylogeny[0].render&&g.phylogeny[0].render[0]){if((g=g.phylogeny[0].render[0])&&
-g.styles){var n=g.styles[0],d;for(d in n)if(d!="_children"&&d!="Text")if(n[d][0].type&&n[d][0].type=="radialGradient"&&Raphael.svg)n[d][0].name=d,Smits.PhyloCanvas.Render.Style[d]=n[d][0],Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList||(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList=[]),Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.push(d);else for(var k in Smits.PhyloCanvas.Render.Style[d]||(Smits.PhyloCanvas.Render.Style[d]={}),n[d][0])k!="_attributes"&&k!="_children"&&k!=
-"type"&&(Smits.PhyloCanvas.Render.Style[d][k.replace("_","-")]=n[d][0][k])}g&&g.parameters&&q(g.parameters[0]);if(g&&g.charts)for(d in g=g.charts[0],g)if(d!="_children"&&d!="Text")for(k in g[d])if(g[d][k].type=="binary")g[d][k].chart=d,Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(g[d][k]);else if(g[d][k].type=="integratedBinary")g[d][k].chart=d,Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(g[d][k]);else if(g[d][k].type=="bar")g[d][k].chart=d,Smits.PhyloCanvas.Render.Parameters.barCharts.push(g[d][k])}b=
-m(b)}}();Smits.PhyloCanvas.PhyloxmlParse.prototype={};
-Smits.PhyloCanvas.NexmlParse=function(){var a=0,c=0,b,f,l,m,q=function(a,d,c){var j=new Smits.PhyloCanvas.Node;if(c)j.level=c.level+1;for(c=0;c<l.length;c++)if(l[c].source==a.id)for(var e=0;e<m.length;e++)l[c].target==m[e].id&&j.children.push(q(m[e],l[c].length,j));if(d&&(j.len=Smits.Common.roundFloat(d,4),j.len==0))j.len=1.0E-4;if(a.label&&(j.type="label",j.name=a.label,a.style))j.style=a.style;j&&j.level>1&&(j.len||(f="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees."));return j},
-g=function(b){if(b.children&&b.children.length)for(var d=0;d<b.children.length;d++){var k=b.children[d];k.newickLen=Math.round((k.len+b.newickLen)*1E4)/1E4;if(k.level>a)a=k.level;if(k.newickLen>c)c=k.newickLen;k.children.length>0&&g(k,b)}return b};return function(n,d){this.getRoot=function(){return b};this.getLevels=function(){return a};this.getNewickLen=function(){return c};this.getValidate=function(){return f};d.tree&&n.trees[0]&&n.trees[0].tree[d.tree-1]?(l=n.trees[0].tree[d.tree-1].edge,m=n.trees[0].tree[d.tree-
-1].node):(l=n.trees[0].tree[0].edge,m=n.trees[0].tree[0].node);for(i=0;i<m.length;i++)m[i].root&&m[i].root=="true"&&(b=m[i]);b?(b=q(b),b=g(b)):f="Error. Currently, only rooted NeXML trees are supported."}}();Smits.PhyloCanvas.NexmlParse.prototype={};
-Smits.PhyloCanvas.NexmlJsonParse=function(){var a=0,c=0,b,f,l=[],m=[],q=function(a,c,j){var e=new Smits.PhyloCanvas.Node;if(j)e.level=j.level+1;for(j=0;j<l.length;j++)if(l[j].source==a.id)for(var b=0;b<m.length;b++)l[j].target==m[b].id&&e.children.push(q(m[b],l[j].length,e));if(c&&(e.len=Smits.Common.roundFloat(c,4),e.len==0))e.len=1.0E-4;if(a.label){e.type="label";e.name=a.label;if(a.accession)e.accession=a.accession;if(a.style)e.style=a.style;if(a.bgStyle)e.bgStyle=a.bgStyle}if(a.chart)e.chart=
-a.chart;e&&e.level>1&&(e.len||(f="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees."));return e},g=function(d){if(d.children&&d.children.length)for(var b=0;b<d.children.length;b++){var j=d.children[b];j.newickLen=Math.round((j.len+d.newickLen)*1E4)/1E4;if(j.level>a)a=j.level;if(j.newickLen>c)c=j.newickLen;j.children.length>0&&g(j,d)}return d},n=function(a,c){for(var b in a)b!="_children"&&b!="Text"&&(b=="rectangular"||b=="circular"?n(a[b],b):(Smits.PhyloCanvas.Render.Parameters[b]||
-(Smits.PhyloCanvas.Render.Parameters[b]={}),Smits.PhyloCanvas.Render.Parameters.set(b,a[b],c)))};return function(d){this.getRoot=function(){return b};this.getLevels=function(){return a};this.getNewickLen=function(){return c};this.getValidate=function(){return f};var k=d.nexmlJson.nexml,j=k.render;if(j&&j.styles){var e=j.styles,h;for(h in e)if(h!="_children"&&h!="Text")if(e[h]["@attributes"].type&&e[h]["@attributes"].type=="radialGradient"&&Raphael.svg)e[h].name=h,e[h].type=e[h]["@attributes"].type,
-Smits.PhyloCanvas.Render.Style[h]=e[h],Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList||(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList=[]),Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.push(h);else for(var o in Smits.PhyloCanvas.Render.Style[h]||(Smits.PhyloCanvas.Render.Style[h]={}),e[h]["@attributes"])o!="_attributes"&&o!="_children"&&o!="type"&&(Smits.PhyloCanvas.Render.Style[h][o.replace("_","-")]=e[h]["@attributes"][o])}j&&j.parameters&&n(j.parameters);if(j&&j.charts)for(h in j=
-j.charts,j)j[h]["@attributes"].chart=h,j[h]["@attributes"].type=="binary"?Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(j[h]["@attributes"]):j[h]["@attributes"].type=="integratedBinary"?Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(j[h]["@attributes"]):j[h]["@attributes"].type=="bar"&&Smits.PhyloCanvas.Render.Parameters.barCharts.push(j[h]["@attributes"]);if(d.tree&&k.trees[0]&&k.trees[0].tree[d.tree-1])l=k.trees[0].tree[d.tree-1].edge,m=k.trees[0].tree[d.tree-1].node;else{for(h=
-0;h<k.trees.tree.edge.length;h++)l.push(k.trees.tree.edge[h]["@attributes"]);for(h=0;h<k.trees.tree.node.length;h++){d=k.trees.tree.node[h]["@attributes"];if(d.label)d.chart=k.trees.tree.node[h].chart;m.push(d)}}for(h=0;h<m.length;h++)m[h].root&&m[h].root=="true"&&(b=m[h]);b?(b=q(b),b=g(b)):f="Error. Currently, only rooted NeXML trees are supported."}}();Smits.PhyloCanvas.NexmlParse.prototype={};Smits.PhyloCanvas.Render={};
-Smits.PhyloCanvas.Render.Style={line:{stroke:"rgb(0,0,0)","stroke-width":1},text:{"font-family":"Verdana","font-size":12,"text-anchor":"start"},path:{stroke:"rgb(0,0,0)","stroke-width":1},connectedDash:{stroke:"rgb(200,200,200)","stroke-dasharray":". "},textSecantBg:{fill:"#EEE",stroke:"#DDD"},highlightedEdgeCircle:{fill:"red"},barChart:{fill:"#003300",stroke:"#DDD"},getStyle:function(a,c){return this[a]?this[a]:this[c]}};
-Smits.PhyloCanvas.Render.Parameters={jsOverride:0,Rectangular:{bufferX:200,bufferY:40,bufferInnerLabels:10,bufferOuterLabels:5,minHeightBetweenLeaves:10,alignPadding:0,alignRight:!1,showScaleBar:!1},Circular:{bufferRadius:0.33,bufferAngle:20,initStartAngle:160,innerCircleRadius:0,minHeightBetweenLeaves:5,bufferInnerLabels:2,bufferOuterLabels:5},binaryCharts:[],integratedBinaryCharts:[],barCharts:[],binaryChartBufferInner:5,binaryChartBufferSiblings:0.01,binaryChartThickness:15,binaryChartDisjointed:!1,
-barChartBufferInner:3,barChartHeight:50,barChartWidth:0.5,mouseRollOver:function(a){if(a.node.edgeCircleHighlight)a.node.edgeCircleHighlight.show();else{var c=a.svg.draw(new Smits.PhyloCanvas.Render.Circle(a.x,a.y,5,{attr:Smits.PhyloCanvas.Render.Style.highlightedEdgeCircle}));a.node.edgeCircleHighlight=c[0]}a.textEl.attr({fill:"red"})},mouseRollOut:function(a){a.node.edgeCircleHighlight.hide();a.textEl.attr({fill:"#000"})},set:function(a,c,b){this.jsOverride||(b?b=="circular"?this.Circular[a]=parseFloat(c):
-b=="rectangular"&&(this.Rectangular[a]=parseFloat(c)):this[a]=parseFloat(c))}};Smits.PhyloCanvas.Render.Line=function(){return function(a,c,b,f,l){this.type="line";this.attr=Smits.PhyloCanvas.Render.Style.line;this.x1=a;this.x2=c;this.y1=b;this.y2=f;if(l&&(Smits.Common.apply(this,l),l.attr))this.attr=l.attr}}();
-Smits.PhyloCanvas.Render.Text=function(){return function(a,c,b,f){this.type="text";this.attr=Smits.PhyloCanvas.Render.Style.text;this.x=a;this.y=c;this.text=b;if(f&&(Smits.Common.apply(this,f),f.attr))this.attr=f.attr}}();Smits.PhyloCanvas.Render.Path=function(){return function(a,c){this.type="path";this.attr=Smits.PhyloCanvas.Render.Style.path;this.path=a;if(c&&(Smits.Common.apply(this,c),c.attr))this.attr=c.attr}}();
-Smits.PhyloCanvas.Render.Circle=function(){return function(a,c,b,f){this.type="circle";this.x=a;this.y=c;this.radius=b;if(f&&(Smits.Common.apply(this,f),f.attr))this.attr=f.attr}}();Smits.PhyloCanvas.Render.SVG=function(){return function(a,c,b){this.canvasSize=[c,b];this.svg=Raphael(a,this.canvasSize[0],this.canvasSize[1])}}();
-Smits.PhyloCanvas.Render.SVG.prototype={render:function(){for(var a=this.phylogramObject.getDrawInstructs(),c=0;c<a.length;c++)if(a[c].type=="line")this.svg.path(["M",a[c].x1,a[c].y1,"L",a[c].x2,a[c].y2]).attr(Smits.PhyloCanvas.Render.Style.line);else if(a[c].type=="path")this.svg.path(a[c].path).attr(a[c].attr);else if(a[c].type=="circle")this.svg.circle(a[c].x,a[c].y,a[c].radius).attr({stroke:"red"});else{var b=this.svg.text(a[c].x,a[c].y,a[c].text).attr(Smits.PhyloCanvas.Render.Style.text);a[c].attr&&
-b.attr(a[c].attr);a[c].rotate&&b.rotate(a[c].rotate);b.getBBox()}},draw:function(a){var c,b;a.type=="line"?c=this.svg.path(["M",a.x1,a.y1,"L",a.x2,a.y2]).attr(Smits.PhyloCanvas.Render.Style.line):a.type=="path"?c=this.svg.path(a.path).attr(a.attr):a.type=="circle"?c=this.svg.circle(a.x,a.y,a.radius).attr({stroke:"red"}):a.type=="text"&&(c=this.svg.text(a.x,a.y,a.text).attr(Smits.PhyloCanvas.Render.Style.text),a.attr&&c.attr(a.attr),a.rotate&&c.rotate(a.rotate),a=c.getBBox(),b=Math.sqrt(a.height*a.height+
-a.width*a.width));return[c,b]}};
-Smits.PhyloCanvas.Render.Phylogram=function(){var a,c=Smits.PhyloCanvas.Render.Parameters.Rectangular,b,f,l,m,q,g,n=!0,d=0,k=0,j,e,h,o,p=[],r=function(b,e){b.len&&(n?n=!1:b.children.length==0&&(d=Smits.Common.roundFloat(d+m,4)));if(b.children.length>0){var j=[],h,f,o,g;b.len&&(h=e,f=e=Smits.Common.roundFloat(e+l*b.len,4),g=o=d+b.getMidbranchPosition()*m,a.draw(new Smits.PhyloCanvas.Render.Line(h,f,o,g)));if(b.name){h={};h=Smits.PhyloCanvas.Render.Style.getStyle("bootstrap","text");if(b.uri)h.href=
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-c.alignPadding:f+c.bufferInnerLabels,g,b.name,{attr:h}));b.style&&console.log([b,h]);k=Math.max(j[1],k);Smits.PhyloCanvas.Render.Parameters.mouseRollOver&&Smits.Common.addEventHandler(j[0].node,"mouseover",Smits.PhyloCanvas.Render.Parameters.mouseRollOver,{svg:a,node:b,x:f,y:g,textEl:j[0]});Smits.PhyloCanvas.Render.Parameters.mouseRollOut&&Smits.Common.addEventHandler(j[0].node,"mouseout",Smits.PhyloCanvas.Render.Parameters.mouseRollOut,{svg:a,node:b,x:f,y:g,textEl:j[0]});Smits.PhyloCanvas.Render.Parameters.onClickAction&&
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-"barChart")}));return d+j+h};return function(p,n){d=0;this.getCanvasSize=function(){return[b,f]};this.getRoot=function(){return n.getRoot()};n.getValidate()&&a.draw(0,0,n.getValidate());a=p;var t=n.getRoot(),C=n.getNewickLen();b=a.canvasSize[0];f=a.canvasSize[1];h=c.bufferX;o=c.bufferY;g=c.minHeightBetweenLeaves;l=Math.round((b-h)/C);m=Math.round((f-o)/(c.showScaleBar?t.getCountAllChildren()+1:t.getCountAllChildren()));m<g&&(m=g);q=Math.round(b-h);if(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length||
-Smits.PhyloCanvas.Render.Parameters.barCharts.length)c.alignRight=!0;r(t,0);c.showScaleBar&&(y=d+m,e=c.showScaleBar*l,a.draw(new Smits.PhyloCanvas.Render.Line(0,e,y,y)),a.draw(new Smits.PhyloCanvas.Render.Text((0+e)/2,y-8,c.showScaleBar)));j=q+k+c.bufferInnerLabels;if(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length){var t=Smits.PhyloCanvas.Render.Parameters.binaryCharts,s;for(s in t)j=u(j,t[s].chart,t[s])}if(Smits.PhyloCanvas.Render.Parameters.barCharts.length)for(s in t=Smits.PhyloCanvas.Render.Parameters.barCharts,
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-"mouseover",Smits.PhyloCanvas.Render.Parameters.mouseRollOver,{svg:j,node:d,x:p[0],y:p[1],textEl:k[0]});Smits.PhyloCanvas.Render.Parameters.mouseRollOut&&Smits.Common.addEventHandler(k[0].node,"mouseout",Smits.PhyloCanvas.Render.Parameters.mouseRollOut,{svg:j,node:d,x:p[0],y:p[1],textEl:k[0]});Smits.PhyloCanvas.Render.Parameters.onClickAction&&Smits.Common.addEventHandler(k[0].node,"click",Smits.PhyloCanvas.Render.Parameters.onClickAction,{svg:j,node:d,x:p[0],y:p[1],textEl:k[0]});z=Math.max(k[1],
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-{attr:Smits.PhyloCanvas.Render.Style.textSecantBg}));a[0].toBack();return s+z+e.bufferOuterLabels}function d(d,b,e){for(var h=e&&e.bufferInner?parseFloat(e.bufferInner):Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner,k=(e&&e.bufferSiblings?e.bufferSiblings*u:0)|(Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings<1?u*Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings:Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings),f=e&&e.thickness?parseFloat(e.thickness):
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+Smits = {};Smits.Common = {
+ nodeIdIncrement : 0,
+ activeNode: 0,
+
+ /* Rounds float to a defined number of decimal places */
+ roundFloat : function(num, digits){
+ var i = 0,
+ dec = 1;
+ while(i < digits){
+ dec *= 10;
+ i++;
+ }
+ return Math.round(num*dec)/dec;
+ },
+
+ /* Copies properties from one object to another */
+ apply : function(obj, extObj){
+ if (obj && typeof extObj == 'object') {
+ for (var key in extObj) {
+ obj[key] = extObj[key];
+ }
+ }
+ return obj;
+ },
+
+ addEventHandler : function(el, eventType, fn, paramsObj){
+ try{
+ el.addEventListener(
+ eventType,
+ (function(fn, args){
+ return(
+ function(e,o) {
+ var params = paramsObj;
+ params.e = e;
+ fn(params);
+ }
+ );
+ }(fn, paramsObj)),
+ false
+ );
+ } catch (err){}
+ },
+
+ isInteger : function(s) {
+ return !isNaN(parseInt(s));
+ },
+
+ isXMLSerializerAvailable : function(){
+ if (typeof(XMLSerializer) == "function"){
+ return true;
+ } else {
+ return false;
+ }
+ },
+
+ createSvgEl : function (el, attr) {
+ el = document.createElementNS("http://www.w3.org/2000/svg", el);
+ if (attr) {
+ for (var key in attr) {
+ if (attr.hasOwnProperty(key)) {
+ el.setAttribute(key, String(attr[key]));
+ }
+ }
+ }
+ return el;
+ },
+
+ createGradientEl : function(name, obj, coords){
+ if(obj.type != "radialGradient") return false;
+
+ var radialEl = Smits.Common.createSvgEl("radialGradient", {
+ id: name,
+ gradientUnits:"userSpaceOnUse",
+ cx: coords[0],
+ cy: coords[1],
+ r: coords[2],
+ fx: coords[0],
+ fy: coords[1]
+ });
+
+ if(obj.stop){
+ var stop = obj.stop;
+ for(var i = 0; i < stop.length; i++){
+ var stopObj = stop[i];
+ if(stopObj['@attributes']){
+ radialEl.appendChild(Smits.Common.createSvgEl("stop", stopObj['@attributes']));
+ } else {
+ if(stopObj['_attributes']) delete stopObj['_attributes'];
+ if(stopObj['_children']) delete stopObj['_children'];
+ if(stopObj['__proto__']) delete stopObj['__proto__'];
+ radialEl.appendChild(Smits.Common.createSvgEl("stop", stopObj));
+ }
+ }
+ }
+
+ return radialEl;
+ },
+
+ setCssStyle : function(selector, rule) {
+ var stylesheet = document.styleSheets[0];
+ if( stylesheet.addRule ){
+ stylesheet.addRule(selector, rule);
+ } else if( stylesheet.insertRule ){
+ stylesheet.insertRule(selector + ' { ' + rule + ' }', stylesheet.cssRules.length);
+ }
+ }
+
+};Smits.PhyloCanvas = function(){
+ var phylogram,
+ divId,
+ newickObject,
+ svg,
+ dataObject;
+
+ return function(inputFormat, sDivId, canvasWidth, canvasHeight, type){
+ /* Privileged Methods */
+ this.getNewickObject = function(){
+ return newickObject;
+ };
+ this.clear = function(){
+
+ };
+ this.scale = function(multiplier){
+ svg.svg.scale(multiplier);
+ };
+ this.getSvg = function(){
+ return svg;
+ };
+ this.getPhylogram = function(){
+ return phylogram;
+ };
+ this.getSvgSource = function(){
+ if(Raphael.svg && Smits.Common.isXMLSerializerAvailable()){
+ var serialize = new XMLSerializer();
+ return serialize.serializeToString(svg.svg.canvas);
+ } else {
+ return false;
+ }
+ }
+
+ /* CONSTRUCTOR */
+
+ // Process dataset -- assume newick format, else needs to provide format
+ if(typeof inputFormat === "object"){
+ if(inputFormat.xml){ // default xml format is phyloXML
+ if(!inputFormat.fileSource){
+ var xj = XMLObjectifier.textToXML(inputFormat.xml); // assume we need to clean it up
+ } else {
+ var xj = inputFormat.xml;
+ }
+ xj = XMLObjectifier.xmlToJSON(xj);
+ dataObject = new Smits.PhyloCanvas.PhyloxmlParse(xj);
+ } else if(inputFormat.phyloxml){
+ if(!inputFormat.fileSource){
+ var xj = XMLObjectifier.textToXML(inputFormat.phyloxml); // assume we need to clean it up
+ } else {
+ var xj = inputFormat.phyloxml;
+ }
+ xj = XMLObjectifier.xmlToJSON(xj);
+ dataObject = new Smits.PhyloCanvas.PhyloxmlParse(xj);
+ } else if(inputFormat.nexml){
+ if(!inputFormat.fileSource){
+ var xj = XMLObjectifier.textToXML(inputFormat.nexml); // assume we need to clean it up
+ } else {
+ var xj = inputFormat.nexml;
+ }
+ xj = XMLObjectifier.xmlToJSON(xj);
+ dataObject = new Smits.PhyloCanvas.NexmlParse(xj, inputFormat)
+ } else if(inputFormat.json){
+ dataObject = new Smits.PhyloCanvas.PhyloxmlParse(inputFormat.json);
+ } else if(inputFormat.newick){
+ dataObject = new Smits.PhyloCanvas.NewickParse(inputFormat.newick);
+ } else if(inputFormat.nexmlJson){
+ dataObject = new Smits.PhyloCanvas.NexmlJsonParse(inputFormat);
+ } else {
+ alert('Please set the format of input data');
+ }
+ } else {
+ dataObject = new Smits.PhyloCanvas.NewickParse(inputFormat);
+ }
+
+ divId = sDivId;
+ svg = new Smits.PhyloCanvas.Render.SVG( divId, canvasWidth, canvasHeight );
+
+ /* FACTORY */
+ if(type == "circular"){
+ phylogram = new Smits.PhyloCanvas.Render.CircularPhylogram(
+ svg,
+ dataObject
+ );
+ } else {
+ phylogram = new Smits.PhyloCanvas.Render.Phylogram(
+ svg,
+ dataObject
+ );
+ }
+
+ }
+
+}();
+
+Smits.PhyloCanvas.prototype = {
+};Smits.PhyloCanvas.Node = function(){
+
+ /**
+ * Node Class
+ * Allows objects to be traversed across children
+ *
+ */
+ return function(o, parentInstance){
+ // initiate object
+ this.id = Smits.Common.nodeIdIncrement += 1;
+ this.level = 0;
+ this.len = 0;
+ this.newickLen = 0;
+ this.name = '';
+ this.type = '';
+ this.chart = {};
+ this.img = [];
+
+ if(o) Smits.Common.apply(this, o);
+
+ this.children = new Array();
+
+ if(parentInstance){
+ parentInstance.children.push(this);
+ }
+ }
+}();
+
+
+Smits.PhyloCanvas.Node.prototype = {
+
+ getCountAllChildren : function(){
+ var nodeCount = 0;
+
+ for (var key in this.children) {
+ if(Smits.Common.isInteger(key)){
+ var child = this.children[key];
+ if(child.children && child.children.length > 0){
+ nodeCount += child.getCountAllChildren();
+ } else {
+ nodeCount ++;
+ }
+ }
+ }
+ return nodeCount;
+ },
+
+ getCountImmediateChildren : function(){
+ var nodeCount = 0;
+
+ for (var key in this.children) {
+ var child = this.children[key];
+ nodeCount += child.length;
+ }
+ return nodeCount;
+ },
+
+ getMidbranchPosition : function(){
+ var y = [0,0]; // bounds
+
+ for (var i = 0; i < this.children.length; i++) {
+ var child = this.children[i];
+
+ if(child.children && child.children.length > 0){
+ if(i == 0){
+ y[0] = child.getMidbranchPosition();
+ y[1] += child.getCountAllChildren();
+ } else if (i == this.children.length - 1){
+ y[1] += child.getMidbranchPosition();
+ } else {
+ y[1] += child.getCountAllChildren();
+ }
+ } else {
+ if(i == 0){
+ y[0] = 1;
+ y[1] += 1;
+ } else if (i == this.children.length - 1){
+ y[1] += 1;
+ } else {
+ y[1] += 1;
+ }
+ }
+ }
+
+ return y[1] >= y[0] ? ((y[1] - y[0]) / 2) + y[0] : y[0];
+ }
+
+};Smits.PhyloCanvas.NewickParse = function(){
+
+ var text,
+ ch,
+ pos,
+ mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+
+ object = function (parentNode) {
+ var node = new Smits.PhyloCanvas.Node();
+
+ while (ch !== ')' && ch !== ',') {
+ if (ch === ':'){
+ next();
+ node.len = Smits.Common.roundFloat(string(), 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ } else if (ch === "'" || ch === '"'){
+ node.type = "label";
+ node.name = quotedString(ch);
+ } else {
+ node.type = "label";
+ node.name = string();
+ }
+ }
+ node.level = parentNode.level + 1;
+ return node;
+ },
+
+ objectIterate = function(parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ while( ch !== ')' ){
+ next()
+ if( ch === '(' ) {
+ node.children.push(objectIterate(node));
+ } else {
+ node.children.push(object(node));
+ }
+ }
+
+ next();
+ if(ch !== ':' && ch !== ')' && ch !== ',' && ch !== ';'){
+ node.type = "label";
+ node.name = string();
+ }
+ if(ch === ':'){
+ next();
+ node.len = Smits.Common.roundFloat(string(), 4);
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ node.type = "stem";
+
+ }
+ return node;
+ },
+
+ string = function(){
+ var string = '';
+
+ while (ch !== ':' && ch !== ')' && ch !== ',' && ch !== ';'){
+ string += ch;
+ next();
+ }
+ return string;
+ },
+
+ quotedString = function(quoteType){
+ var string = '';
+
+ while (ch !== quoteType){
+ string += ch;
+ next();
+ }
+ return string;
+ },
+
+ next = function() {
+ ch = text.charAt(pos);
+ pos += 1;
+ return ch;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++ ){
+ var child = node.children[i];
+ if(child.len === 0) { // Dendogram
+ child.len = 1;
+ }
+ child.newickLen = Smits.Common.roundFloat(child.len + node.newickLen, 4);
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ };
+
+ return function(parseText){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+
+ /* CONSTRUCTOR */
+ text = parseText;
+ pos = 0;
+
+ next();
+ root = objectIterate();
+ root = recursiveProcessRoot(root);
+ }
+
+}();
+
+Smits.PhyloCanvas.NewickParse.prototype = {
+
+};Smits.PhyloCanvas.PhyloxmlParse = function(){
+
+ var mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+
+ recursiveParse = function(clade, parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ if(clade.clade && clade.clade.length){
+ for(var i = 0; i < clade.clade.length; i++){
+ var thisClade = clade.clade[i];
+ node.children.push(recursiveParse(thisClade, node));
+ }
+ }
+ if(clade.branch_length){ // Branches can be attributes or own element
+ if(typeof clade.branch_length === 'object'){
+ clade.branch_length = clade.branch_length[0].Text;
+ }
+
+ node.len = Smits.Common.roundFloat(clade.branch_length, 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ }
+ if(clade.name){
+ node.type = 'label';
+ node.name = clade.name[0].Text;
+ if(clade.name[0] && clade.name[0].style){
+ node.style = clade.name[0].style;
+ }
+ if(clade.name[0] && clade.name[0].bgStyle){
+ node.bgStyle = clade.name[0].bgStyle;
+ }
+ } else if(clade.confidence){
+ node.name = clade.confidence[0].Text;
+ }
+
+ /* Collect further info that might be used as a label */
+ if (clade.sequence && clade.sequence[0] && clade.sequence[0].name && clade.sequence[0].name[0] && clade.sequence[0].name[0].Text){
+ node.sequenceName = clade.sequence[0].name[0].Text;
+ }
+ if (clade.taxonomy && clade.taxonomy[0]){
+ if(clade.taxonomy[0].scientific_name && clade.taxonomy[0].scientific_name[0] && clade.taxonomy[0].scientific_name[0].Text){
+ node.taxonomyScientificName = clade.taxonomy[0].scientific_name[0].Text;
+ }
+ if (clade.taxonomy[0].common_name && clade.taxonomy[0].common_name[0] && clade.taxonomy[0].common_name[0].Text){
+ node.taxonomyCommonName = clade.taxonomy[0].common_name[0].Text;
+ }
+ }
+ if (clade.sequence && clade.sequence[0] && clade.sequence[0].accession && clade.sequence[0].accession[0] && clade.sequence[0].accession[0].Text){
+ node.sequenceAccession = clade.sequence[0].accession[0].Text;
+ }
+ if (clade.point ){
+ node.LatLong = [clade.point[0].lat[0].Text, clade.point[0]['long'][0].Text];
+ }
+
+
+ /* Prioritization of Label */
+ if(!node.name){
+ if(node.sequenceName){
+ node.name = node.sequenceName;
+ } else if (node.taxonomyScientificName){
+ node.name = node.taxonomyScientificName;
+ } else if (node.taxonomyCommonName){
+ node.name = node.taxonomyCommonName;
+ } else if (node.sequenceAccession){
+ node.name = node.sequenceAccession;
+ }
+ if(node.name){ // if name is now set, type is 'label'
+ node.type = 'label';
+ }
+ }
+
+ if(clade.annotation){
+ if(clade.annotation[0] && clade.annotation[0].desc && clade.annotation[0].desc[0] && clade.annotation[0].desc[0].Text){
+ node.description = clade.annotation[0].desc[0].Text;
+ }
+ if(clade.annotation[0] && clade.annotation[0].uri && clade.annotation[0].uri[0] && clade.annotation[0].uri[0].Text){
+ node.uri = clade.annotation[0].uri[0].Text;
+ }
+ if(clade.annotation[0] && clade.annotation[0].img){
+ for(var i in clade.annotation[0].img){
+ if(Smits.Common.isInteger(i)){
+ node.img[i] = clade.annotation[0].img[i].Text;
+ }
+ }
+ }
+ }
+ if(clade.chart){
+ if(clade.chart[0]){
+ for(var i in clade.chart[0]){
+ if(i != 'Text' && i != '_children'){
+ node.chart[i] = clade.chart[0][i][0].Text;
+ }
+ }
+ }
+
+ }
+
+ // Validation
+ if(node && node.level > 1){
+ if(!node.len){
+ validate = 'Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.';
+ }
+ }
+
+ return node;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++){
+ var child = node.children[i];
+ child.newickLen = Math.round( (child.len + node.newickLen) *10000)/10000;
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ },
+
+ recursiveProcessParameters = function(parametersEl, treeType){
+ for (var i in parametersEl){
+ if(i != '_children' && i != 'Text'){
+ if(i == 'rectangular' || i == 'circular'){
+ recursiveProcessParameters(parametersEl[i][0], i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Parameters[i]) { Smits.PhyloCanvas.Render.Parameters[i] = {}; };
+ Smits.PhyloCanvas.Render.Parameters.set(i, parametersEl[i][0].Text, treeType);
+ }
+ }
+ }
+ return;
+ };
+
+ return function(jsonString){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+
+ /* CONSTRUCTOR */
+ if(jsonString.phylogeny && jsonString.phylogeny[0] && jsonString.phylogeny[0].clade){
+ root = recursiveParse(jsonString.phylogeny[0].clade[0]);
+ }
+
+ if(jsonString.phylogeny && jsonString.phylogeny[0] && jsonString.phylogeny[0].render && jsonString.phylogeny[0].render[0]){
+ var render = jsonString.phylogeny[0].render[0];
+
+ // Custom Styles
+ if(render && render.styles){
+ var styles = render.styles[0];
+ for (var i in styles){
+ if(i != '_children' && i != 'Text'){
+ if(styles[i][0]['type'] && styles[i][0]['type'] == "radialGradient" && Raphael.svg){
+ // radialGradient only supported by SVG
+ styles[i][0]['name'] = i;
+ Smits.PhyloCanvas.Render.Style[i] = styles[i][0];
+ if(!Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList']) { Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'] = [] };
+ Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'].push(i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Style[i]) { Smits.PhyloCanvas.Render.Style[i] = {}; };
+ for(var j in styles[i][0]){
+ if(j != '_attributes' && j != '_children' && j != 'type'){
+ Smits.PhyloCanvas.Render.Style[i][j.replace('_', '-')] = styles[i][0][j]; // This is quite painful, as xml does not allow dashes
+ }
+ }
+ }
+
+ }
+ }
+ }
+
+ // Custom Parameters
+ if(render && render.parameters){
+ recursiveProcessParameters(render.parameters[0]);
+ }
+
+ // Charts
+ if(render && render.charts){
+ var charts = render.charts[0];
+ for (var i in charts){
+ if(i != '_children' && i != 'Text'){
+ for(var j in charts[i]){
+ if(charts[i][j].type == "binary"){
+ charts[i][j].chart = i;
+ Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(charts[i][j]);
+ } else if (charts[i][j].type == "integratedBinary"){
+ charts[i][j].chart = i;
+ Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(charts[i][j]);
+ } else if (charts[i][j].type == "bar"){
+ charts[i][j].chart = i;
+ Smits.PhyloCanvas.Render.Parameters.barCharts.push(charts[i][j]);
+ }
+ }
+ }
+ }
+ }
+
+ }
+
+ root = recursiveProcessRoot(root);
+
+ }
+
+}();
+
+Smits.PhyloCanvas.PhyloxmlParse.prototype = {
+
+};Smits.PhyloCanvas.NexmlParse = function(){
+
+ var mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+ nexEdges,
+ nexNodes,
+
+ recursiveParse = function(nexnode, nexlen, parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ for(var i = 0; i < nexEdges.length; i++){
+ if(nexEdges[i].source == nexnode.id){
+ for(var j = 0; j < nexNodes.length; j++){
+ if(nexEdges[i].target == nexNodes[j].id){
+ node.children.push(recursiveParse(nexNodes[j], nexEdges[i].length, node));
+ }
+ }
+ }
+ }
+
+ if(nexlen) {
+ node.len = Smits.Common.roundFloat(nexlen, 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ }
+
+ if(nexnode.label){
+ node.type = 'label';
+ node.name = nexnode.label;
+ if(nexnode.style){
+ node.style = nexnode.style;
+ }
+ }
+
+
+ // Validation
+ if(node && node.level > 1){
+ if(!node.len){
+ validate = 'Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.';
+ }
+ }
+
+ return node;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++){
+ var child = node.children[i];
+ child.newickLen = Math.round( (child.len + node.newickLen) *10000)/10000;
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ },
+ recursiveProcessParameters = function(parametersEl, treeType){
+ for (var i in parametersEl){
+ if(i != '_children' && i != 'Text'){
+ if(i == 'rectangular' || i == 'circular'){
+ recursiveProcessParameters(parametersEl[i][0], i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Parameters[i]) { Smits.PhyloCanvas.Render.Parameters[i] = {}; };
+ Smits.PhyloCanvas.Render.Parameters.set(i, parametersEl[i][0].Text, treeType);
+ }
+ }
+ }
+ return;
+ };
+
+ return function(jsonString, inputFormat){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+
+ if(inputFormat.tree && jsonString.trees[0] && jsonString.trees[0].tree[(inputFormat.tree-1)]){
+ nexEdges = jsonString.trees[0].tree[(inputFormat.tree-1)].edge;
+ nexNodes = jsonString.trees[0].tree[(inputFormat.tree-1)].node;
+ } else {
+ nexEdges = jsonString.trees[0].tree[0].edge;
+ nexNodes = jsonString.trees[0].tree[0].node;
+ }
+
+ for(i = 0; i < nexNodes.length; i++){
+ if(nexNodes[i].root && nexNodes[i].root == "true"){
+ root = nexNodes[i];
+ }
+ }
+
+ if(root){
+ root = recursiveParse(root);
+
+ root = recursiveProcessRoot(root);
+ } else {
+ validate = 'Error. Currently, only rooted NeXML trees are supported.';
+ }
+
+ };
+
+}();
+
+Smits.PhyloCanvas.NexmlParse.prototype = {
+
+};Smits.PhyloCanvas.NexmlJsonParse = function(){
+
+ var mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+ nexEdges = [], nexNodes = [],
+
+ recursiveParse = function(nexnode, nexlen, parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ for(var i = 0; i < nexEdges.length; i++){
+ if(nexEdges[i].source == nexnode.id){
+ for(var j = 0; j < nexNodes.length; j++){
+ if(nexEdges[i].target == nexNodes[j].id){
+ node.children.push(recursiveParse(nexNodes[j], nexEdges[i].length, node));
+ }
+ }
+ }
+ }
+
+ if(nexlen) {
+ node.len = Smits.Common.roundFloat(nexlen, 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ }
+
+ if(nexnode.label){
+ node.type = 'label';
+ node.name = nexnode.label;
+ if(nexnode.accession){
+ node.accession = nexnode.accession;
+ }
+ if(nexnode.style){
+ node.style = nexnode.style;
+ }
+ if(nexnode.bgStyle){
+ node.bgStyle = nexnode.bgStyle;
+ }
+ }
+
+ if(nexnode.chart){
+ node.chart = nexnode.chart;
+ }
+
+ // Validation
+ if(node && node.level > 1){
+ if(!node.len){
+ validate = 'Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.';
+ }
+ }
+
+ return node;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++){
+ var child = node.children[i];
+ child.newickLen = Math.round( (child.len + node.newickLen) *10000)/10000;
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ },
+
+ recursiveProcessParameters = function(parametersEl, treeType){
+ for (var i in parametersEl){
+ if(i != '_children' && i != 'Text'){
+ if(i == 'rectangular' || i == 'circular'){
+ recursiveProcessParameters(parametersEl[i], i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Parameters[i]) { Smits.PhyloCanvas.Render.Parameters[i] = {}; };
+ Smits.PhyloCanvas.Render.Parameters.set(i, parametersEl[i], treeType);
+ }
+ }
+ }
+ return;
+ };
+
+ return function(inputFormat){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+ var jsonString = inputFormat.nexmlJson.nexml;
+
+
+ /* RENDER STYLES */
+ var render = jsonString.render;
+
+ // Custom Styles
+ if(render && render.styles){
+ var styles = render.styles;
+ for (var i in styles){
+ if(i != '_children' && i != 'Text'){
+ if(styles[i]['@attributes']['type'] && styles[i]['@attributes']['type'] == "radialGradient" && Raphael.svg){
+ // radialGradient only supported by SVG
+ styles[i]['name'] = i;
+ styles[i]['type'] = styles[i]['@attributes']['type'];
+ Smits.PhyloCanvas.Render.Style[i] = styles[i];
+ if(!Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList']) { Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'] = [] };
+ Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'].push(i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Style[i]) { Smits.PhyloCanvas.Render.Style[i] = {}; };
+ for(var j in styles[i]['@attributes']){
+ if(j != '_attributes' && j != '_children' && j != 'type'){
+ Smits.PhyloCanvas.Render.Style[i][j.replace('_', '-')] = styles[i]['@attributes'][j]; // This is quite painful, as xml does not allow dashes
+ }
+ }
+ }
+ }
+ }
+ }
+ // Custom Parameters
+ if(render && render.parameters){
+ recursiveProcessParameters(render.parameters);
+ }
+
+ // Charts
+ if(render && render.charts){
+ var charts = render.charts;
+ for (var i in charts){
+ charts[i]['@attributes'].chart = i;
+ if(charts[i]['@attributes'].type == "binary"){
+ Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(charts[i]['@attributes']);
+ } else if(charts[i]['@attributes'].type == "integratedBinary"){
+ Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(charts[i]['@attributes']);
+ } else if(charts[i]['@attributes'].type == "bar"){
+ Smits.PhyloCanvas.Render.Parameters.barCharts.push(charts[i]['@attributes']);
+ }
+ }
+ }
+
+ if(inputFormat.tree && jsonString.trees[0] && jsonString.trees[0].tree[(inputFormat.tree-1)]){
+ nexEdges = jsonString.trees[0].tree[(inputFormat.tree-1)].edge;
+ nexNodes = jsonString.trees[0].tree[(inputFormat.tree-1)].node;
+ } else {
+ for(var i = 0; i < jsonString.trees.tree.edge.length; i++){
+ nexEdges.push(jsonString.trees.tree.edge[i]['@attributes']);
+ }
+ for(var i = 0; i < jsonString.trees.tree.node.length; i++){
+ var node = jsonString.trees.tree.node[i]['@attributes'];
+ if(node.label){
+ node.chart = jsonString.trees.tree.node[i].chart;
+ }
+ nexNodes.push(node);
+ }
+ }
+
+ for(var i = 0; i < nexNodes.length; i++){
+ if(nexNodes[i].root && nexNodes[i].root == "true"){
+ root = nexNodes[i];
+ }
+ }
+
+ if(root){
+ root = recursiveParse(root);
+
+ root = recursiveProcessRoot(root);
+ } else {
+ validate = 'Error. Currently, only rooted NeXML trees are supported.';
+ }
+
+ };
+
+}();
+
+Smits.PhyloCanvas.NexmlParse.prototype = {
+
+};Smits.PhyloCanvas.Render = {};Smits.PhyloCanvas.Render.Style = {
+
+ /* Default Styles */
+
+ line: {
+ "stroke": 'rgb(0,0,0)',
+ "stroke-width": 1
+ },
+
+ text: {
+ "font-family": 'Verdana',
+ "font-size": 12,
+ "text-anchor": 'start'
+ },
+
+ path: {
+ "stroke": 'rgb(0,0,0)',
+ "stroke-width": 1
+ },
+
+ connectedDash : {
+ "stroke": 'rgb(200,200,200)',
+ "stroke-dasharray": ". "
+ },
+
+ textSecantBg : {
+ "fill": '#EEE',
+ "stroke": '#DDD'
+ },
+
+ highlightedEdgeCircle : {
+ "fill": 'red'
+ },
+
+ barChart : {
+ fill: '#003300',
+ stroke: '#DDD'
+ },
+
+ getStyle : function(requestStyle, fallbackStyle){
+ if...
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