Smits={};Smits.Common={nodeIdIncrement:0,activeNode:0,roundFloat:function(c,e){for(var k=0,s=1;k<e;){s*=10;k++}return Math.round(c*s)/s},apply:function(c,e){if(c&&typeof e=="object")for(var k in e)c[k]=e[k];return c},addEventHandler:function(c,e,k,s){try{c.addEventListener(e,function(u){return function(B){s.e=B;u(s)}}(k,s),false)}catch(p){}},isInteger:function(c){return!isNaN(parseInt(c))},isXMLSerializerAvailable:function(){return typeof XMLSerializer=="function"?true:false}};
Smits.PhyloCanvas=function(){var c,e,k,s;return function(p,u,B,f,x){this.getNewickObject=function(){};this.clear=function(){};this.scale=function(a){k.svg.scale(a)};this.getSvg=function(){return k};this.getPhylogram=function(){return c};this.getSvgSource=function(){return Raphael.svg&&Smits.Common.isXMLSerializerAvailable()?(new XMLSerializer).serializeToString(k.svg.canvas):false};if(typeof p==="object")if(p.xml){var b=p.fileSource?p.xml:XMLObjectifier.textToXML(p.xml);b=XMLObjectifier.xmlToJSON(b);
s=new Smits.PhyloCanvas.PhyloxmlParse(b)}else if(p.phyloxml){b=p.fileSource?p.phyloxml:XMLObjectifier.textToXML(p.phyloxml);b=XMLObjectifier.xmlToJSON(b);s=new Smits.PhyloCanvas.PhyloxmlParse(b)}else if(p.nexml){b=p.fileSource?p.nexml:XMLObjectifier.textToXML(p.nexml);b=XMLObjectifier.xmlToJSON(b);s=new Smits.PhyloCanvas.NexmlParse(b,p)}else if(p.json)s=new Smits.PhyloCanvas.PhyloxmlParse(p.json);else if(p.newick)s=new Smits.PhyloCanvas.NewickParse(p.newick);else if(p.nexmlJson){console.log("load nexmlJson");
s=new Smits.PhyloCanvas.NexmlJsonParse(p)}else alert("Please set the format of input data");else s=new Smits.PhyloCanvas.NewickParse(p);e=u;k=new Smits.PhyloCanvas.Render.SVG(e,B,f);c=x=="circular"?new Smits.PhyloCanvas.Render.CircularPhylogram(k,s):new Smits.PhyloCanvas.Render.Phylogram(k,s)}}();Smits.PhyloCanvas.prototype={};
Smits.PhyloCanvas.Node=function(){return function(c,e){this.id=Smits.Common.nodeIdIncrement+=1;this.newickLen=this.len=this.level=0;this.type=this.name="";this.chart={};this.img=[];c&&Smits.Common.apply(this,c);this.children=[];e&&e.children.push(this)}}();
Smits.PhyloCanvas.Node.prototype={getCountAllChildren:function(){var c=0;for(var e in this.children)if(Smits.Common.isInteger(e)){var k=this.children[e];if(k.children&&k.children.length>0)c+=k.getCountAllChildren();else c++}return c},getCountImmediateChildren:function(){var c=0;for(var e in this.children)c+=this.children[e].length;return c},getMidbranchPosition:function(){for(var c=[0,0],e=0;e<this.children.length;e++){var k=this.children[e];if(k.children&&k.children.length>0)if(e==0){c[0]=k.getMidbranchPosition();
c[1]+=k.getCountAllChildren()}else c[1]+=e==this.children.length-1?k.getMidbranchPosition():k.getCountAllChildren();else{if(e==0)c[0]=1;c[1]+=1}}return c[1]>=c[0]?(c[1]-c[0])/2+c[0]:c[0]}};
Smits.PhyloCanvas.NewickParse=function(){var c,e,k,s=0,p=0,u,B=function(h){for(var d=new Smits.PhyloCanvas.Node;e!==")"&&e!==",";)if(e===":"){a();d.len=Smits.Common.roundFloat(x(),4);if(d.len==0)d.len=1.0E-4}else if(e==="'"||e==='"'){d.type="label";d.name=b(e)}else{d.type="label";d.name=x()}d.level=h.level+1;return d},f=function(h){var d=new Smits.PhyloCanvas.Node;if(h)d.level=h.level+1;for(;e!==")";){a();e==="("?d.children.push(f(d)):d.children.push(B(d))}a();if(e!==":"&&e!==")"&&e!==","&&e!==";"){d.type=
"label";d.name=x()}if(e===":"){a();d.len=Smits.Common.roundFloat(x(),4);if(d.len==0)d.len=1.0E-4;d.type="stem"}return d},x=function(){for(var h="";e!==":"&&e!==")"&&e!==","&&e!==";";){h+=e;a()}return h},b=function(h){for(var d="";e!==h;){d+=e;a()}return d},a=function(){e=c.charAt(k);k+=1;return e},g=function(h){if(h.children&&h.children.length)for(var d=0;d<h.children.length;d++){var j=h.children[d];if(j.len===0)j.len=1;j.newickLen=Smits.Common.roundFloat(j.len+h.newickLen,4);if(j.level>s)s=j.level;
if(j.newickLen>p)p=j.newickLen;j.children.length>0&&g(j,h)}return h};return function(h){this.getRoot=function(){return u};this.getLevels=function(){return s};this.getNewickLen=function(){return p};this.getValidate=function(){};c=h;k=0;a();u=f();u=g(u)}}();Smits.PhyloCanvas.NewickParse.prototype={};
Smits.PhyloCanvas.PhyloxmlParse=function(){var c=0,e=0,k,s,p=function(f,x){var b=new Smits.PhyloCanvas.Node;if(x)b.level=x.level+1;if(f.clade&&f.clade.length)for(var a=0;a<f.clade.length;a++)b.children.push(p(f.clade[a],b));if(f.branch_length){if(typeof f.branch_length==="object")f.branch_length=f.branch_length[0].Text;b.len=Smits.Common.roundFloat(f.branch_length,4);if(b.len==0)b.len=1.0E-4}if(f.name){b.type="label";b.name=f.name[0].Text;if(f.name[0]&&f.name[0].style)b.style=f.name[0].style;if(f.name[0]&&
f.name[0].bgStyle)b.bgStyle=f.name[0].bgStyle}else if(f.confidence)b.name=f.confidence[0].Text;if(f.sequence&&f.sequence[0]&&f.sequence[0].name&&f.sequence[0].name[0]&&f.sequence[0].name[0].Text)b.sequenceName=f.sequence[0].name[0].Text;if(f.taxonomy&&f.taxonomy[0]){if(f.taxonomy[0].scientific_name&&f.taxonomy[0].scientific_name[0]&&f.taxonomy[0].scientific_name[0].Text)b.taxonomyScientificName=f.taxonomy[0].scientific_name[0].Text;if(f.taxonomy[0].common_name&&f.taxonomy[0].common_name[0]&&f.taxonomy[0].common_name[0].Text)b.taxonomyCommonName=
f.taxonomy[0].common_name[0].Text}if(f.sequence&&f.sequence[0]&&f.sequence[0].accession&&f.sequence[0].accession[0]&&f.sequence[0].accession[0].Text)b.sequenceAccession=f.sequence[0].accession[0].Text;if(f.point)b.LatLong=[f.point[0].lat[0].Text,f.point[0]["long"][0].Text];if(!b.name){if(b.sequenceName)b.name=b.sequenceName;else if(b.taxonomyScientificName)b.name=b.taxonomyScientificName;else if(b.taxonomyCommonName)b.name=b.taxonomyCommonName;else if(b.sequenceAccession)b.name=b.sequenceAccession;
if(b.name)b.type="label"}if(f.annotation){if(f.annotation[0]&&f.annotation[0].desc&&f.annotation[0].desc[0]&&f.annotation[0].desc[0].Text)b.description=f.annotation[0].desc[0].Text;if(f.annotation[0]&&f.annotation[0].uri&&f.annotation[0].uri[0]&&f.annotation[0].uri[0].Text)b.uri=f.annotation[0].uri[0].Text;if(f.annotation[0]&&f.annotation[0].img)for(a in f.annotation[0].img)if(Smits.Common.isInteger(a))b.img[a]=f.annotation[0].img[a].Text}if(f.chart)if(f.chart[0])for(a in f.chart[0])if(a!="Text"&&
a!="_children")b.chart[a]=f.chart[0][a][0].Text;if(b&&b.level>1)b.len||(s="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.");return b},u=function(f){if(f.children&&f.children.length)for(var x=0;x<f.children.length;x++){var b=f.children[x];b.newickLen=Math.round((b.len+f.newickLen)*1E4)/1E4;if(b.level>c)c=b.level;if(b.newickLen>e)e=b.newickLen;b.children.length>0&&u(b,f)}return f},B=function(f,x){for(var b in f)if(b!="_children"&&b!="Text")if(b=="rectangular"||b=="circular")B(f[b][0],
b);else{Smits.PhyloCanvas.Render.Parameters[b]||(Smits.PhyloCanvas.Render.Parameters[b]={});Smits.PhyloCanvas.Render.Parameters.set(b,f[b][0].Text,x)}};return function(f){this.getRoot=function(){return k};this.getLevels=function(){return c};this.getNewickLen=function(){return e};this.getValidate=function(){return s};if(f.phylogeny&&f.phylogeny[0]&&f.phylogeny[0].clade)k=p(f.phylogeny[0].clade[0]);if(f.phylogeny&&f.phylogeny[0]&&f.phylogeny[0].render&&f.phylogeny[0].render[0]){if((f=f.phylogeny[0].render[0])&&
f.styles){var x=f.styles[0];for(var b in x)if(b!="_children"&&b!="Text"){Smits.PhyloCanvas.Render.Style[b]||(Smits.PhyloCanvas.Render.Style[b]={});for(var a in x[b][0])if(a!="_attributes")Smits.PhyloCanvas.Render.Style[b][a.replace("_","-")]=x[b][0][a]}}f&&f.parameters&&B(f.parameters[0]);if(f&&f.charts){f=f.charts[0];for(b in f)if(b!="_children"&&b!="Text")for(a in f[b])if(f[b][a].type=="binary"){f[b][a].chart=b;Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(f[b][a])}else if(f[b][a].type==
"bar"){f[b][a].chart=b;Smits.PhyloCanvas.Render.Parameters.barCharts.push(f[b][a])}}}k=u(k)}}();Smits.PhyloCanvas.PhyloxmlParse.prototype={};
Smits.PhyloCanvas.NexmlParse=function(){var c=0,e=0,k,s,p,u,B=function(b,a,g){var h=new Smits.PhyloCanvas.Node;if(g)h.level=g.level+1;for(g=0;g<p.length;g++)if(p[g].source==b.id)for(var d=0;d<u.length;d++)p[g].target==u[d].id&&h.children.push(B(u[d],p[g].length,h));if(a){h.len=Smits.Common.roundFloat(a,4);if(h.len==0)h.len=1.0E-4}if(b.label){h.type="label";h.name=b.label;if(b.style)h.style=b.style}if(h&&h.level>1)h.len||(s="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.");
return h},f=function(b){if(b.children&&b.children.length)for(var a=0;a<b.children.length;a++){var g=b.children[a];g.newickLen=Math.round((g.len+b.newickLen)*1E4)/1E4;if(g.level>c)c=g.level;if(g.newickLen>e)e=g.newickLen;g.children.length>0&&f(g,b)}return b},x=function(b,a){for(var g in b)if(g!="_children"&&g!="Text")if(g=="rectangular"||g=="circular")x(b[g][0],g);else{Smits.PhyloCanvas.Render.Parameters[g]||(Smits.PhyloCanvas.Render.Parameters[g]={});Smits.PhyloCanvas.Render.Parameters.set(g,b[g][0].Text,
a)}};return function(b,a){this.getRoot=function(){return k};this.getLevels=function(){return c};this.getNewickLen=function(){return e};this.getValidate=function(){return s};if(a.tree&&b.trees[0]&&b.trees[0].tree[a.tree-1]){p=b.trees[0].tree[a.tree-1].edge;u=b.trees[0].tree[a.tree-1].node}else{p=b.trees[0].tree[0].edge;u=b.trees[0].tree[0].node}for(i=0;i<u.length;i++)if(u[i].root&&u[i].root=="true")k=u[i];if(k){k=B(k);k=f(k)}else s="Error. Currently, only rooted NeXML trees are supported."}}();
Smits.PhyloCanvas.NexmlParse.prototype={};
Smits.PhyloCanvas.NexmlJsonParse=function(){var c=0,e=0,k,s,p=[],u=[],B=function(b,a,g){var h=new Smits.PhyloCanvas.Node;if(g)h.level=g.level+1;for(g=0;g<p.length;g++)if(p[g].source==b.id)for(var d=0;d<u.length;d++)p[g].target==u[d].id&&h.children.push(B(u[d],p[g].length,h));if(a){h.len=Smits.Common.roundFloat(a,4);if(h.len==0)h.len=1.0E-4}if(b.label){h.type="label";h.name=b.label;if(b.style)h.style=b.style;if(b.bgStyle)h.bgStyle=b.bgStyle}if(h&&h.level>1)h.len||(s="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.");
return h},f=function(b){if(b.children&&b.children.length)for(var a=0;a<b.children.length;a++){var g=b.children[a];g.newickLen=Math.round((g.len+b.newickLen)*1E4)/1E4;if(g.level>c)c=g.level;if(g.newickLen>e)e=g.newickLen;g.children.length>0&&f(g,b)}return b},x=function(b){for(var a in b)if(a!="_children"&&a!="Text"){console.log([a,b]);if(a=="rectangular"||a=="circular")x(b[a],a);else{Smits.PhyloCanvas.Render.Parameters[a]||(Smits.PhyloCanvas.Render.Parameters[a]={});console.log([a,b[a]])}}};return function(b){this.getRoot=
function(){return k};this.getLevels=function(){return c};this.getNewickLen=function(){return e};this.getValidate=function(){return s};var a=b.nexmlJson.nexml,g=a.render;if(g&&g.styles){var h=g.styles;for(var d in h)if(d!="_children"&&d!="Text"){Smits.PhyloCanvas.Render.Style[d]||(Smits.PhyloCanvas.Render.Style[d]={});for(var j in h[d]["@attributes"])if(j!="_attributes")Smits.PhyloCanvas.Render.Style[d][j.replace("_","-")]=h[d]["@attributes"][j]}}g&&g.parameters&&x(g.parameters);if(b.tree&&a.trees[0]&&
a.trees[0].tree[b.tree-1]){p=a.trees[0].tree[b.tree-1].edge;u=a.trees[0].tree[b.tree-1].node}else{for(d=0;d<a.trees.tree.edge.length;d++)p.push(a.trees.tree.edge[d]["@attributes"]);for(d=0;d<a.trees.tree.node.length;d++)u.push(a.trees.tree.node[d]["@attributes"])}for(d=0;d<u.length;d++)if(u[d].root&&u[d].root=="true")k=u[d];if(k){k=B(k);k=f(k)}else s="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(c,e){return this[c]?this[c]:this[e]}};
Smits.PhyloCanvas.Render.Parameters={jsOverride:0,Rectangular:{bufferX:200,bufferY:40,bufferInnerLabels:10,bufferOuterLabels:5,minHeightBetweenLeaves:10,alignPadding:0,alignRight:false,showScaleBar:false},Circular:{bufferRadius:0.33,bufferAngle:20,initStartAngle:160,innerCircleRadius:0,minHeightBetweenLeaves:5,bufferInnerLabels:2,bufferOuterLabels:5},binaryCharts:[],barCharts:[],binaryChartBufferInner:5,binaryChartBufferSiblings:0.01,binaryChartThickness:15,binaryChartDisjointed:false,barChartBufferInner:3,
barChartHeight:50,barChartWidth:0.5,mouseRollOver:function(c){if(c.node.edgeCircleHighlight)c.node.edgeCircleHighlight.show();else{var e=c.svg.draw(new Smits.PhyloCanvas.Render.Circle(c.x,c.y,5,{attr:Smits.PhyloCanvas.Render.Style.highlightedEdgeCircle}));c.node.edgeCircleHighlight=e[0]}c.textEl.attr({fill:"red"})},mouseRollOut:function(c){c.node.edgeCircleHighlight.hide();c.textEl.attr({fill:"#000"})},set:function(c,e,k){if(!this.jsOverride)if(k)if(k=="circular")this.Circular[c]=parseFloat(e);else{if(k==
"rectangular")this.Rectangular[c]=parseFloat(e)}else this[c]=parseFloat(e)}};Smits.PhyloCanvas.Render.Line=function(){return function(c,e,k,s,p){this.type="line";this.attr=Smits.PhyloCanvas.Render.Style.line;this.x1=c;this.x2=e;this.y1=k;this.y2=s;if(p){Smits.Common.apply(this,p);if(p.attr)this.attr=p.attr}}}();
Smits.PhyloCanvas.Render.Text=function(){return function(c,e,k,s){this.type="text";this.attr=Smits.PhyloCanvas.Render.Style.text;this.x=c;this.y=e;this.text=k;if(s){Smits.Common.apply(this,s);if(s.attr)this.attr=s.attr}}}();Smits.PhyloCanvas.Render.Path=function(){return function(c,e){this.type="path";this.attr=Smits.PhyloCanvas.Render.Style.path;this.path=c;if(e){Smits.Common.apply(this,e);if(e.attr)this.attr=e.attr}}}();
Smits.PhyloCanvas.Render.Circle=function(){return function(c,e,k,s){this.type="circle";this.x=c;this.y=e;this.radius=k;if(s){Smits.Common.apply(this,s);if(s.attr)this.attr=s.attr}}}();Smits.PhyloCanvas.Render.SVG=function(){return function(c,e,k){this.canvasSize=[e,k];this.svg=Raphael(c,this.canvasSize[0],this.canvasSize[1])}}();
Smits.PhyloCanvas.Render.SVG.prototype={render:function(){for(var c=this.phylogramObject.getDrawInstructs(),e=0;e<c.length;e++)if(c[e].type=="line")this.svg.path(["M",c[e].x1,c[e].y1,"L",c[e].x2,c[e].y2]).attr(Smits.PhyloCanvas.Render.Style.line);else if(c[e].type=="path")this.svg.path(c[e].path).attr(c[e].attr);else if(c[e].type=="circle")this.svg.circle(c[e].x,c[e].y,c[e].radius).attr({stroke:"red"});else{var k=this.svg.text(c[e].x,c[e].y,c[e].text).attr(Smits.PhyloCanvas.Render.Style.text);c[e].attr&&
k.attr(c[e].attr);c[e].rotate&&k.rotate(c[e].rotate);k=k.getBBox();Math.sqrt(k.height*k.height+k.width*k.width)}},draw:function(c){var e,k;if(c.type=="line")e=this.svg.path(["M",c.x1,c.y1,"L",c.x2,c.y2]).attr(Smits.PhyloCanvas.Render.Style.line);else if(c.type=="path")e=this.svg.path(c.path).attr(c.attr);else if(c.type=="circle")e=this.svg.circle(c.x,c.y,c.radius).attr({stroke:"red"});else if(c.type=="text"){e=this.svg.text(c.x,c.y,c.text).attr(Smits.PhyloCanvas.Render.Style.text);c.attr&&e.attr(c.attr);
c.rotate&&e.rotate(c.rotate);c=e.getBBox();k=Math.sqrt(c.height*c.height+c.width*c.width)}return[e,k]}};
Smits.PhyloCanvas.Render.Phylogram=function(){var c,e=Smits.PhyloCanvas.Render.Parameters.Rectangular,k,s,p,u,B,f,x=true,b=0,a=0,g,h,d,j,o=[],z=function(m,w,t,r){return["M",m,w,"L",t,w,"L",t,r,"L",m,r,"Z"]},J=function(m,w){if(m.len)if(x)x=false;else if(m.children.length==0)b=Smits.Common.roundFloat(b+u,4);if(m.children.length>0){var t=[],r,C,E,D;if(m.len){r=w;C=w=Smits.Common.roundFloat(w+p*m.len,4);D=E=b+m.getMidbranchPosition()*u;c.draw(new Smits.PhyloCanvas.Render.Line(r,C,E,D))}if(m.name){r={};
r=Smits.PhyloCanvas.Render.Style.getStyle("bootstrap","text");if(m.uri)r.href=m.uri;if(m.description)r.title=m.description;if(m.level==0){C=2;var I=b+m.getMidbranchPosition()*u}else{C=C;I=D}c.draw(new Smits.PhyloCanvas.Render.Text(C+5,I,m.name,{attr:r}))}if(m.children&&m.children.length)for(r=0;r<m.children.length;r++)t.push(J(m.children[r],w));m=[];for(r=0;r<t.length;r++){t[r][0]&&m.push(t[r][0]);t[r][1]&&m.push(t[r][1])}t=Math.min.apply(null,m);m=Math.max.apply(null,m);c.draw(new Smits.PhyloCanvas.Render.Path(["M",
w+1.0E-4,t,"L",w,t,"L",w,m,"L",w+1.0E-4,m],{attr:Smits.PhyloCanvas.Render.Style.line}))}else{r=w;C=Smits.Common.roundFloat(w+p*m.len,2);D=E=b;m.y=b;o.push(m);c.draw(new Smits.PhyloCanvas.Render.Line(r,C,E,D));e.alignRight&&c.draw(new Smits.PhyloCanvas.Render.Path(["M",C,E,"L",e.alignPadding+B,D],{attr:Smits.PhyloCanvas.Render.Style.connectedDash}));if(m.name){r={};if(m.style)r=Smits.PhyloCanvas.Render.Style.getStyle(m.style,"text");r["text-anchor"]="start";if(m.uri)r.href=m.uri;if(m.description)r.title=
m.description;w=c.draw(new Smits.PhyloCanvas.Render.Text(e.alignRight?B+e.bufferInnerLabels+e.alignPadding:C+e.bufferInnerLabels,D,m.name,{attr:r}));m.style&&console.log([m,r]);a=Math.max(w[1],a);Smits.PhyloCanvas.Render.Parameters.mouseRollOver&&Smits.Common.addEventHandler(w[0].node,"mouseover",Smits.PhyloCanvas.Render.Parameters.mouseRollOver,{svg:c,node:m,x:C,y:D,textEl:w[0]});Smits.PhyloCanvas.Render.Parameters.mouseRollOut&&Smits.Common.addEventHandler(w[0].node,"mouseout",Smits.PhyloCanvas.Render.Parameters.mouseRollOut,
{svg:c,node:m,x:C,y:D,textEl:w[0]});Smits.PhyloCanvas.Render.Parameters.onClickAction&&Smits.Common.addEventHandler(w[0].node,"click",Smits.PhyloCanvas.Render.Parameters.onClickAction,{svg:c,node:m,x:C,y:D,textEl:w[0]})}}return[E,D]},N=function(){y=b+u;h=e.showScaleBar*p;c.draw(new Smits.PhyloCanvas.Render.Line(0,h,y,y));c.draw(new Smits.PhyloCanvas.Render.Text((0+h)/2,y-8,e.showScaleBar))},K=function(m,w,t){var r=(t&&t.bufferInner?t.bufferInner:0)|Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner,
C=(t&&t.bufferSiblings?t.bufferSiblings*u:0)|(Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings<1?u*Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings:Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings);t=(t&&t.thickness?t.thickness:0)|Smits.PhyloCanvas.Render.Parameters.binaryChartThickness;for(var E=0;E<o.length;E++){var D=o[E];c.draw(new Smits.PhyloCanvas.Render.Path(z(m+r,D.y-u/2+C/2,m+r+t,D.y+u/2-C/2),{attr:Smits.PhyloCanvas.Render.Style.getStyle(D.chart[w],
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