jsphylosvg-color-min.js

Smits={},Smits.Common={nodeIdIncrement:0,activeNode:0,roundFloat:function(e,t){for(var n=0,r=1;t>n;)r*=10,n++;return Math.round(e*r)/r},apply:function(e,t){if(e&&"object"==typeof t)for(var n in t)e[n]=t[n];return e},addRaphEventHandler:function(e,t,n,r){try{e[t](function(e,t){return function(n,r){var a=t;a.e=n,e(a)}}(n,r))}catch(a){}},isInteger:function(e){return!isNaN(parseInt(e))},isXMLSerializerAvailable:function(){return"function"==typeof XMLSerializer?!0:!1},createSvgEl:function(e,t){if(e=document.createElementNS("http://www.w3.org/2000/svg",e),t)for(var n in t)t.hasOwnProperty(n)&&e.setAttribute(n,String(t[n]));return e},createGradientEl:function(e,t,n){if("radialGradient"!=t.type)return!1;var r=Smits.Common.createSvgEl("radialGradient",{id:e,gradientUnits:"userSpaceOnUse",cx:n[0],cy:n[1],r:n[2],fx:n[0],fy:n[1]});if(t.stop)for(var a=t.stop,i=0;i<a.length;i++){var s=a[i];s["@attributes"]?r.appendChild(Smits.Common.createSvgEl("stop",s["@attributes"])):(s._attributes&&delete s._attributes,s._children&&delete s._children,s.__proto__&&delete s.__proto__,r.appendChild(Smits.Common.createSvgEl("stop",s)))}return r},setCssStyle:function(e,t){var n=document.styleSheets[0];n.addRule?n.addRule(e,t):n.insertRule&&n.insertRule(e+" { "+t+" }",n.cssRules.length)}},Smits.PhyloCanvas=function(){var e,t,n,r,a;return function(i,s,l,o,h){if(this.getNewickObject=function(){return n},this.clear=function(){},this.scale=function(e){r.svg.scale(e)},this.getSvg=function(){return r},this.getPhylogram=function(){return e},this.getSvgSource=function(){if(Raphael.svg&&Smits.Common.isXMLSerializerAvailable()){var e=new XMLSerializer;return e.serializeToString(r.svg.canvas)}return!1},"object"==typeof i)if(i.xml){if(i.fileSource)var c=i.xml;else var c=XMLObjectifier.textToXML(i.xml);c=XMLObjectifier.xmlToJSON(c),a=new Smits.PhyloCanvas.PhyloxmlParse(c)}else if(i.phyloxml){if(i.fileSource)var c=i.phyloxml;else var c=XMLObjectifier.textToXML(i.phyloxml);c=XMLObjectifier.xmlToJSON(c),a=new Smits.PhyloCanvas.PhyloxmlParse(c)}else if(i.nexml){if(i.fileSource)var c=i.nexml;else var c=XMLObjectifier.textToXML(i.nexml);c=XMLObjectifier.xmlToJSON(c),a=new Smits.PhyloCanvas.NexmlParse(c,i)}else i.json?a=new Smits.PhyloCanvas.PhyloxmlParse(i.json):i.newick?a=new Smits.PhyloCanvas.NewickParse(i.newick):i.nexmlJson?a=new Smits.PhyloCanvas.NexmlJsonParse(i):alert("Please set the format of input data");else a=new Smits.PhyloCanvas.NewickParse(i);t=s,r=new Smits.PhyloCanvas.Render.SVG(t,l,o),e="circular"==h?new Smits.PhyloCanvas.Render.CircularPhylogram(r,a):new Smits.PhyloCanvas.Render.Phylogram(r,a)}}(),Smits.PhyloCanvas.prototype={},Smits.PhyloCanvas.Node=function(){return function(e,t){this.id=Smits.Common.nodeIdIncrement+=1,this.level=0,this.len=0,this.newickLen=0,this.name="",this.type="",this.chart={},this.img=[],e&&Smits.Common.apply(this,e),this._countAllChildren=!1,this._countImmediateChildren=!1,this._midBranchPosition=!1,this.children=new Array,t&&t.children.push(this)}}(),Smits.PhyloCanvas.Node.prototype={getCountAllChildren:function(){if(this._countAllChildren!==!1)return this._countAllChildren;var e=0;for(var t in this.children)if(Smits.Common.isInteger(t)){var n=this.children[t];n.children&&n.children.length>0?e+=n.getCountAllChildren():e++}return this._countAllChildren=e,e},getCountImmediateChildren:function(){if(this._countImmediateChildren!==!1)return this._countImmediateChildren;var e=0;for(var t in this.children){var n=this.children[t];e+=n.length}return this._countImmediateChildren=e,e},getMidbranchPosition:function(e){if(this._midBranchPosition!==!1)return this._midBranchPosition;for(var t=[0,0],n=0;n<this.children.length;n++){var r=this.children[n];r.children&&r.children.length>0?0==n&&e?(t[0]=r.getMidbranchPosition(!0),t[1]+=r.getCountAllChildren()-1):0==n?(t[0]=r.getMidbranchPosition(),t[1]+=r.getCountAllChildren()):n==this.children.length-1?t[1]+=r.getMidbranchPosition():t[1]+=r.getCountAllChildren():0==n&&e?t[0]=0:0==n?(t[0]=1,t[1]+=1):n==this.children.length-1?t[1]+=1:t[1]+=1}return this._midBranchPosition=t[1]>=t[0]?(t[1]+t[0])/2:t[0],this._midBranchPosition}},Smits.PhyloCanvas.NewickParse=function(){var e,t,n,r,a,i=0,s=0,l=function(e){for(var n=new Smits.PhyloCanvas.Node;")"!==t&&","!==t;)":"===t?(d(),n.len=Smits.Common.roundFloat(h(),4),0==n.len&&(n.len=1e-4)):"'"===t||'"'===t?(n.type="label",n.name=c(t)):(n.type="label",n.name=h());return n.level=e.level+1,n},o=function(e){var n=new Smits.PhyloCanvas.Node;for(e&&(n.level=e.level+1);")"!==t;)d(),"("===t?n.children.push(o(n)):n.children.push(l(n));return d(),":"!==t&&")"!==t&&","!==t&&";"!==t&&(n.type="label",n.name=h()),":"===t&&(d(),n.len=Smits.Common.roundFloat(h(),4),0==n.len&&(n.len=1e-4),n.type="stem"),n},h=function(){for(var e="";":"!==t&&")"!==t&&","!==t&&";"!==t;)e+=t,d();return e},c=function(e){for(var n="";t!==e;)n+=t,d();return n},d=function(){return t=e.charAt(n),n+=1,t},u=function(e,t){if(e.children&&e.children.length)for(var n=0;n<e.children.length;n++){var r=e.children[n];0===r.len&&(r.len=1),r.newickLen=Smits.Common.roundFloat(r.len+e.newickLen,4),r.level>i&&(i=r.level),r.newickLen>s&&(s=r.newickLen),r.children.length>0&&u(r,e)}return e};return function(t){this.getRoot=function(){return r},this.getLevels=function(){return i},this.getNewickLen=function(){return s},this.getValidate=function(){return a},i=0,s=0,e=t,n=0,d(),r=o(),r=u(r)}}(),Smits.PhyloCanvas.NewickParse.prototype={},Smits.PhyloCanvas.PhyloxmlParse=function(){var e,t,n=0,r=0,a=function(e,n){var r=new Smits.PhyloCanvas.Node;if(n&&(r.level=n.level+1),e.clade&&e.clade.length)for(var i=0;i<e.clade.length;i++){var s=e.clade[i];r.children.push(a(s,r))}if(e.branch_length&&("object"==typeof e.branch_length&&(e.branch_length=e.branch_length[0].Text),r.len=Smits.Common.roundFloat(e.branch_length,4),0==r.len&&(r.len=1e-4)),e.color?(r.red=e.color[0].red[0].Text,r.green=e.color[0].green[0].Text,r.blue=e.color[0].blue[0].Text):(r.red=0,r.green=0,r.blue=0),e.property&&"node"==e.property[0].applies_to&&"style:font_color"==e.property[0].ref&&(r.font_color_hex=e.property[0].Text),e.name?(r.type="label",r.name=e.name[0].Text,e.name[0]&&e.name[0].style&&(r.style=e.name[0].style),e.name[0]&&e.name[0].bgStyle&&(r.bgStyle=e.name[0].bgStyle)):e.confidence&&(r.name=e.confidence[0].Text),e.sequence&&e.sequence[0]&&e.sequence[0].name&&e.sequence[0].name[0]&&e.sequence[0].name[0].Text&&(r.sequenceName=e.sequence[0].name[0].Text),e.taxonomy&&e.taxonomy[0]&&(e.taxonomy[0].scientific_name&&e.taxonomy[0].scientific_name[0]&&e.taxonomy[0].scientific_name[0].Text&&(r.taxonomyScientificName=e.taxonomy[0].scientific_name[0].Text),e.taxonomy[0].common_name&&e.taxonomy[0].common_name[0]&&e.taxonomy[0].common_name[0].Text&&(r.taxonomyCommonName=e.taxonomy[0].common_name[0].Text)),e.sequence&&e.sequence[0]&&e.sequence[0].accession&&e.sequence[0].accession[0]&&e.sequence[0].accession[0].Text&&(r.sequenceAccession=e.sequence[0].accession[0].Text),e.point&&(r.LatLong=[e.point[0].lat[0].Text,e.point[0]["long"][0].Text]),r.name||(r.sequenceName?r.name=r.sequenceName:r.taxonomyScientificName?r.name=r.taxonomyScientificName:r.taxonomyCommonName?r.name=r.taxonomyCommonName:r.sequenceAccession&&(r.name=r.sequenceAccession),r.name&&(r.type="label")),e.annotation&&(e.annotation[0]&&e.annotation[0].desc&&e.annotation[0].desc[0]&&e.annotation[0].desc[0].Text&&(r.description=e.annotation[0].desc[0].Text),e.annotation[0]&&e.annotation[0].uri&&e.annotation[0].uri[0]&&e.annotation[0].uri[0].Text&&(r.uri=e.annotation[0].uri[0].Text),e.annotation[0]&&e.annotation[0].img))for(var i in e.annotation[0].img)Smits.Common.isInteger(i)&&(r.img[i]=e.annotation[0].img[i].Text);if(e.chart&&e.chart[0])for(var i in e.chart[0])"Text"!=i&&"_children"!=i&&(r.chart[i]=e.chart[0][i][0].Text);return r&&r.level>1&&(r.len||(t="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.")),r},i=function(e,t){if(e.children&&e.children.length)for(var a=0;a<e.children.length;a++){var s=e.children[a];s.newickLen=Math.round(1e4*(s.len+e.newickLen))/1e4,s.level>n&&(n=s.level),s.newickLen>r&&(r=s.newickLen),s.children.length>0&&i(s,e)}return e},s=function(e,t){for(var n in e)"_children"!=n&&"Text"!=n&&("rectangular"==n||"circular"==n?s(e[n][0],n):(Smits.PhyloCanvas.Render.Parameters[n]||(Smits.PhyloCanvas.Render.Parameters[n]={}),Smits.PhyloCanvas.Render.Parameters.set(n,e[n][0].Text,t)))};return function(l){if(this.getRoot=function(){return e},this.getLevels=function(){return n},this.getNewickLen=function(){return r},this.getValidate=function(){return t},l.phylogeny&&l.phylogeny[0]&&l.phylogeny[0].clade&&(e=a(l.phylogeny[0].clade[0])),l.phylogeny&&l.phylogeny[0]&&l.phylogeny[0].render&&l.phylogeny[0].render[0]){var o=l.phylogeny[0].render[0];if(o&&o.styles){var h=o.styles[0];for(var c in h)if("_children"!=c&&"Text"!=c)if(h[c][0].type&&"radialGradient"==h[c][0].type&&Raphael.svg)h[c][0].name=c,Smits.PhyloCanvas.Render.Style[c]=h[c][0],Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList||(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList=[]),Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.push(c);else{Smits.PhyloCanvas.Render.Style[c]||(Smits.PhyloCanvas.Render.Style[c]={});for(var d in h[c][0])"_attributes"!=d&&"_children"!=d&&"type"!=d&&(Smits.PhyloCanvas.Render.Style[c][d.replace("_","-")]=h[c][0][d])}}if(o&&o.parameters&&s(o.parameters[0]),o&&o.charts){var u=o.charts[0];for(var c in u)if("_children"!=c&&"Text"!=c)for(var d in u[c])"binary"==u[c][d].type?(u[c][d].chart=c,Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(u[c][d])):"integratedBinary"==u[c][d].type?(u[c][d].chart=c,Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(u[c][d])):"bar"==u[c][d].type&&(u[c][d].chart=c,1==Smits.PhyloCanvas.Render.Parameters.barCharts.length&&Smits.PhyloCanvas.Render.Parameters.barCharts.shift(),Smits.PhyloCanvas.Render.Parameters.barCharts.push(u[c][d]))}}e=i(e)}}(),Smits.PhyloCanvas.PhyloxmlParse.prototype={},Smits.PhyloCanvas.NexmlParse=function(){var e,t,n,r,a=0,i=0,s=function(e,t,a){var i=new Smits.PhyloCanvas.Node;a&&(i.level=a.level+1);for(var l=0;l<n.length;l++)if(n[l].source==e.id)for(var o=0;o<r.length;o++)n[l].target==r[o].id&&i.children.push(s(r[o],n[l].length,i));return i&&i.level>0&&!i.len&&(i.len=1),t&&(i.len=Smits.Common.roundFloat(t,4),0==i.len&&(i.len=1e-4)),e.label&&(i.type="label",i.name=e.label,e.style&&(i.style=e.style)),i},l=function(e,t){if(e.children&&e.children.length)for(var n=0;n<e.children.length;n++){var r=e.children[n];r.newickLen=Math.round(1e4*(r.len+e.newickLen))/1e4,r.level>a&&(a=r.level),r.newickLen>i&&(i=r.newickLen),r.children.length>0&&l(r,e)}return e};return function(o,h){this.getRoot=function(){return e},this.getLevels=function(){return a},this.getNewickLen=function(){return i},this.getValidate=function(){return t},h.tree&&o.trees[0]&&o.trees[0].tree[h.tree-1]?(n=o.trees[0].tree[h.tree-1].edge,r=o.trees[0].tree[h.tree-1].node):(n=o.trees[0].tree[0].edge,r=o.trees[0].tree[0].node);for(var c=0;c<r.length;c++){var d=0;if(r[c].root&&"true"==r[c].root){e=r[c];break}for(var u=0;u<n.length;u++)n[u].target==r[c].id&&d++;if(0==d){e=r[c];break}}e?(e=s(e),e=l(e)):t="Error. Currently, only rooted NeXML trees are supported."}}(),Smits.PhyloCanvas.NexmlParse.prototype={},Smits.PhyloCanvas.NexmlJsonParse=function(){var e,t,n=0,r=0,a=[],i=[],s=function(e,n,r){var l=new Smits.PhyloCanvas.Node;r&&(l.level=r.level+1);for(var o=0;o<a.length;o++)if(a[o].source==e.id)for(var h=0;h<i.length;h++)a[o].target==i[h].id&&l.children.push(s(i[h],a[o].length,l));return n&&(l.len=Smits.Common.roundFloat(n,4),0==l.len&&(l.len=1e-4)),e.label&&(l.type="label",l.name=e.label,e.accession&&(l.accession=e.accession),e.style&&(l.style=e.style),e.bgStyle&&(l.bgStyle=e.bgStyle)),e.chart&&(l.chart=e.chart),l&&l.level>1&&(l.len||(t="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.")),l},l=function(e,t){if(e.children&&e.children.length)for(var a=0;a<e.children.length;a++){var i=e.children[a];i.newickLen=Math.round(1e4*(i.len+e.newickLen))/1e4,i.level>n&&(n=i.level),i.newickLen>r&&(r=i.newickLen),i.children.length>0&&l(i,e)}return e},o=function(e,t){for(var n in e)"_children"!=n&&"Text"!=n&&("rectangular"==n||"circular"==n?o(e[n],n):(Smits.PhyloCanvas.Render.Parameters[n]||(Smits.PhyloCanvas.Render.Parameters[n]={}),Smits.PhyloCanvas.Render.Parameters.set(n,e[n],t)))};return function(h){this.getRoot=function(){return e},this.getLevels=function(){return n},this.getNewickLen=function(){return r},this.getValidate=function(){return t};var c=h.nexmlJson.nexml,d=c.render;if(d&&d.styles){var u=d.styles;for(var m in u)if("_children"!=m&&"Text"!=m)if(u[m]["@attributes"].type&&"radialGradient"==u[m]["@attributes"].type&&Raphael.svg)u[m].name=m,u[m].type=u[m]["@attributes"].type,Smits.PhyloCanvas.Render.Style[m]=u[m],Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList||(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList=[]),Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.push(m);else{Smits.PhyloCanvas.Render.Style[m]||(Smits.PhyloCanvas.Render.Style[m]={});for(var y in u[m]["@attributes"])"_attributes"!=y&&"_children"!=y&&"type"!=y&&(Smits.PhyloCanvas.Render.Style[m][y.replace("_","-")]=u[m]["@attributes"][y])}}if(d&&d.parameters&&o(d.parameters),d&&d.charts){var v=d.charts;for(var m in v)v[m]["@attributes"].chart=m,"binary"==v[m]["@attributes"].type?Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(v[m]["@attributes"]):"integratedBinary"==v[m]["@attributes"].type?Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(v[m]["@attributes"]):"bar"==v[m]["@attributes"].type&&Smits.PhyloCanvas.Render.Parameters.barCharts.push(v[m]["@attributes"])}if(h.tree&&c.trees[0]&&c.trees[0].tree[h.tree-1])a=c.trees[0].tree[h.tree-1].edge,i=c.trees[0].tree[h.tree-1].node;else{for(var m=0;m<c.trees.tree.edge.length;m++)a.push(c.trees.tree.edge[m]["@attributes"]);for(var m=0;m<c.trees.tree.node.length;m++){var f=c.trees.tree.node[m]["@attributes"];f.label&&(f.chart=c.trees.tree.node[m].chart),i.push(f)}}for(var m=0;m<i.length;m++)i[m].root&&"true"==i[m].root&&(e=i[m]);e?(e=s(e),e=l(e)):t="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":". 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Smits.PhyloCanvas.Render.Path(["M",n+1e-4,w,"L",n,w,"L",n,L,"L",n+1e-4,L],{attr:Smits.PhyloCanvas.Render.Style.line})))}else{if(l=n,o=Smits.Common.roundFloat(n+a*t.len,2),h=C,c=C,r=t.red,g=t.green,b=t.blue,t.y=C,p.push(t),e.draw(new Smits.PhyloCanvas.Render.Line(l,o,h,c,r,g,b)),f.alignRight&&e.draw(new Smits.PhyloCanvas.Render.Path(["M",o,h,"L",f.alignPadding+s,c],{attr:Smits.PhyloCanvas.Render.Style.connectedDash})),t.name){var u={};t.style&&(u=Smits.PhyloCanvas.Render.Style.getStyle(t.style,"text")),t.font_color_hex?u.fill=t.font_color_hex:u.fill="#000000",u["text-anchor"]="start",t.uri&&(u.href=t.uri),t.description&&(u.title=t.description);var O=e.draw(new Smits.PhyloCanvas.Render.Text(f.alignRight?s+f.bufferInnerLabels+f.alignPadding:o+f.bufferInnerLabels,c,t.name,{attr:u}));P=Math.max(O[1],P),Smits.PhyloCanvas.Render.Parameters.mouseRollOver&&Smits.Common.addRaphEventHandler(O[0],"mouseover",Smits.PhyloCanvas.Render.Parameters.mouseRollOver,{svg:e,node:t,x:o,y:c,textEl:O[0]}),Smits.PhyloCanvas.Render.Parameters.mouseRollOut&&Smits.Common.addRaphEventHandler(O[0],"mouseout",Smits.PhyloCanvas.Render.Parameters.mouseRollOut,{svg:e,node:t,x:o,y:c,textEl:O[0]}),Smits.PhyloCanvas.Render.Parameters.onClickAction&&Smits.Common.addRaphEventHandler(O[0],"click",Smits.PhyloCanvas.Render.Parameters.onClickAction,{svg:e,node:t,x:o,y:c,textEl:O[0]})}S&&(S=!1)}return[h,c]},w=function(){y=C+i,c=0,d=f.showScaleBar*a,e.draw(new Smits.PhyloCanvas.Render.Line(c,d,y,y)),e.draw(new Smits.PhyloCanvas.Render.Text((c+d)/2,y-8,f.showScaleBar))},L=function(t,n,r){for(var a=(r&&r.bufferInner?r.bufferInner:0)|Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner,s=(r&&r.bufferSiblings?r.bufferSiblings*i:0)|(Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings<1?i*Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings:Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings),l=(r&&r.thickness?r.thickness:0)|Smits.PhyloCanvas.Render.Parameters.binaryChartThickness,o=0;o<p.length;o++){var h=p[o];e.draw(new Smits.PhyloCanvas.Render.Path(R(t+a,h.y-i/2+s/2,t+a+l,h.y+i/2-s/2),{attr:Smits.PhyloCanvas.Render.Style.getStyle(h.chart[n],"textSecantBg")}))}return t+a+l},k=function(t,n,r){for(var a,s=[],l=r&&r.bufferInner?r.bufferInner:0|Smits.PhyloCanvas.Render.Parameters.barChartBufferInner,o=r&&r.height?r.height:0|Smits.PhyloCanvas.Render.Parameters.barChartHeight,h=r&&r.width?r.width<1?i*r.width:r.width:0|(Smits.PhyloCanvas.Render.Parameters.barChartWidth<1?i*Smits.PhyloCanvas.Render.Parameters.barChartWidth:Smits.PhyloCanvas.Render.Parameters.barChartWidth),c=0,d=0;d<p.length;d++)s.push(p[d].chart[n]);a=Math.max.apply(null,s),c=Smits.Common.roundFloat(o/a,4);for(var d=0;d<p.length;d++){var u=p[d];e.draw(new Smits.PhyloCanvas.Render.Path(R(t+l,u.y-h/2,t+l+c*u.chart[n],u.y+h/2),{attr:Smits.PhyloCanvas.Render.Style.getStyle(u.chart[n],"barChart")}))}return t+l+o};return function(r,c){this.getCanvasSize=function(){return[t,n]},this.getRoot=function(){return c.getRoot()},c.getValidate()&&e.draw(0,0,c.getValidate()),e=r;var d=c.getRoot(),y=c.getNewickLen();if(t=e.canvasSize[0],n=e.canvasSize[1],u=f.bufferX,m=f.paddingX,v=f.paddingY,l=f.minHeightBetweenLeaves,C=v,a=Math.round((t-u-2*m)/y),i=Math.round((n-2*v)/(f.showScaleBar?d.getCountAllChildren():d.getCountAllChildren()-1)),l>i&&(i=l),s=Math.round(t-u-2*m),(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length||Smits.PhyloCanvas.Render.Parameters.barCharts.length)&&(f.alignRight=!0),x(d,m),f.showScaleBar&&w(),o=s+P+f.bufferInnerLabels,Smits.PhyloCanvas.Render.Parameters.binaryCharts.length){var g=Smits.PhyloCanvas.Render.Parameters.binaryCharts;for(var S in g)o=L(o,g[S].chart,g[S])}if(Smits.PhyloCanvas.Render.Parameters.barCharts.length){var b=Smits.PhyloCanvas.Render.Parameters.barCharts;for(var S in b)h=k(o,b[S].chart,b[S])}p=[],bgLabelsHold=[]}}(),Smits.PhyloCanvas.Render.Phylogram.prototype={},Smits.PhyloCanvas.Render.CircularPhylogram=function(){function e(e,t){return 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y=a.children[m],g=s(y,i);g>0&&u.push(g)}var S=Smits.Common.roundFloat(Math.min.apply(null,u),4),C=Smits.Common.roundFloat(Math.max.apply(null,u),4);0!=a.level&&d.draw(new Smits.PhyloCanvas.Render.Path(l("M",e(i+.01,S),"L",n(i,S,C,{noMove:!0}),"L",e(i+.01,C)))),a.len&&(c=Smits.Common.roundFloat(S+(C-S)/2,4),d.draw(new Smits.PhyloCanvas.Render.Path(r(c,o,h))))}else if(a.y=k,_.push(a),o=i,h=i=Smits.Common.roundFloat(i+v*a.len),c=k,d.draw(new Smits.PhyloCanvas.Render.Path(r(c,o,h))),d.draw(new Smits.PhyloCanvas.Render.Path(r(c,h,p),{attr:Smits.PhyloCanvas.Render.Style.connectedDash})),a.name){var P=e(p+w.bufferInnerLabels,c),R=t(c),x=R[0],T=R[1],N={};a.style&&Smits.Common.apply(N,Smits.PhyloCanvas.Render.Style.getStyle(a.style,"text")),a.font_color_hex?N.fill=a.font_color_hex:N.fill="#000000",N["text-anchor"]=T,a.uri&&(N.href=a.uri),a.description&&(N.title=a.description);var O=d.draw(new Smits.PhyloCanvas.Render.Text(P[0],P[1],a.name,{attr:N,rotate:[x,P[0],P[1]]}));a.bgStyle&&M.push([a.bgStyle,c]);var P=e(h,c);Smits.PhyloCanvas.Render.Parameters.mouseRollOver&&Smits.Common.addRaphEventHandler(O[0],"mouseover",Smits.PhyloCanvas.Render.Parameters.mouseRollOver,{svg:d,node:a,x:P[0],y:P[1],textEl:O[0]}),Smits.PhyloCanvas.Render.Parameters.mouseRollOut&&Smits.Common.addRaphEventHandler(O[0],"mouseout",Smits.PhyloCanvas.Render.Parameters.mouseRollOut,{svg:d,node:a,x:P[0],y:P[1],textEl:O[0]}),Smits.PhyloCanvas.Render.Parameters.onClickAction&&Smits.Common.addRaphEventHandler(O[0],"click",Smits.PhyloCanvas.Render.Parameters.onClickAction,{svg:d,node:a,x:P[0],y:P[1],textEl:O[0]}),B=Math.max(O[1],B)}return L&&(L=!1),c}function l(e){for(var t=e,n=1;n<arguments.length;n++)t=t.concat(arguments[n]);return t}function o(){var e=[];if(M.length>0){if(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList)for(var t=0;t<Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.length;t++){var 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