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[Treebase-guts] SF.net SVN: treebase:[935] trunk/treebase-web/src/main/webapp/scripts/ jsphylosvg-min.js
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From: <lol...@us...> - 2011-08-01 20:18:16
|
Revision: 935
http://treebase.svn.sourceforge.net/treebase/?rev=935&view=rev
Author: loloyohe
Date: 2011-08-01 20:18:08 +0000 (Mon, 01 Aug 2011)
Log Message:
-----------
Updated the jsphylosvg-min.js with the most recent version hoping to see what happens with the tree visualizer.
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 2011-07-27 21:58:58 UTC (rev 934)
+++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-08-01 20:18:08 UTC (rev 935)
@@ -1,2505 +1,75 @@
-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;
- }
-
- // RAV: it is more robust to search for the root by the tree topology
- // then by looking for a @root attribute. Valid NeXML tree structures
- // always have one node without normal edges pointing into it. The
- // root attribute is used to indicate that this tree is actually rooted.
- // Compare this with nexus/newick: newick strings are always implicitly
- // rooted, even if the tree is called a utree or the [&U] token is used.
- for(i = 0; i < nexNodes.length; i++){
- for(i = 0; i < nexNodes.length; i++) {
- var targetCount = 0;
- for(j = 0; j < nexEdges.length; j++) {
- if(nexEdges[j].target == nexNodes[i].id) {
- targetCount++;
- }
- }
- if ( targetCount == 0 ) {
- 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(this[requestStyle]){
- return this[requestStyle];
- } else {
- return this[fallbackStyle];
- }
-
- }
-
-
-
-};Smits.PhyloCanvas.Render.Parameters = {
-
- /* DEFAULT PARAMETERS */
- jsOverride: 0, // If set, js will override chart's file setting
-
- /** Phylogram parameters are separated because they behave very differently **/
-
- /* Rectangular Phylogram */
- Rectangular : {
- bufferX : 200, // Reduces the available canvas space for tree branches, allowing
- // for more space for the textual/charting components
- bufferY : 40,
- bufferInnerLabels : 10, // Pixels
- bufferOuterLabels : 5, // Pixels
- minHeightBetweenLeaves : 10, // Should probably set pretty low, as clipping may occur if it needs to be implemented
-
- alignPadding : 0, // Pixels to push the labels out by - this extension should be
- // compensated by an increase in bufferX too
- alignRight : false,
-
- showScaleBar : false // (STRING, e.g. "0.05") Shows a scale bar at the bottom of the tree
- },
-
- /* Circular Phylogram */
- Circular : {
- bufferRadius : 0.33, // Margins of Tree Circle
- // If > 1, it is in pixels
- // If < 1, it is a percentage of the full canvas size
- bufferAngle : 20, // controls split size in circle
- initStartAngle : 160,
- innerCircleRadius : 0,
- minHeightBetweenLeaves : 5,
-
- /* Labels */
- bufferInnerLabels : 2, // Pixels
- bufferOuterLabels : 5 // Pixels
- },
-
- /* Charts */
- binaryCharts : [],
- integratedBinaryCharts : [],
- barCharts : [],
-
- /* Binary Defaults */
- binaryChartBufferInner : 5,
- binaryChartBufferSiblings : 0.01,
- binaryChartThickness : 15,
- binaryChartDisjointed : false,
-
- /* Bar Defaults */
- barChartBufferInner : 3,
- barChartHeight : 50,
- barChartWidth : 0.5, // If > 1, it is in pixels
- // If < 1, it is a percentage of the node width
-
- /*
- Rollover Events
- At minimum, the params object has the following properties:
- .svg
- .node
- .x
- .y
- .textEl
- */
- mouseRollOver : function(params) {
- if(params.node.edgeCircleHighlight){
- params.node.edgeCircleHighlight.show();
- } else {
- var circleObject = params.svg.draw(
- new Smits.PhyloCanvas.Render.Circle(
- params.x, params.y, 5,
- { attr: Smits.PhyloCanvas.Render.Style.highlightedEdgeCircle }
- )
- );
- params.node.edgeCircleHighlight = circleObject[0];
- }
- params.textEl.attr({ fill: 'red' });
- },
- mouseRollOut : function(params) {
- params.node.edgeCircleHighlight.hide();
- params.textEl.attr({ fill: '#000' });
- },
-
- set : function(param, value, treeType){
- if(!this.jsOverride){
- if(treeType){
- if(treeType == 'circular'){
- this['Circular'][param] = parseFloat(value);
- } else if (treeType == 'rectangular'){
- this['Rectangular'][param] = parseFloat(value);
- }
- } else {
- this[param] = parseFloat(value);
- }
- }
- }
-};Smits.PhyloCanvas.Render.Line = function(){
-
- return function(x1, x2, y1, y2, params){
- /* Defaults */
- this.type = 'line';
- this.attr = Smits.PhyloCanvas.Render.Style.line;
-
- this.x1 = x1;
- this.x2 = x2;
- this.y1 = y1;
- this.y2 = y2;
-
- if(params) {
- Smits.Common.apply(this, params);
- if(params.attr) this.attr = params.attr;
- }
-
- }
-}();Smits.PhyloCanvas.Render.Text = function(){
-
- return function(x, y, text, params){
- /* Defaults */
- this.type = 'text';
- this.attr = Smits.PhyloCanvas.Render.Style.text;
-
- this.x = x;
- this.y = y;
- this.text = text;
-
- if(params) {
- Smits.Common.apply(this, params);
- if(params.attr) this.attr = params.attr;
- }
- }
-}();Smits.PhyloCanvas.Render.Path = function(){
- var attr = Smits.PhyloCanvas.Render.Style.path;
-
- return function(path, params){
- /* Defaults */
- this.type = 'path';
- this.attr = Smits.PhyloCanvas.Render.Style.path;
-
- this.path = path;
- if(params) {
- Smits.Common.apply(this, params);
- if(params.attr) this.attr = params.attr;
- }
-
- }
-}();Smits.PhyloCanvas.Render.Circle = function(){
-
- return function(x, y, radius, params){
- /* Defaults */
- this.type = 'circle';
-
- this.x = x;
- this.y = y;
- this.radius = radius;
-
- if(params) {
- Smits.Common.apply(this, params);
- if(params.attr) this.attr = params.attr;
- }
-
- }
-}();Smits.PhyloCanvas.Render.SVG = function(){
- var divId,
- canvasSize;
-
- return function(sDivId, canvasWidth, canvasHeight){
-
- /* CONSTRUCTOR */
- divId = sDivId;
- this.canvasSize = [canvasWidth, canvasHeight];
-
- this.svg = Raphael(sDivId, this.canvasSize[0], this.canvasSize[1]);
-
- }
-
-}();
-
-Smits.PhyloCanvas.Render.SVG.prototype = {
-
- render : function(){
- var instructs = this.phylogramObject.getDrawInstructs();
-
- for (var i = 0; i < instructs.length; i++) {
- if(instructs[i].type == 'line'){
- var line = this.svg.path(["M", instructs[i].x1, instructs[i].y1, "L", instructs[i].x2, instructs[i].y2]).attr(Smits.PhyloCanvas.Render.Style.line);
- } else if(instructs[i].type == 'path'){
- var path = this.svg.path(instructs[i].path).attr(instructs[i].attr);
- } else if(instructs[i].type == 'circle'){
- var path = this.svg.circle(instructs[i].x, instructs[i].y, instructs[i].radius).attr({
- "stroke": 'red'
- });
- } else {
- var text = this.svg.text(instructs[i].x, instructs[i].y, instructs[i].text).attr(Smits.PhyloCanvas.Render.Style.text);
- if(instructs[i].attr){
- text.attr(instructs[i].attr);
- }
- if(instructs[i].rotate){
- text.rotate(instructs[i].rotate);
- }
-
- var bbox = text.getBBox();
- var hyp = Math.sqrt( (bbox.height * bbox.height) + (bbox.width * bbox.width) ); // get hypotenuse
-
- }
- }
- },
-
- draw : function(instruct){
- var obj,
- param;
- if(instruct.type == 'line'){
- obj = this.svg.path(["M", instruct.x1, instruct.y1, "L", instruct.x2, instruct.y2]).attr(Smits.PhyloCanvas.Render.Style.line);
- } else if(instruct.type == 'path'){
- obj = this.svg.path(instruct.path).attr(instruct.attr);
- } else if(instruct.type == 'circle'){
- obj = this.svg.circle(instruct.x, instruct.y, instruct.radius).attr({
- "stroke": 'red'
- });
- } else if(instruct.type == 'text'){
- obj = this.svg.text(instruct.x, instruct.y, instruct.text).attr(Smits.PhyloCanvas.Render.Style.text);
- if(instruct.attr){
- obj.attr(instruct.attr);
- }
- if(instruct.rotate){
- obj.rotate(instruct.rotate);
- }
-
- var bbox = obj.getBBox();
- param = Math.sqrt( (bbox.height * bbox.height) + (bbox.width * bbox.width) ); // get hypotenuse
- }
-
- return [obj, param];
- }
-
-};Smits.PhyloCanvas.Render.Phylogram = function(){
-
- var svg,
- sParams = Smits.PhyloCanvas.Render.Parameters.Rectangular, // Easy Reference
- canvasX, canvasY,
- scaleX, scaleY, maxBranch,
- minHeightBetweenLeaves,
- firstBranch = true,
- absoluteY = 0, maxLabelLength = 0,
- outerX, outerY, outerRadius,
- x1, x2, y1, y2,
- positionX, positionY,
- bufferX, bufferY, labelsHold = [],
-
- textPadding = function (y){
- return y + Math.round(y / 4);
- },
-
- rectLinePathArray = function (x1, y1, x2, y2){
- return ["M", x1, y1, "L", x2, y1, "L", x2, y2, "L", x1, y2, "Z"];
- },
-
- recursiveCalculateNodePositions = function (node, positionX){
- if(node.len){
- if(firstBranch){
- firstBranch = false;
- } else {
- if(node.children.length == 0) absoluteY = Smits.Common.roundFloat(absoluteY + scaleY, 4);
- }
- }
-
- if(node.children.length > 0){
- var nodeCoords = [], x1,x2,y1,y2;
- if(node.len){ // draw stem
- x1 = positionX;
- x2 = positionX = Smits.Common.roundFloat(positionX + (scaleX * node.len), 4);
- y1 = absoluteY + (node.getMidbranchPosition() * scaleY);
- y2 = y1;
-
- svg.draw(new Smits.PhyloCanvas.Render.Line(x1, x2, y1, y2));
- }
-
- if(node.name){ // draw bootstrap values
- var attr = {};
- attr = Smits.PhyloCanvas.Render.Style.getStyle('bootstrap', 'text');
- if(node.uri) { attr.href = node.uri };
- if(node.description) {attr.title = node.description };
- if(node.level == 0){
- var innerX2 = 2;
- var innerY2 = absoluteY + (node.getMidbranchPosition() * scaleY);
- } else {
- var innerX2 = x2;
- var innerY2 = y2;
- }
-
- svg.draw(
- new Smits.PhyloCanvas.Render.Text(
- innerX2 + 5, innerY2,
- node.name,
- {
- attr: attr
- }
- )
- );
- //svg.draw(new Smits.PhyloCanvas.Render.Text(x2 + 5, y2, node.name));
- }
-
- if(node.children && node.children.length){
- for(var i = 0; i < node.children.length; i++){
- var child = node.children[i];
- nodeCoords.push(recursiveCalculateNodePositions(child, positionX));
- }
- }
-
- var flatNodeCoords = []; // establish vertical bounds
- for ( var i = 0; i < nodeCoords.length; i++ ){
- if(nodeCoords[i][0]) flatNodeCoords.push(nodeCoords[i][0]);
- if(nodeCoords[i][1]) flatNodeCoords.push(nodeCoords[i][1]);
- }
- var verticalY1 = Math.min.apply(null, flatNodeCoords );
- var verticalY2 = Math.max.apply(null, flatNodeCoords);
-
- // draw vertical
- // hack: little elbows at ends in order to prevent stair-effects at edges
- svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- [
- "M", positionX + 0.0001, verticalY1,
- "L", positionX, verticalY1,
- "L", positionX, verticalY2,
- "L", positionX + 0.0001, verticalY2
- ],
- { attr : Smits.PhyloCanvas.Render.Style.line }
- )
- );
-
- } else {
- // label
- x1 = positionX;
- x2 = Smits.Common.roundFloat(positionX + (scaleX * node.len), 2);
- y1 = absoluteY;
- y2 = absoluteY;
-
- // preserve for later processing
- node.y = absoluteY;
- labelsHold.push(node);
-
- svg.draw(new Smits.PhyloCanvas.Render.Line(x1, x2, y1, y2));
- if(sParams.alignRight){
- svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- ["M", x2, y1, "L", sParams.alignPadding + maxBranch, y2],
- { attr : Smits.PhyloCanvas.Render.Style.connectedDash }
- )
- );
- }
-
- if(node.name){
- var attr = {};
- if(node.style){
- attr = Smits.PhyloCanvas.Render.Style.getStyle(node.style, 'text');
- }
- attr["text-anchor"] = 'start';
- if(node.uri) { attr.href = node.uri };
- if(node.description) {attr.title = node.description };
-
- var draw = svg.draw(
- new Smits.PhyloCanvas.Render.Text(
- sParams.alignRight ? maxBranch + sParams.bufferInnerLabels + sParams.alignPadding : x2 + sParams.bufferInnerLabels, y2,
- node.name,
- {
- attr: attr
- }
- )
- );
- if(node.style){
- console.log([node, attr]);
- }
- maxLabelLength = Math.max(draw[1], maxLabelLength);
-
- // Rollover, Rollout and Click Events
- if(Smits.PhyloCanvas.Render.Parameters.mouseRollOver){
- Smits.Common.addEventHandler(
- draw[0].node,
- 'mouseover',
- Smits.PhyloCanvas.Render.Parameters.mouseRollOver,
- { svg: svg, node: node, x: x2, y: y2, textEl: draw[0] }
- );
- }
- if(Smits.PhyloCanvas.Render.Parameters.mouseRollOut){
- Smits.Common.addEventHandler(
- draw[0].node,
- 'mouseout',
- Smits.PhyloCanvas.Render.Parameters.mouseRollOut,
- { svg: svg, node: node, x: x2, y: y2, textEl: draw[0] }
- );
- }
- if(Smits.PhyloCanvas.Render.Parameters.onClickAction){
- Smits.Common.addEventHandler(
- draw[0].node,
- 'click',
- Smits.PhyloCanvas.Render.Parameters.onClickAction,
- { svg: svg, node: node, x: x2, y: y2, textEl: draw[0] }
- );
- }
- }
-
- }
-
- return [y1, y2];
-
- },
-
- drawScaleBar = function (){
- y = absoluteY + scaleY;
- x1 = 0;
- x2 = sParams.showScaleBar * scaleX;
- svg.draw(new Smits.PhyloCanvas.Render.Line(x1, x2, y, y));
- svg.draw(new Smits.PhyloCanvas.Render.Text(
- (x1+x2)/2,
- y-8,
- sParams.showScaleBar)
- );
- },
-
- renderBinaryChart = function(x, groupName, params){
- var bufferInner = (params && params.bufferInner ? params.bufferInner : 0) | Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner,
- bufferSiblings = (params && params.bufferSiblings ? params.bufferSiblings * scaleY : 0) | (Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings < 1 ? scaleY * Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings : Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings),
- thickness = (params && params.thickness ? params.thickness : 0) | Smits.PhyloCanvas.Render.Parameters.binaryChartThickness,
- beginY;
-
- for(var i = 0; i < labelsHold.length; i++){
- var node = labelsHold[i];
- svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- rectLinePathArray(
- x + bufferInner,
- node.y - (scaleY/2) + (bufferSiblings/2),
- x + bufferInner + thickness,
- node.y + (scaleY/2) - (bufferSiblings/2)
- ),
- { attr: Smits.PhyloCanvas.Render.Style.getStyle(node.chart[groupName], 'textSecantBg') }
- )
- );
- }
- return x + bufferInner + thickness;
- },
-
- renderBarChart = function(x, groupName, params){
- var allValues = [], maxValue,
- bufferInner = params && params.bufferInner ? params.bufferInner : 0 | Smits.PhyloCanvas.Render.Parameters.barChartBufferInner,
- height = params && params.height ? params.height : 0 | Smits.PhyloCanvas.Render.Parameters.barChartHeight,
- width = params && params.width ? (params.width < 1 ? scaleY * params.width : params.width ) : 0 | (Smits.PhyloCanvas.Render.Parameters.barChartWidth < 1 ? scaleY * Smits.PhyloCanvas.Render.Parameters.barChartWidth : Smits.PhyloCanvas.Render.Parameters.barChartWidth),
- scaleHeight = 0;
-
- // Need to get max value
- for(var i = 0; i < labelsHold.length; i++){
- allValues.push(labelsHold[i].chart[groupName]);
- }
- maxValue = Math.max.apply(null, allValues);
- scaleHeight = Smits.Common.roundFloat(height / maxValue, 4);
-
- for(var i = 0; i < labelsHold.length; i++){
- var node = labelsHold[i];
- svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- rectLinePathArray(
- x + bufferInner,
- node.y - (width/2),
- x + bufferInner + (scaleHeight * node.chart[groupName]),
- node.y + (width/2)
- ),
- { attr: Smits.PhyloCanvas.Render.Style.getStyle(node.chart[groupName], 'barChart') }
- )
- );
- }
-
- return x + bufferInner + height;
- };
-
- return function(sSvg, dataObject){
- absoluteY = 0;
-
- /* Privileged Methods */
- this.getCanvasSize = function(){
- return [canvasX, canvasY];
- };
- this.getRoot = function(){
- return dataObject.getRoot();
- };
-
- /* CONSTRUCTOR */
- if(dataObject.getValidate()){ // Validate
- svg.draw(0,0, dataObject.getValidate());
- }
-
- svg = sSvg;
- var node = dataObject.getRoot();
- var mNewickLen = dataObject.getNewickLen();
-
- canvasX = svg.canvasSize[0]; // Full Canvas Width
- canvasY = svg.canvasSize[1]; // Full Canvas Height
-
- bufferX = sParams.bufferX;
- bufferY = sParams.bufferY;
- minHeightBetweenLeaves = sParams.minHeightBetweenLeaves;
-
- scaleX = Math.round((canvasX - bufferX) / mNewickLen);
- scaleY = Math.round((canvasY - bufferY) / (sParams.showScaleBar ? node.getCountAllChildren() + 1 : node.getCountAllChildren()) );
- if(scaleY < minHeightBetweenLeaves){
- scaleY = minHeightBetweenLeaves;
- }
- maxBranch = Math.round( canvasX - bufferX );
-
- if(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length || Smits.PhyloCanvas.Render.Parameters.barCharts.length){
- sParams.alignRight = true;
- }
-
- recursiveCalculateNodePositions(node, 0);
-
- // Draw Scale Bar
- if(sParams.showScaleBar){
- drawScaleBar();
- }
-
- outerX = maxBranch + maxLabelLength + sParams.bufferInnerLabels;
- // Draw secant highlights
- if(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length){
- var binaryCharts = Smits.PhyloCanvas.Render.Parameters.binaryCharts;
- for(var i in binaryCharts){
- outerX = renderBinaryChart(outerX, binaryCharts[i].chart, binaryCharts[i]);
- }
- }
-
- // Draw Bar Chart
- if(Smits.PhyloCanvas.Render.Parameters.barCharts.length){
- var barCharts = Smits.PhyloCanvas.Render.Parameters.barCharts;
- for(var i in barCharts){
- outerRadius = renderBarChart(outerX, barCharts[i].chart, barCharts[i]);
- }
- }
-
- }
-}();
-
-Smits.PhyloCanvas.Render.Phylogram.prototype = {
-
-};Smits.PhyloCanvas.Render.CircularPhylogram = (function(){
-
- var svg,
- sParams = Smits.PhyloCanvas.Render.Parameters.Circular, // Easy Reference
- canvasX, canvasY, canvasMinEdge,
- scaleRadius, scaleAngle,
- minHeightBetweenLeaves,
- innerCircleRadius,
- firstBranch = true,
- absoluteY = 0, cx, cy, maxBranch,
- labelsHold = [], bgLabelsHold = [],
- bufferRadius, bufferAngle, outerRadius,
- maxLabelLength = 0,
- initStartAngle,
- rad = (Math.PI / 180);
-
- function secPosition(r, deg){
- deg += initStartAngle;
- return [
- Smits.Common.roundFloat(cx + r * Math.sin(deg * rad), 4),
- Smits.Common.roundFloat(cy + r * Math.cos(deg * rad), 4)
- ]; // x,y
- };
- function rotateTextByY(yCoord){
- var rotateAngle = normalizeAngle( 90 - yCoord - initStartAngle );
-
- if(rotateAngle > 90 && rotateAngle < 270){
- rotateAngle += 180;
- var alignment = "end";
- } else {
- var alignment = "start";
- }
-
- return [rotateAngle, alignment];
- };
- function secant(r, startAngle, endAngle, params){
- var startPos = secPosition(r, startAngle);
- var endPos = secPosition(r, endAngle);
- var arr = [],
- n, inv = 0;
-
- if(Math.abs(normalizeAngle(endAngle-startAngle)) > 180) {
- n = 1;
- } else {
- n = -1;
- }
-
- // Parameter changes
- if(params && params.invertSecant){
- n *= -1;
- inv = 1;
- }
- if(params && params.noMove){
- } else {
- arr.push('M');
- }
-
- arr.push(startPos[0], startPos[1], "A", r, r, 0, n < 1 ? 0 : 1, inv, endPos[0], endPos[1]);
- return arr;
- };
- function secLinePath(deg, x1, x2, params){
- var arr = [];
- var startPos = secPosition(x1, deg);
- var endPos = secPosition(x2, deg);
- if(params && params.noMove){
- } else {
- arr.push('M');
- }
- arr.push(startPos[0], startPos[1], "L", endPos[0], endPos[1]);
- return arr;
- };
- function normalizeAngle(ang){
- while(ang > 360 || ang < 0){
- if(ang > 360){
- ang -= 360;
- } else if (ang < 0){
- ang += 360;
- }
- }
- return ang;
- };
- function sector(r1, r2, y1, y2){
- if(!r2 && r1.length > 1){
- var y2 = r1[3];
- var y1 = r1[2];
- var r2 = r1[1];
- var r1 = r1[0];
- }
- var arr = array_merge( "M",
- secant(
- r1,
- y1,
- y2,
- { noMove: 1, invertSecant: 0}
- ), "L",
- secant(
- r2,
- y2,
- y1,
- { noMove: 1, invertSecant: 1}
- ),
- 'Z'
- );
- return arr;
- };
-
- function recursiveCalculateNodePositions(node, positionX){
- positionX = positionX;
-
- if(node.len){ // If first branch, pad only margin
- if(firstBranch){
- absoluteY = bufferAngle || 1; // Has to be at least 1
- firstBranch = false;
- } else {
- if(node.children.length == 0) absoluteY = Smits.Common.roundFloat(absoluteY + scaleAngle, 4);
- }
- }
-
- if(node.children.length > 0){
- var nodeCoords = [], x1,x2,y1,y2;
- x1 = positionX;
- x2 = positionX += Smits.Common.roundFloat(scaleRadius * node.len, 4);
-
-
- if(node.name){ // draw bootstrap values
-
- }
-
- if(node.children && node.children.length){
- for(var i = 0; i < node.children.length; i++){
- var child = node.children[i];
- var y = recursiveCalculateNodePositions(child, positionX);
- if(y > 0) nodeCoords.push(y);
- }
- }
-
- var minAngle = Smits.Common.roundFloat(Math.min.apply(null, nodeCoords ), 4);
- var maxAngle = Smits.Common.roundFloat(Math.max.apply(null, nodeCoords ), 4);
-
- // hack: little elbows at ends in order to prevent stair-effects at edges
- svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- array_merge(
- "M", secPosition(positionX + 0.01, minAngle),
- "L", secant(positionX, minAngle, maxAngle, {noMove: true}),
- "L", secPosition(positionX + 0.01, maxAngle)
- )
- )
- );
-
- if(node.len){ // draw stem
- y1 = Smits.Common.roundFloat( minAngle + (maxAngle-minAngle)/2, 4 );
- svg.draw(new Smits.PhyloCanvas.Render.Path(secLinePath(y1, x1, x2)));
- }
-
- } else {
- // LABEL
-
- // preserve for later processing
- node.y = absoluteY;
- labelsHold.push(node);
-
- x1 = positionX;
- x2 = positionX = Smits.Common.roundFloat(positionX + (scaleRadius * node.len));
- y1 = absoluteY;
-
- svg.draw(new Smits.PhyloCanvas.Render.Path(secLinePath(y1, x1, x2)));
- svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- secLinePath(y1, x2, maxBranch),
- { attr : Smits.PhyloCanvas.Render.Style.connectedDash }
- )
- );
-
-
-
- if(node.name){
- var pos = secPosition(maxBranch + sParams.bufferInnerLabels, y1);
- var rotateParam = rotateTextByY(y1);
- var rotateAngle = rotateParam[0];
- var alignment = rotateParam[1];
-
- var attr = {};
- if(node.style){
- Smits.Common.apply(attr, Smits.PhyloCanvas.Render.Style.getStyle(node.style, 'text'));
- }
- attr["text-anchor"] = alignment;
- if(node.uri) { attr.href = node.uri };
- if(node.description) {attr.title = node.description };
-
- var draw = svg.draw(
- new Smits.PhyloCanvas.Render.Text(
- pos[0], pos[1],
- node.name,
- {
- attr: attr,
- rotate: [rotateAngle, pos[0], pos[1]]
- }
- )
- );
-
- // Background Style
- if(node.bgStyle){
- bgLabelsHold.push([node.bgStyle, y1]);
- }
-
- // Rollover, Rollout and Click Events
- var pos = secPosition(x2, y1);
- if(Smits.PhyloCanvas.Render.Parameters.mouseRollOver){
- Smits.Common.addEventHandler(
- draw[0].node,
- 'mouseover',
- Smits.PhyloCanvas.Render.Parameters.mouseRollOver,
- { svg: svg, node: node, x: pos[0], y: pos[1], textEl: draw[0] }
- );
- }
- if(Smits.PhyloCanvas.Render.Parameters.mouseRollOut){
- Smits.Common.addEventHandler(
- draw[0].node,
- 'mouseout',
- Smits.PhyloCanvas.Render.Parameters.mouseRollOut,
- { svg: svg, node: node, x: pos[0], y: pos[1], textEl: draw[0] }
- );
- }
- if(Smits.PhyloCanvas.Render.Parameters.onClickAction){
- Smits.Common.addEventHandler(
- draw[0].node,
- 'click',
- Smits.PhyloCanvas.Render.Parameters.onClickAction,
- { svg: svg, node: node, x: pos[0], y: pos[1], textEl: draw[0] }
- );
- }
-
- maxLabelLength = Math.max(draw[1], maxLabelLength);
- }
- }
- return y1;
- };
-
-
- function array_merge(arr) {
- var merged = arr;
- for (var i = 1; i < arguments.length; i++) {
- merged = merged.concat(arguments[i]);
- }
- return merged;
- };
-
- function renderBackground(){
- var arr = [];
-
- // Highlighted Labels
- if(bgLabelsHold.length > 0){
-
- // Setup Gradients if defined
- if(Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList']){
- for(var i = 0; i < Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'].length; i++){
- var gradientName = Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'][i];
- var radialEl = Smits.Common.createGradientEl(gradientName, Smits.PhyloCanvas.Render.Style[gradientName], [cx, cy, maxBranch + maxLabelLength + sParams.bufferOuterLabels]);
- svg.svg.defs.appendChild(radialEl);
- }
- }
-
- for(var i = 0; i < bgLabelsHold.length; i++){
- if(i != bgLabelsHold.length - 1 && bgLabelsHold[i][0] == bgLabelsHold[(i+1)][0]){
- bgLabelsHold[(i+1)][2] = bgLabelsHold[i][2] ? bgLabelsHold[i][2] : bgLabelsHold[i][1];
- continue;
- }
-
- var arr = sector(
- maxBranch,
- maxBranch + maxLabelLength + sParams.bufferOuterLabels,
- bgLabelsHold[i][2] ? bgLabelsHold[i][2] - scaleAngle/2 : bgLabelsHold[i][1] - scaleAngle/2,
- bgLabelsHold[i][1] + scaleAngle/2
- );
- var attr = Smits.PhyloCanvas.Render.Style.getStyle(bgLabelsHold[i][0], 'textSecantBg');
- var bgObj = svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- arr,
- { attr: attr.type ? {} : attr}
- )
- );
- //if(attr.type && attr.type == "radialGradient") { bgObj[0].node.setAttribute('class', 'jsphylosvg-' + attr.name); };
- if(attr.type && attr.type == "radialGradient") { bgObj[0].node.setAttribute('fill', 'url(#' + attr.name + ')'); };
- if(attr.type && attr.type == "radialGradient") { bgObj[0].node.setAttribute('stroke', 'none'); };
- bgObj[0].toBack(); // Put it behind the labels
- }
- }
-
- // Neutral Background
- var arr = sector(
- maxBranch,
- maxBranch + maxLabelLength + sParams.bufferOuterLabels,
- (bufferAngle || 1) + (scaleAngle/2),
- 360 + (scaleAngle/2)
- );
- var bgObj = svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- arr,
- { attr: Smits.PhyloCanvas.Render.Style.textSecantBg }
- )
- );
-
- bgObj[0].toBack(); // Put it behind the labels
-
- return maxBranch + maxLabelLength + sParams.bufferOuterLabels;
- };
-
- function renderBinaryChart(outerRadius, groupName, params){
- var bufferInner = (params && params.bufferInner) ? parseFloat(params.bufferInner) : Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner,
- bufferSiblings = (params && params.bufferSiblings ? params.bufferSiblings * scaleAngle : 0) | (Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings < 1 ? scaleAngle * Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings : Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings),
- thickness = (params && params.thickness) ? parseFloat(params.thickness) : Smits.PhyloCanvas.Render.Parameters.binaryChartThickness,
- disjointed = (params && params.disjointed ? params.disjointed : false) | Smits.PhyloCanvas.Render.Parameters.binaryChartDisjointed,
- isInternal = (params && params.isInternal) ? params.isInternal : false,
- isFirst = true,
- beginY;
-
-
- for(var i = 0; i < labelsHold.length; i++){
- var node = labelsHold[i];
- if( (!labelsHold[i+1] || node.chart[groupName] !== labelsHold[i+1].chart[groupName] || disjointed) && node.chart[groupName] != "none" ){
- var attr = Smits.PhyloCanvas.Render.Style.getStyle(node.chart[groupName], 'textSecantBg');
- if(isInternal){
- var sectorCoords = [
- maxBranch - bufferInner - thickness,
- maxBranch - bufferInner,
- (beginY ? beginY : node.y) - (scaleAngle/2) + (isFirst && !disjointed ? 0 : (bufferSiblings/2)),
- node.y + (scaleAngle/2) - (i == labelsHold.length-1 && !disjointed ? 0 : (bufferSiblings/2))
- ];
- } else {
- var sectorCoords = [
- outerRadius + bufferInner,
- outerRadius + bufferInner + thickness,
- (beginY ? beginY : node.y) - (scaleAngle/2) + (isFirst && !disjointed ? 0 : (bufferSiblings/2)),
- node.y + (scaleAngle/2) - (i == labelsHold.length-1 && !disjointed ? 0 : (bufferSiblings/2))
- ];
- }
-
- if(attr.label){
- var textAttr = Smits.PhyloCanvas.Render.Style.getStyle(attr.labelStyle, 'text');
- var pos = secPosition( (sectorCoords[0] + sectorCoords[1]) / 2, (sectorCoords[2] + sectorCoords[3]) / 2 );
- var rotateParam = rotateTextByY((sectorCoords[2] + sectorCoords[3]) / 2);
- var rotateLabelBy = normalizeAngle(rotateParam[0] + (textAttr["rotate"] ? parseFloat(textAttr["rotate"]) : 0));
-
- var rotateAngle = normalizeAngle( 90 - (sectorCoords[2] + sectorCoords[3])/2 - initStartAngle );
- if(rotateAngle > 90 && rotateAngle < 270){
- rotateLabelBy += 180;
- }
-
- if(!textAttr["text-anchor"]){
- textAttr["text-anchor"] = "middle";
- }
-
- var binText = svg.draw(
- new Smits.PhyloCanvas.Render.Text(
- pos[0],
- pos[1],
- attr.label,
- {
- attr: textAttr,
- rotate: rotateLabelBy
- }
- )
- );
- binText[0].toBack();
- }
-
- if(attr.borderStyle){
- var borderAttr = Smits.PhyloCanvas.Render.Style.getStyle(attr.borderStyle, 'textSecantBg');
- var borderSectorCoords = [
- maxBranch,
- borderAttr.fullsize ? sectorCoords[1] : sectorCoords[0],
- sectorCoords[2],
- sectorCoords[3]
- ];
- var binBorder = svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- sector(
- borderSectorCoords
- ),
- { attr: borderAttr }
- )
- );
- binBorder[0].toBack();
- }
-
- var binObj = svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- sector(
- sectorCoords
- ),
- { attr: attr }
- )
- );
- binObj[0].toBack();
-
- beginY = 0;
- isFirst = false;
- } else {
- if(!beginY){ beginY = node.y; }
- if(node.chart[groupName] == "none"){
- beginY = 0;
- }
- }
- isFirst = false;
- }
- return isInternal ? outerRadius : outerRadius + bufferInner + thickness;
- };
-
- function renderBarChart(outerRadius, groupName, params){
- var allValues = [], maxValue,
- bufferInner = params && params.bufferInner ? parseFloat(params.bufferInner) : Smits.PhyloCanvas.Render.Parameters.barChartBufferInner,
- height = params && params.height ? parseFloat(params.height) : (Smits.PhyloCanvas.Render.Parameters.barChartHeight ? Smits.PhyloCanvas.Render.Parameters.barChartHeight : 0),
- width = params && params.width ? (parseFloat(params.width) < 1 ? scaleAngle * parseFloat(params.width) : parseFloat(params.width) ) : 0 | (Smits.PhyloCanvas.Render.Parameters.barChartWidth < 1 ? scaleAngle * Smits.PhyloCanvas.Render.Parameters.barChartWidth : Smits.PhyloCanvas.Render.Parameters.barChartWidth),
- scaleHeight = 0;
-
- // Need to get max value
- for(var i = 0; i < labelsHold.length; i++){
- allValues.push(labelsHold[i].chart[groupName]);
- }
- maxValue = Math.max.apply(null, allValues);
- scaleHeight = Smits.Common.roundFloat(height / maxValue, 4);
-
- for(var i = 0; i < labelsHold.length; i++){
- var node = labelsHold[i];
- if(node.chart[groupName] > 0){
- svg.draw(
- new Smits.PhyloCanvas.Render.Path(
- sector(
- outerRadius + bufferInner,
- outerRadius + bufferInner + (scaleHeight * node.chart[groupName]),
- node.y - (width/2),
- node.y + (width/2)
- ),
- { attr: Smits.PhyloCanvas.Render.Style.getStyle(node.chart[groupName], 'barChart') }
- )
- );
- }
- }
-
- return outerRadius + bufferInner + height;
- };
-
- return function(sSvg, dataObject, bufferRadius){
- /* Privileged Methods */
- this.getCanvasSize = function(){
- return [canvasX, canvasY];
- };
- this.getRoot = function(){
- return dataObject.getRoot();
- };
-
- /* CONSTRUCTOR */
- // Validation
- if(dataObject.getValidate()){
- sSvg.draw({type: 'text', x: 0, y: sSvg.canvasSize[1] / 3, text: dataObject.getValidate() });
- return
- }
-
- // Properties Setup
- svg = sSvg;
- var node = dataObject.getRoot();
- var mNewickLen = dataObject.getNewickLen();
- canvasX = svg.canvasSize[0]; // Full Canvas Width
- canvasY = svg.canvasSize[1]; // Full Canvas Height
- cx = canvasX / 2; // Set Center Position
- cy = canvasY / 2;
- canvasMinEdge = Math.min.apply(null, [canvasX,canvasY]);
-
- bufferRadius = (sParams.bufferRadius > 1) ? sParams.bufferRadius : Smits.Common.roundFloat(canvasMinEdge * sParams.bufferRadius, 4);
- bufferAngle = sParams.bufferAngle; // controls split size in circle
- innerCircleRadius = sParams.innerCircleRadius;
- minHeightBetweenLeaves = sParams.minHeightBetweenLeaves;
- initStartAngle = sParams.initStartAngle; // Angle at which the entire tree is rotated
-
- maxBranch = Math.round( (canvasMinEdge - bufferRadius - innerCircleRadius) / 2); // maximum branch length
- scaleRadius = (maxBranch - innerCircleRadius) / mNewickLen; // scale multiplier to use
- scaleAngle = Smits.Common.roundFloat( (360 - bufferAngle) / node.getCountAllChildren(), 4 );
-
- // Draw Nodes and Labels
- recursiveCalculateNodePositions(node, innerCircleRadius);
- outerRadius = maxBranch + maxLabelLength + sParams.bufferOuterLabels;
-
- // Draw integrated secant highlights
- if(Smits.PhyloCanvas.Render.Parameters.integratedBina...
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