Demonstration of two common tree visualizations using d3 and newick.js. I hadn't found any examples of these kinds of right-angle trees so I figured I'd share. Input data is a Newick-formatted guide tree from a clustalw multiple sequence alignment on some cytochrome b sequences from several North American snakes. And it turns out the creator of newick.js also has an implementation of this kind of radial tree: check out http://www.jasondavies.com/tree-of-life/
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|
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| /* | |
| d3.phylogram.js | |
| Wrapper around a d3-based phylogram (tree where branch lengths are scaled) | |
| Also includes a radial dendrogram visualization (branch lengths not scaled) | |
| along with some helper methods for building angled-branch trees. | |
| Copyright (c) 2013, Ken-ichi Ueda | |
| All rights reserved. | |
| Redistribution and use in source and binary forms, with or without | |
| modification, are permitted provided that the following conditions are met: | |
| Redistributions of source code must retain the above copyright notice, this | |
| list of conditions and the following disclaimer. Redistributions in binary | |
| form must reproduce the above copyright notice, this list of conditions and | |
| the following disclaimer in the documentation and/or other materials | |
| provided with the distribution. | |
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | |
| AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE | |
| LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | |
| CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | |
| SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS | |
| INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN | |
| CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | |
| ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE | |
| POSSIBILITY OF SUCH DAMAGE. | |
| DOCUEMENTATION | |
| d3.phylogram.build(selector, nodes, options) | |
| Creates a phylogram. | |
| Arguments: | |
| selector: selector of an element that will contain the SVG | |
| nodes: JS object of nodes | |
| Options: | |
| width | |
| Width of the vis, will attempt to set a default based on the width of | |
| the container. | |
| height | |
| Height of the vis, will attempt to set a default based on the height | |
| of the container. | |
| vis | |
| Pre-constructed d3 vis. | |
| tree | |
| Pre-constructed d3 tree layout. | |
| children | |
| Function for retrieving an array of children given a node. Default is | |
| to assume each node has an attribute called "branchset" | |
| diagonal | |
| Function that creates the d attribute for an svg:path. Defaults to a | |
| right-angle diagonal. | |
| skipTicks | |
| Skip the tick rule. | |
| skipBranchLengthScaling | |
| Make a dendrogram instead of a phylogram. | |
| d3.phylogram.buildRadial(selector, nodes, options) | |
| Creates a radial dendrogram. | |
| Options: same as build, but without diagonal, skipTicks, and | |
| skipBranchLengthScaling | |
| d3.phylogram.rightAngleDiagonal() | |
| Similar to d3.diagonal except it create an orthogonal crook instead of a | |
| smooth Bezier curve. | |
| d3.phylogram.radialRightAngleDiagonal() | |
| d3.phylogram.rightAngleDiagonal for radial layouts. | |
| */ | |
| if (!d3) { throw "d3 wasn't included!"}; | |
| (function() { | |
| d3.phylogram = {} | |
| d3.phylogram.rightAngleDiagonal = function() { | |
| var projection = function(d) { return [d.y, d.x]; } | |
| var path = function(pathData) { | |
| return "M" + pathData[0] + ' ' + pathData[1] + " " + pathData[2]; | |
| } | |
| function diagonal(diagonalPath, i) { | |
| var source = diagonalPath.source, | |
| target = diagonalPath.target, | |
| midpointX = (source.x + target.x) / 2, | |
| midpointY = (source.y + target.y) / 2, | |
| pathData = [source, {x: target.x, y: source.y}, target]; | |
| pathData = pathData.map(projection); | |
| return path(pathData) | |
| } | |
| diagonal.projection = function(x) { | |
| if (!arguments.length) return projection; | |
| projection = x; | |
| return diagonal; | |
| }; | |
| diagonal.path = function(x) { | |
| if (!arguments.length) return path; | |
| path = x; | |
| return diagonal; | |
| }; | |
| return diagonal; | |
| } | |
| d3.phylogram.radialRightAngleDiagonal = function() { | |
| return d3.phylogram.rightAngleDiagonal() | |
| .path(function(pathData) { | |
| var src = pathData[0], | |
| mid = pathData[1], | |
| dst = pathData[2], | |
| radius = Math.sqrt(src[0]*src[0] + src[1]*src[1]), | |
| srcAngle = d3.phylogram.coordinateToAngle(src, radius), | |
| midAngle = d3.phylogram.coordinateToAngle(mid, radius), | |
| clockwise = Math.abs(midAngle - srcAngle) > Math.PI ? midAngle <= srcAngle : midAngle > srcAngle, | |
| rotation = 0, | |
| largeArc = 0, | |
| sweep = clockwise ? 0 : 1; | |
| return 'M' + src + ' ' + | |
| "A" + [radius,radius] + ' ' + rotation + ' ' + largeArc+','+sweep + ' ' + mid + | |
| 'L' + dst; | |
| }) | |
| .projection(function(d) { | |
| var r = d.y, a = (d.x - 90) / 180 * Math.PI; | |
| return [r * Math.cos(a), r * Math.sin(a)]; | |
| }) | |
| } | |
| // Convert XY and radius to angle of a circle centered at 0,0 | |
| d3.phylogram.coordinateToAngle = function(coord, radius) { | |
| var wholeAngle = 2 * Math.PI, | |
| quarterAngle = wholeAngle / 4 | |
| var coordQuad = coord[0] >= 0 ? (coord[1] >= 0 ? 1 : 2) : (coord[1] >= 0 ? 4 : 3), | |
| coordBaseAngle = Math.abs(Math.asin(coord[1] / radius)) | |
| // Since this is just based on the angle of the right triangle formed | |
| // by the coordinate and the origin, each quad will have different | |
| // offsets | |
| switch (coordQuad) { | |
| case 1: | |
| coordAngle = quarterAngle - coordBaseAngle | |
| break | |
| case 2: | |
| coordAngle = quarterAngle + coordBaseAngle | |
| break | |
| case 3: | |
| coordAngle = 2*quarterAngle + quarterAngle - coordBaseAngle | |
| break | |
| case 4: | |
| coordAngle = 3*quarterAngle + coordBaseAngle | |
| } | |
| return coordAngle | |
| } | |
| d3.phylogram.styleTreeNodes = function(vis) { | |
| vis.selectAll('g.leaf.node') | |
| .append("svg:circle") | |
| .attr("r", 4.5) | |
| .attr('stroke', 'yellowGreen') | |
| .attr('fill', 'greenYellow') | |
| .attr('stroke-width', '2px'); | |
| vis.selectAll('g.root.node') | |
| .append('svg:circle') | |
| .attr("r", 4.5) | |
| .attr('fill', 'steelblue') | |
| .attr('stroke', '#369') | |
| .attr('stroke-width', '2px'); | |
| } | |
| function scaleBranchLengths(nodes, w) { | |
| // Visit all nodes and adjust y pos width distance metric | |
| var visitPreOrder = function(root, callback) { | |
| callback(root) | |
| if (root.children) { | |
| for (var i = root.children.length - 1; i >= 0; i--){ | |
| visitPreOrder(root.children[i], callback) | |
| }; | |
| } | |
| } | |
| visitPreOrder(nodes[0], function(node) { | |
| node.rootDist = (node.parent ? node.parent.rootDist : 0) + (node.length || 0) | |
| }) | |
| var rootDists = nodes.map(function(n) { return n.rootDist; }); | |
| var yscale = d3.scale.linear() | |
| .domain([0, d3.max(rootDists)]) | |
| .range([0, w]); | |
| visitPreOrder(nodes[0], function(node) { | |
| node.y = yscale(node.rootDist) | |
| }) | |
| return yscale | |
| } | |
| d3.phylogram.build = function(selector, nodes, options) { | |
| options = options || {} | |
| var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'), | |
| h = options.height || d3.select(selector).style('height') || d3.select(selector).attr('height'), | |
| w = parseInt(w), | |
| h = parseInt(h); | |
| var tree = options.tree || d3.layout.cluster() | |
| .size([h, w]) | |
| .sort(function(node) { return node.children ? node.children.length : -1; }) | |
| .children(options.children || function(node) { | |
| return node.branchset | |
| }); | |
| var diagonal = options.diagonal || d3.phylogram.rightAngleDiagonal(); | |
| var vis = options.vis || d3.select(selector).append("svg:svg") | |
| .attr("width", w + 300) | |
| .attr("height", h + 30) | |
| .append("svg:g") | |
| .attr("transform", "translate(20, 20)"); | |
| var nodes = tree(nodes); | |
| if (options.skipBranchLengthScaling) { | |
| var yscale = d3.scale.linear() | |
| .domain([0, w]) | |
| .range([0, w]); | |
| } else { | |
| var yscale = scaleBranchLengths(nodes, w) | |
| } | |
| if (!options.skipTicks) { | |
| vis.selectAll('line') | |
| .data(yscale.ticks(10)) | |
| .enter().append('svg:line') | |
| .attr('y1', 0) | |
| .attr('y2', h) | |
| .attr('x1', yscale) | |
| .attr('x2', yscale) | |
| .attr("stroke", "#ddd"); | |
| vis.selectAll("text.rule") | |
| .data(yscale.ticks(10)) | |
| .enter().append("svg:text") | |
| .attr("class", "rule") | |
| .attr("x", yscale) | |
| .attr("y", 0) | |
| .attr("dy", -3) | |
| .attr("text-anchor", "middle") | |
| .attr('font-size', '8px') | |
| .attr('fill', '#ccc') | |
| .text(function(d) { return Math.round(d*100) / 100; }); | |
| } | |
| var link = vis.selectAll("path.link") | |
| .data(tree.links(nodes)) | |
| .enter().append("svg:path") | |
| .attr("class", "link") | |
| .attr("d", diagonal) | |
| .attr("fill", "none") | |
| .attr("stroke", "#aaa") | |
| .attr("stroke-width", "4px"); | |
| var node = vis.selectAll("g.node") | |
| .data(nodes) | |
| .enter().append("svg:g") | |
| .attr("class", function(n) { | |
| if (n.children) { | |
| if (n.depth == 0) { | |
| return "root node" | |
| } else { | |
| return "inner node" | |
| } | |
| } else { | |
| return "leaf node" | |
| } | |
| }) | |
| .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; }) | |
| d3.phylogram.styleTreeNodes(vis) | |
| if (!options.skipLabels) { | |
| vis.selectAll('g.inner.node') | |
| .append("svg:text") | |
| .attr("dx", -6) | |
| .attr("dy", -6) | |
| .attr("text-anchor", 'end') | |
| .attr('font-size', '8px') | |
| .attr('fill', '#ccc') | |
| .text(function(d) { return d.length; }); | |
| vis.selectAll('g.leaf.node').append("svg:text") | |
| .attr("dx", 8) | |
| .attr("dy", 3) | |
| .attr("text-anchor", "start") | |
| .attr('font-family', 'Helvetica Neue, Helvetica, sans-serif') | |
| .attr('font-size', '10px') | |
| .attr('fill', 'black') | |
| .text(function(d) { return d.name + ' ('+d.length+')'; }); | |
| } | |
| return {tree: tree, vis: vis} | |
| } | |
| d3.phylogram.buildRadial = function(selector, nodes, options) { | |
| options = options || {} | |
| var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'), | |
| r = w / 2, | |
| labelWidth = options.skipLabels ? 10 : options.labelWidth || 120; | |
| var vis = d3.select(selector).append("svg:svg") | |
| .attr("width", r * 2) | |
| .attr("height", r * 2) | |
| .append("svg:g") | |
| .attr("transform", "translate(" + r + "," + r + ")"); | |
| var tree = d3.layout.tree() | |
| .size([360, r - labelWidth]) | |
| .sort(function(node) { return node.children ? node.children.length : -1; }) | |
| .children(options.children || function(node) { | |
| return node.branchset | |
| }) | |
| .separation(function(a, b) { return (a.parent == b.parent ? 1 : 2) / a.depth; }); | |
| var phylogram = d3.phylogram.build(selector, nodes, { | |
| vis: vis, | |
| tree: tree, | |
| skipBranchLengthScaling: true, | |
| skipTicks: true, | |
| skipLabels: options.skipLabels, | |
| diagonal: d3.phylogram.radialRightAngleDiagonal() | |
| }) | |
| vis.selectAll('g.node') | |
| .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + d.y + ")"; }) | |
| if (!options.skipLabels) { | |
| vis.selectAll('g.leaf.node text') | |
| .attr("dx", function(d) { return d.x < 180 ? 8 : -8; }) | |
| .attr("dy", ".31em") | |
| .attr("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; }) | |
| .attr("transform", function(d) { return d.x < 180 ? null : "rotate(180)"; }) | |
| .attr('font-family', 'Helvetica Neue, Helvetica, sans-serif') | |
| .attr('font-size', '10px') | |
| .attr('fill', 'black') | |
| .text(function(d) { return d.data.name; }); | |
| vis.selectAll('g.inner.node text') | |
| .attr("dx", function(d) { return d.x < 180 ? -6 : 6; }) | |
| .attr("text-anchor", function(d) { return d.x < 180 ? "end" : "start"; }) | |
| .attr("transform", function(d) { return d.x < 180 ? null : "rotate(180)"; }); | |
| } | |
| return {tree: tree, vis: vis} | |
| } | |
| }()); |
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| <!DOCTYPE html> | |
| <html lang='en' xml:lang='en' xmlns='http://www.w3.org/1999/xhtml'> | |
| <head> | |
| <meta content='text/html;charset=UTF-8' http-equiv='content-type'> | |
| <title>Right-angle phylograms and dendrograms with d3</title> | |
| <script src="http://d3js.org/d3.v3.min.js" type="text/javascript"></script> | |
| <script src="newick.js" type="text/javascript"></script> | |
| <script src="d3.phylogram.js" type="text/javascript"></script> | |
| <script> | |
| function load() { | |
| var newick = Newick.parse("(((Crotalus_oreganus_oreganus_cytochrome_b:0.00800,Crotalus_horridus_cytochrome_b:0.05866):0.04732,(Thamnophis_elegans_terrestris_cytochrome_b:0.00366,Thamnophis_atratus_cytochrome_b:0.00172):0.06255):0.00555,(Pituophis_catenifer_vertebralis_cytochrome_b:0.00552,Lampropeltis_getula_cytochrome_b:0.02035):0.05762,((Diadophis_punctatus_cytochrome_b:0.06486,Contia_tenuis_cytochrome_b:0.05342):0.01037,Hypsiglena_torquata_cytochrome_b:0.05346):0.00779);") | |
| var newickNodes = [] | |
| function buildNewickNodes(node, callback) { | |
| newickNodes.push(node) | |
| if (node.branchset) { | |
| for (var i=0; i < node.branchset.length; i++) { | |
| buildNewickNodes(node.branchset[i]) | |
| } | |
| } | |
| } | |
| buildNewickNodes(newick) | |
| d3.phylogram.buildRadial('#radialtree', newick, { | |
| width: 400, | |
| skipLabels: true | |
| }) | |
| d3.phylogram.build('#phylogram', newick, { | |
| width: 300, | |
| height: 400 | |
| }); | |
| } | |
| </script> | |
| <style type="text/css" media="screen"> | |
| body { font-family: "Helvetica Neue", Helvetica, sans-serif; } | |
| td { vertical-align: top; } | |
| </style> | |
| </head> | |
| <body onload="load()"> | |
| <table> | |
| <tr> | |
| <td> | |
| <h2>Circular Dendrogram</h2> | |
| <div id='radialtree'></div> | |
| </td> | |
| <td> | |
| <h2>Phylogram</h2> | |
| <div id='phylogram'></div> | |
| </td> | |
| </tr> | |
| </table> | |
| </body> | |
| </html> |
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| { | |
| "kind": "fusiontables#sqlresponse", | |
| "columns": [ | |
| "tg_ecotypeid", | |
| "country", | |
| "latitude", | |
| "longitude", | |
| "name" | |
| ], | |
| "rows": [ | |
| [ | |
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| [ | |
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| 13.2, | |
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| 15.8, | |
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| "Västervik" | |
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| "SWE", | |
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| "Bar 1" | |
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| "SWE", | |
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| "SWE", | |
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| "SWE", | |
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| "SWE", | |
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| "SWE", | |
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| "FäL 1" | |
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| "SWE", | |
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| 13.3742, | |
| "FlyA 3" | |
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| "Fri 1" | |
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| "SWE", | |
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| "SWE", | |
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| 15.0105, | |
| "Hal-1" | |
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| "SWE", | |
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| 13.9905, | |
| "Ham-1" | |
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| "SWE", | |
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| 14.8549, | |
| "Hel-3" | |
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| "SWE", | |
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| 13.399, | |
| "HolA-1 1" | |
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| "SWE", | |
| 55.7491, | |
| 13.399, | |
| "HolA-1 2" | |
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| "SWE", | |
| 55.7491, | |
| 13.399, | |
| "HolA-2 2" | |
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| "SWE", | |
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| 13.9519, | |
| "Kal 1" | |
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| "SWE", | |
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| 14.302, | |
| "Kia 1" | |
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| "SWE", | |
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| 16.1494, | |
| "Kor 3" | |
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| "SWE", | |
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| 16.1494, | |
| "Kor 4" | |
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| "SWE", | |
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| 18.3837, | |
| "Kru-3" | |
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| "SWE", | |
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| 18.154, | |
| "Kva 2" | |
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| "SWE", | |
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| 14.3997, | |
| "Lan 1" | |
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| "SWE", | |
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| 18.4055, | |
| "Näs 2" | |
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| "SWE", | |
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| 18.2763, | |
| "Nyl 13" | |
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| "SWE", | |
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| 18.3659, | |
| "Öde 2" | |
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| "SWE", | |
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| 14.6806, | |
| "Puk-1" | |
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| "SWE", | |
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| 14.6806, | |
| "Puk-2" | |
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| "SWE", | |
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| 14.3398, | |
| "Sim-1" | |
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| "SWE", | |
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| 18.2109, | |
| "Spro 1" | |
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| "SWE", | |
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| 18.2109, | |
| "Spro 2" | |
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| "SWE", | |
| 57.2545, | |
| 18.2109, | |
| "Spro 3" | |
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| "SWE", | |
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| 18.5162, | |
| "Ste 2" | |
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| "SWE", | |
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| 18.5162, | |
| "Ste 3" | |
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| "SWE", | |
| 57.8009, | |
| 18.5162, | |
| "Ste 4" | |
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| "SWE", | |
| 57.6511, | |
| 14.8043, | |
| "Tur-4" | |
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| "SWE", | |
| 56.0648, | |
| 13.9707, | |
| "Ull-A-1" | |
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| "SWE", | |
| 55.5796, | |
| 14.3336, | |
| "VårA 1" | |
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| "SWE", | |
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| 13.8484, | |
| "Yst-1" | |
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| "FRA", | |
| 44.65, | |
| -1.16667, | |
| "PYL-6" | |
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| 47.35, | |
| 3.93333, | |
| "MAR2-3" | |
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| -4.06667, | |
| "LDV-18" | |
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| "FRA", | |
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| -4.06667, | |
| "LDV-46" | |
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| "FRA", | |
| 46.6667, | |
| 4.11667, | |
| "TOU-A1-88" | |
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| "FRA", | |
| 46.6667, | |
| 4.11667, | |
| "TOU-A1-89" | |
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| "FRA", | |
| 47.4, | |
| 0.683333, | |
| "CYR" | |
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| "FRA", | |
| 48.5, | |
| -1.41, | |
| "Ren-1" | |
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| "FRA", | |
| 48.5, | |
| -1.41, | |
| "Ren-11" | |
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| "FRA", | |
| 45.9, | |
| 6.13028, | |
| "Ann-1" | |
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| "FRA", | |
| 45.0, | |
| 1.3, | |
| "Ag-0" | |
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| [ | |
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| "FRA", | |
| 49.0, | |
| 0.5, | |
| "Cen-0" | |
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| [ | |
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| "FRA", | |
| 48.0717, | |
| 1.33867, | |
| "Chat-1" | |
| ], | |
| [ | |
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| "FRA", | |
| 49.416, | |
| 2.823, | |
| "Com-1" | |
| ], | |
| [ | |
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| "FRA", | |
| 47.3239, | |
| 5.04278, | |
| "Di-G" | |
| ], | |
| [ | |
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| "FRA", | |
| 44.6447, | |
| 2.56481, | |
| "Et-0" | |
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| [ | |
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| "FRA", | |
| 48.0, | |
| 0.5, | |
| "Lm-2" | |
| ], | |
| [ | |
| "8343", | |
| "FRA", | |
| 47.5, | |
| 1.5, | |
| "Na-1" | |
| ], | |
| [ | |
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| "Rib-1" | |
| ], | |
| [ | |
| "9891", | |
| "ESP", | |
| 41.93, | |
| 2.92, | |
| "Sal-0" | |
| ], | |
| [ | |
| "9892", | |
| "ESP", | |
| 42.68, | |
| -6.96, | |
| "Sam-0" | |
| ], | |
| [ | |
| "9893", | |
| "ESP", | |
| 37.96, | |
| -5.37, | |
| "Sca-0" | |
| ], | |
| [ | |
| "9894", | |
| "ESP", | |
| 42.59, | |
| 0.76, | |
| "Sen-0" | |
| ], | |
| [ | |
| "9895", | |
| "ESP", | |
| 41.78, | |
| 2.57, | |
| "Sfb-6" | |
| ], | |
| [ | |
| "9897", | |
| "ESP", | |
| 40.95, | |
| -5.63, | |
| "Smt-1" | |
| ], | |
| [ | |
| "9898", | |
| "ESP", | |
| 41.14, | |
| -3.58, | |
| "Som-0" | |
| ], | |
| [ | |
| "9899", | |
| "ESP", | |
| 42.54, | |
| 0.84, | |
| "Tau-0" | |
| ], | |
| [ | |
| "9900", | |
| "ESP", | |
| 37.38, | |
| -6.01, | |
| "Tri-0" | |
| ], | |
| [ | |
| "9901", | |
| "ESP", | |
| 42.27, | |
| -2.98, | |
| "Urd-1" | |
| ], | |
| [ | |
| "9902", | |
| "ESP", | |
| 40.71, | |
| -3.24, | |
| "Usa-0" | |
| ], | |
| [ | |
| "9903", | |
| "ESP", | |
| 42.31, | |
| -3.1, | |
| "Val-0" | |
| ], | |
| [ | |
| "9904", | |
| "ESP", | |
| 40.95, | |
| -3.31, | |
| "Vas-0" | |
| ], | |
| [ | |
| "9905", | |
| "ESP", | |
| 40.76, | |
| -4.01, | |
| "Ven-0" | |
| ], | |
| [ | |
| "9906", | |
| "ESP", | |
| 40.0, | |
| 4.25, | |
| "Mah-6" | |
| ], | |
| [ | |
| "9907", | |
| "FRA", | |
| 50.86, | |
| 3.6, | |
| "ENC-2-1" | |
| ], | |
| [ | |
| "9908", | |
| "FRA", | |
| 50.72, | |
| 3.47, | |
| "ESP-1-11" | |
| ], | |
| [ | |
| "9909", | |
| "FRA", | |
| 50.59, | |
| 3.3, | |
| "GEN-8" | |
| ], | |
| [ | |
| "9910", | |
| "FRA", | |
| 50.68, | |
| 3.52, | |
| "BRI-2" | |
| ], | |
| [ | |
| "9911", | |
| "FRA", | |
| 47.16, | |
| 4.28, | |
| "ARGE-1-15" | |
| ], | |
| [ | |
| "9912", | |
| "FRA", | |
| 46.67, | |
| 4.55, | |
| "CIRY-13" | |
| ], | |
| [ | |
| "9913", | |
| "FRA", | |
| 47.24, | |
| 4.43, | |
| "CON-7" | |
| ], | |
| [ | |
| "9914", | |
| "FRA", | |
| 47.58, | |
| 5.33, | |
| "IST-29" | |
| ], | |
| [ | |
| "9915", | |
| "FRA", | |
| 47.45, | |
| 3.94, | |
| "MAR-4-16" | |
| ], | |
| [ | |
| "9916", | |
| "FRA", | |
| 47.1, | |
| 4.22, | |
| "MOL-1" | |
| ], | |
| [ | |
| "9917", | |
| "FRA", | |
| 46.69, | |
| 4.34, | |
| "RAD-21" | |
| ], | |
| [ | |
| "9918", | |
| "FRA", | |
| 47.43, | |
| 5.21, | |
| "SAUL-24" | |
| ], | |
| [ | |
| "9919", | |
| "FRA", | |
| 48.85, | |
| 4.45, | |
| "BRE-14" | |
| ], | |
| [ | |
| "9920", | |
| "FRA", | |
| 48.54, | |
| 4.32, | |
| "DIR-9" | |
| ], | |
| [ | |
| "9921", | |
| "FRA", | |
| 48.57, | |
| 4.41, | |
| "FOR-23" | |
| ], | |
| [ | |
| "9922", | |
| "FRA", | |
| 48.52, | |
| 4.7, | |
| "MIL-2" | |
| ], | |
| [ | |
| "9923", | |
| "FRA", | |
| 48.58, | |
| 4.46, | |
| "PLO-1" | |
| ], | |
| [ | |
| "9924", | |
| "FRA", | |
| 48.59, | |
| 4.24, | |
| "PLY-20" | |
| ], | |
| [ | |
| "9925", | |
| "FRA", | |
| 48.91, | |
| 4.52, | |
| "RUM-20" | |
| ], | |
| [ | |
| "9926", | |
| "FRA", | |
| 48.86, | |
| 4.1, | |
| "TRE-1" | |
| ], | |
| [ | |
| "9927", | |
| "FRA", | |
| 44.05, | |
| 3.69, | |
| "ARR-17" | |
| ], | |
| [ | |
| "9928", | |
| "FRA", | |
| 44.12, | |
| 3.77, | |
| "BEZ-9" | |
| ], | |
| [ | |
| "9929", | |
| "FRA", | |
| 43.92, | |
| 3.71, | |
| "ISS-20" | |
| ], | |
| [ | |
| "9930", | |
| "FRA", | |
| 43.91, | |
| 4.14, | |
| "LEC-25" | |
| ], | |
| [ | |
| "9931", | |
| "FRA", | |
| 43.98, | |
| 4.31, | |
| "MOU2-25" | |
| ], | |
| [ | |
| "9932", | |
| "FRA", | |
| 44.12, | |
| 4.33, | |
| "NOZ-6" | |
| ], | |
| [ | |
| "9933", | |
| "FRA", | |
| 43.74, | |
| 3.89, | |
| "VED-10" | |
| ], | |
| [ | |
| "9934", | |
| "FRA", | |
| 44.07, | |
| 4.08, | |
| "QUI-8" | |
| ], | |
| [ | |
| "9935", | |
| "FRA", | |
| 50.6, | |
| 2.93, | |
| "BAU-15" | |
| ], | |
| [ | |
| "9936", | |
| "FRA", | |
| 50.47, | |
| 3.46, | |
| "LCL-16" | |
| ], | |
| [ | |
| "9937", | |
| "FRA", | |
| 50.79, | |
| 2.69, | |
| "CATS-6" | |
| ], | |
| [ | |
| "9938", | |
| "FRA", | |
| 50.65, | |
| 2.99, | |
| "WAV-8" | |
| ] | |
| ] | |
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| /** | |
| * Newick format parser in JavaScript. | |
| * | |
| * Copyright (c) Jason Davies 2010. | |
| * | |
| * Permission is hereby granted, free of charge, to any person obtaining a copy | |
| * of this software and associated documentation files (the "Software"), to deal | |
| * in the Software without restriction, including without limitation the rights | |
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| * copies of the Software, and to permit persons to whom the Software is | |
| * furnished to do so, subject to the following conditions: | |
| * | |
| * The above copyright notice and this permission notice shall be included in | |
| * all copies or substantial portions of the Software. | |
| * | |
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| * THE SOFTWARE. | |
| * | |
| * Example tree (from http://en.wikipedia.org/wiki/Newick_format): | |
| * | |
| * +--0.1--A | |
| * F-----0.2-----B +-------0.3----C | |
| * +------------------0.5-----E | |
| * +---------0.4------D | |
| * | |
| * Newick format: | |
| * (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; | |
| * | |
| * Converted to JSON: | |
| * { | |
| * name: "F", | |
| * branchset: [ | |
| * {name: "A", length: 0.1}, | |
| * {name: "B", length: 0.2}, | |
| * { | |
| * name: "E", | |
| * length: 0.5, | |
| * branchset: [ | |
| * {name: "C", length: 0.3}, | |
| * {name: "D", length: 0.4} | |
| * ] | |
| * } | |
| * ] | |
| * } | |
| * | |
| * Converted to JSON, but with no names or lengths: | |
| * { | |
| * branchset: [ | |
| * {}, {}, { | |
| * branchset: [{}, {}] | |
| * } | |
| * ] | |
| * } | |
| */ | |
| (function(exports) { | |
| exports.parse = function(s) { | |
| var ancestors = []; | |
| var tree = {}; | |
| var tokens = s.split(/\s*(;|\(|\)|,|:)\s*/); | |
| for (var i=0; i<tokens.length; i++) { | |
| var token = tokens[i]; | |
| switch (token) { | |
| case '(': // new branchset | |
| var subtree = {}; | |
| tree.branchset = [subtree]; | |
| ancestors.push(tree); | |
| tree = subtree; | |
| break; | |
| case ',': // another branch | |
| var subtree = {}; | |
| ancestors[ancestors.length-1].branchset.push(subtree); | |
| tree = subtree; | |
| break; | |
| case ')': // optional name next | |
| tree = ancestors.pop(); | |
| break; | |
| case ':': // optional length next | |
| break; | |
| default: | |
| var x = tokens[i-1]; | |
| if (x == ')' || x == '(' || x == ',') { | |
| tree.name = token; | |
| } else if (x == ':') { | |
| tree.length = parseFloat(token); | |
| } | |
| } | |
| } | |
| return tree; | |
| }; | |
| })( | |
| // exports will be set in any commonjs platform; use it if it's available | |
| typeof exports !== "undefined" ? | |
| exports : | |
| // otherwise construct a name space. outside the anonymous function, | |
| // "this" will always be "window" in a browser, even in strict mode. | |
| this.Newick = {} | |
| ); |
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