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benjeffery/d3.phylogram.js

Forked from kueda/d3.phylogram.js
Last active August 29, 2015 14:15
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index.html
<!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>NJT</title>
<script src="https://code.jquery.com/jquery-2.1.3.min.js" type="text/javascript"></script>
<script src="http://d3js.org/d3.v3.min.js" type="text/javascript"></script>
<script src="newick.js" type="text/javascript"></script>
<script>
var w = 500;
var scale = 12;
var newicks = [
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];
var population = {'AB0085-C':'BFS','AB0087-C':'BFM','AB0088-C':'BFM','AB0089-C':'BFM','AB0090-C':'BFM','AB0091-C':'BFM','AB0092-C':'BFM','AB0094-C':'BFM','AB0095-C':'BFM','AB0097-C':'BFM','AB0098-C':'BFM','AB0099-C':'BFM','AB0100-C':'BFM','AB0101-C':'BFM','AB0103-C':'BFS','AB0104-C':'BFS','AB0109-C':'BFM','AB0110-C':'BFM','AB0111-C':'BFM','AB0112-C':'BFM','AB0113-C':'BFM','AB0114-C':'BFM','AB0117-C':'BFS','AB0119-C':'BFS','AB0122-C':'BFM','AB0123-C':'BFM','AB0124-C':'BFM','AB0126-C':'BFS','AB0127-C':'BFS','AB0128-C':'BFS','AB0129-C':'BFS','AB0130-C':'BFS','AB0133-C':'BFS','AB0134-C':'BFS','AB0135-C':'BFS','AB0136-C':'BFS','AB0137-C':'BFM','AB0138-C':'BFM','AB0139-C':'BFM','AB0140-C':'BFM','AB0142-C':'BFM','AB0143-C':'BFS','AB0145-C':'BFS','AB0146-C':'BFS','AB0147-C':'BFS','AB0148-C':'BFS','AB0151-C':'BFS','AB0153-C':'BFS','AB0155-C':'BFS','AB0157-C':'BFS','AB0158-C':'BFS','AB0159-C':'BFS','AB0160-C':'BFS','AB0161-C':'BFS','AB0164-C':'BFS','AB0166-C':'BFS','AB0169-C':'BFS','AB0170-C':'BFS','AB0171-C':'BFS','AB0172-C':'BFS','AB0173-C':'BFS','AB0174-C':'BFS','AB0175-C':'BFS','AB0176-C':'BFS','AB0177-C':'BFS','AB0178-C':'BFS','AB0179-C':'BFS','AB0181-C':'BFM','AB0182-C':'BFM','AB0183-C':'BFM','AB0184-C':'BFM','AB0185-C':'BFM','AB0186-C':'BFM','AB0187-C':'BFM','AB0188-C':'BFM','AB0189-C':'BFM','AB0190-C':'BFM','AB0191-C':'BFM','AB0192-C':'BFM','AB0197-C':'BFS','AB0198-C':'BFS','AB0199-C':'BFS','AB0201-C':'BFS','AB0202-C':'BFS','AB0203-C':'BFS','AB0204-C':'BFM','AB0205-C':'BFS','AB0206-C':'BFS','AB0207-C':'BFS','AB0208-C':'BFS','AB0209-C':'BFM','AB0210-C':'BFM','AB0211-C':'BFS','AB0212-C':'BFM','AB0213-C':'BFM','AB0217-C':'BFS','AB0219-C':'BFM','AB0221-C':'BFM','AB0222-C':'BFM','AB0223-C':'BFM','AB0224-C':'BFM','AB0226-C':'BFM','AB0227-C':'BFM','AB0228-C':'BFS','AB0229-C':'BFM','AB0231-C':'BFS','AB0233-C':'BFS','AB0234-C':'BFM','AB0235-C':'BFS','AB0236-C':'BFS','AB0237-C':'BFM','AB0238-C':'BFS','AB0239-C':'BFS','AB0240-C':'BFM','AB0241-C':'BFS','AB0242-C':'BFM','AB0243-C':'BFM','AB0244-C':'BFS','AB0246-C':'BFM','AB0249-C':'BFM','AB0250-C':'BFM','AB0251-C':'BFS','AB0252-C':'BFS','AB0253-C':'BFS','AB0256-C':'BFS','AB0257-C':'BFM','AB0258-C':'BFM','AB0260-C':'BFS','AB0261-C':'BFS','AB0262-C':'BFM','AB0263-C':'BFM','AB0264-C':'BFS','AB0265-C':'BFS','AB0266-C':'BFM','AB0267-C':'BFM','AB0268-C':'BFS','AB0270-C':'BFS','AB0271-C':'BFS','AB0272-C':'BFS','AB0273-C':'BFS','AB0274-C':'BFS','AB0276-C':'BFM','AB0277-C':'BFS','AB0278-C':'BFS','AB0279-C':'BFM','AB0280-C':'BFS','AB0281-C':'BFS','AB0282-C':'BFM','AB0283-C':'BFS','AB0284-C':'BFS','AC0090-C':'UGS','AC0091-C':'UGS','AC0092-C':'UGS','AC0093-C':'UGS','AC0094-C':'UGS','AC0095-C':'UGS','AC0096-C':'UGS','AC0097-C':'UGS','AC0098-C':'UGS','AC0099-C':'UGS','AC0100-C':'UGS','AC0101-C':'UGS','AC0102-C':'UGS','AC0103-C':'UGS','AC0104-C':'UGS','AC0106-C':'UGS','AC0107-C':'UGS','AC0108-C':'UGS','AC0109-C':'UGS','AC0110-C':'UGS','AC0111-C':'UGS','AC0112-C':'UGS','AC0113-C':'UGS','AC0114-C':'UGS','AC0115-C':'UGS','AC0116-C':'UGS','AC0117-C':'UGS','AC0118-C':'UGS','AC0119-C':'UGS','AC0120-C':'UGS','AC0121-C':'UGS','AC0122-C':'UGS','AC0123-C':'UGS','AC0124-C':'UGS','AC0125-C':'UGS','AC0126-C':'UGS','AC0127-C':'UGS','AC0128-C':'UGS','AC0129-C':'UGS','AC0130-C':'UGS','AC0131-C':'UGS','AC0132-C':'UGS','AC0133-C':'UGS','AC0135-C':'UGS','AC0136-C':'UGS','AC0137-C':'UGS','AC0138-C':'UGS','AC0139-C':'UGS','AC0140-C':'UGS','AC0142-C':'UGS','AC0143-C':'UGS','AC0144-C':'UGS','AC0145-C':'UGS','AC0147-C':'UGS','AC0148-C':'UGS','AC0149-C':'UGS','AC0150-C':'UGS','AC0151-C':'UGS','AC0152-C':'UGS','AC0153-C':'UGS','AC0154-C':'UGS','AC0156-C':'UGS','AC0158-C':'UGS','AC0159-C':'UGS','AC0160-C':'UGS','AC0161-C':'UGS','AC0162-C':'UGS','AC0163-C':'UGS','AC0164-C':'UGS','AC0166-C':'UGS','AC0167-C':'UGS','AC0168-C':'UGS','AC0169-C':'UGS','AC0170-C':'UGS','AC0171-C':'UGS','AC0172-C':'UGS','AC0173-C':'UGS','AC0174-C':'UGS','AC0176-C':'UGS','AC0178-C':'UGS','AC0179-C':'UGS','AC0180-C':'UGS','AC0181-C':'UGS','AC0182-C':'UGS','AC0183-C':'UGS','AC0184-C':'UGS','AC0186-C':'UGS','AC0187-C':'UGS','AC0188-C':'UGS','AC0189-C':'UGS','AC0190-C':'UGS','AC0191-C':'UGS','AC0192-C':'UGS','AC0193-C':'UGS','AC0194-C':'UGS','AC0195-C':'UGS','AC0196-C':'UGS','AC0197-C':'UGS','AC0199-C':'UGS','AC0200-C':'UGS','AC0201-C':'UGS','AC0202-C':'UGS','AC0203-C':'UGS','AJ0023-C':'GWA','AJ0024-C':'GWA','AJ0032-C':'GWA','AJ0035-C':'GWA','AJ0036-C':'GWA','AJ0039-C':'GWA','AJ0043-C':'GWA','AJ0044-C':'GWA','AJ0045-C':'GWA','AJ0047-C':'GWA','AJ0051-C':'GWA','AJ0052-C':'GWA','AJ0056-C':'GWA','AJ0061-C':'GWA','AJ0063-C':'GWA','AJ0064-C':'GWA','AJ0066-C':'GWA','AJ0070-C':'GWA','AJ0071-C':'GWA','AJ0072-C':'GWA','AJ0074-C':'GWA','AJ0075-C':'GWA','AJ0076-C':'GWA','AJ0077-C':'GWA','AJ0078-C':'GWA','AJ0081-C':'GWA','AJ0084-C':'GWA','AJ0085-C':'GWA','AJ0086-C':'GWA','AJ0088-C':'GWA','AJ0090-C':'GWA','AJ0092-C':'GWA','AJ0093-C':'GWA','AJ0096-C':'GWA','AJ0097-C':'GWA','AJ0098-C':'GWA','AJ0100-C':'GWA','AJ0101-C':'GWA','AJ0102-C':'GWA','AJ0103-C':'GWA','AJ0105-C':'GWA','AJ0107-C':'GWA','AJ0109-C':'GWA','AJ0113-C':'GWA','AJ0115-C':'GWA','AJ0116-C':'GWA','AK0065-C':'KES','AK0066-C':'KES','AK0067-C':'KES','AK0068-C':'KES','AK0069-C':'KES','AK0070-C':'KES','AK0072-C':'KES','AK0073-C':'KES','AK0074-C':'KES','AK0075-C':'KES','AK0076-C':'KES','AK0077-C':'KES','AK0078-C':'KES','AK0079-C':'KES','AK0080-C':'KES','AK0081-C':'KES','AK0082-C':'KES','AK0085-C':'KES','AK0086-C':'KES','AK0087-C':'KES','AK0088-C':'KES','AK0089-C':'KES','AK0090-C':'KES','AK0091-C':'KES','AK0092-C':'KES','AK0093-C':'KES','AK0094-C':'KES','AK0095-C':'KES','AK0096-C':'KES','AK0098-C':'KES','AK0099-C':'KES','AK0100-C':'KES','AK0101-C':'KES','AK0102-C':'KES','AK0103-C':'KES','AK0104-C':'KES','AK0105-C':'KES','AK0106-C':'KES','AK0108-C':'KES','AK0109-C':'KES','AK0110-C':'KES','AK0116-C':'KES','AK0119-C':'KES','AK0127-C':'KES','AN0007-C':'CMS','AN0008-C':'CMS','AN0009-C':'CMS','AN0010-C':'CMS','AN0011-C':'CMS','AN0012-C':'CMS','AN0014-C':'CMS','AN0016-C':'CMS','AN0017-C':'CMS','AN0018-C':'CMS','AN0019-C':'CMS','AN0020-C':'CMS','AN0022-C':'CMS','AN0023-C':'CMS','AN0024-C':'CMS','AN0025-C':'CMS','AN0026-C':'CMS','AN0027-C':'CMS','AN0028-C':'CMS','AN0029-C':'CMS','AN0030-C':'CMS','AN0031-C':'CMS','AN0032-C':'CMS','AN0033-C':'CMS','AN0034-C':'CMS','AN0035-C':'CMS','AN0036-C':'CMS','AN0037-C':'CMS','AN0038-C':'CMS','AN0039-C':'CMS','AN0040-C':'CMS','AN0041-C':'CMS','AN0042-C':'CMS','AN0043-C':'CMS','AN0045-C':'CMS','AN0046-C':'CMS','AN0047-C':'CMS','AN0048-C':'CMS','AN0049-C':'CMS','AN0050-C':'CMS','AN0051-C':'CMS','AN0053-C':'CMS','AN0054-C':'CMS','AN0055-C':'CMS','AN0056-C':'CMS','AN0057-C':'CMS','AN0058-C':'CMS','AN0059-C':'CMS','AN0060-C':'CMS','AN0063-C':'CMS','AN0064-C':'CMS','AN0065-C':'CMS','AN0066-C':'CMS','AN0067-C':'CMS','AN0068-C':'CMS','AN0069-C':'CMS','AN0070-C':'CMS','AN0071-C':'CMS','AN0072-C':'CMS','AN0073-C':'CMS','AN0074-C':'CMS','AN0075-C':'CMS','AN0076-C':'CMS','AN0077-C':'CMS','AN0079-C':'CMS','AN0080-C':'CMS','AN0081-C':'CMS','AN0082-C':'CMS','AN0083-C':'CMS','AN0084-C':'CMS','AN0085-C':'CMS','AN0086-C':'CMS','AN0087-C':'CMS','AN0088-C':'CMS','AN0089-C':'CMS','AN0090-C':'CMS','AN0091-C':'CMS','AN0092-C':'CMS','AN0093-C':'CMS','AN0094-C':'CMS','AN0095-C':'CMS','AN0096-C':'CMS','AN0097-C':'CMS','AN0098-C':'CMS','AN0099-C':'CMS','AN0100-C':'CMS','AN0101-C':'CMS','AN0102-C':'CMS','AN0103-C':'CMS','AN0104-C':'CMS','AN0105-C':'CMS','AN0106-C':'CMS','AN0107-C':'CMS','AN0108-C':'CMS','AN0109-C':'CMS','AN0111-C':'CMS','AN0112-C':'CMS','AN0113-C':'CMS','AN0114-C':'CMS','AN0115-C':'CMS','AN0117-C':'CMS','AN0120-C':'CMS','AN0121-C':'CMS','AN0122-C':'CMS','AN0123-C':'CMS','AN0124-C':'CMS','AN0125-C':'CMS','AN0126-C':'CMS','AN0127-C':'CMS','AN0128-C':'CMS','AN0129-C':'CMS','AN0130-C':'CMS','AN0131-C':'CMS','AN0132-C':'CMS','AN0134-C':'CMS','AN0135-C':'CMS','AN0136-C':'CMS','AN0137-C':'CMS','AN0138-C':'CMS','AN0139-C':'CMS','AN0140-C':'CMS','AN0141-C':'CMS','AN0143-C':'CMS','AN0147-C':'CMS','AN0149-C':'CMS','AN0151-C':'CMS','AN0152-C':'CMS','AN0153-C':'CMS','AN0154-C':'CMS','AN0155-C':'CMS','AN0156-C':'CMS','AN0157-C':'CMS','AN0158-C':'CMS','AN0159-C':'CMS','AN0160-C':'CMS','AN0162-C':'CMS','AN0163-C':'CMS','AN0164-C':'CMS','AN0165-C':'CMS','AN0166-C':'CMS','AN0167-C':'CMS','AN0168-C':'CMS','AN0169-C':'CMS','AN0170-C':'CMS','AN0171-C':'CMS','AN0172-C':'CMS','AN0173-C':'CMS','AN0174-C':'CMS','AN0175-C':'CMS','AN0176-C':'CMS','AN0177-C':'CMS','AN0178-C':'CMS','AN0179-C':'CMS','AN0180-C':'CMS','AN0181-C':'CMS','AN0182-C':'CMS','AN0183-C':'CMS','AN0184-C':'CMS','AN0185-C':'CMS','AN0186-C':'CMS','AN0187-C':'CMS','AN0188-C':'CMS','AN0189-C':'CMS','AN0190-C':'CMS','AN0191-C':'CMS','AN0192-C':'CMS','AN0193-C':'CMS','AN0194-C':'CMS','AN0196-C':'CMS','AN0197-C':'CMS','AN0198-C':'CMS','AN0199-C':'CMS','AN0200-C':'CMS','AN0201-C':'CMS','AN0202-C':'CMS','AN0203-C':'CMS','AN0204-C':'CMS','AN0205-C':'CMS','AN0206-C':'CMS','AN0207-C':'CMS','AN0208-C':'CMS','AN0209-C':'CMS','AN0210-C':'CMS','AN0212-C':'CMS','AN0213-C':'CMS','AN0214-C':'CMS','AN0215-C':'CMS','AN0217-C':'CMS','AN0218-C':'CMS','AN0219-C':'CMS','AN0220-C':'CMS','AN0221-C':'CMS','AN0222-C':'CMS','AN0223-C':'CMS','AN0224-C':'CMS','AN0225-C':'CMS','AN0226-C':'CMS','AN0227-C':'CMS','AN0228-C':'CMS','AN0229-C':'CMS','AN0230-C':'CMS','AN0231-C':'CMS','AN0233-C':'CMS','AN0234-C':'CMS','AN0235-C':'CMS','AN0236-C':'CMS','AN0237-C':'CMS','AN0238-C':'CMS','AN0239-C':'CMS','AN0240-C':'CMS','AN0241-C':'CMS','AN0242-C':'CMS','AN0243-C':'CMS','AN0244-C':'CMS','AN0245-C':'CMS','AN0246-C':'CMS','AN0247-C':'CMS','AN0248-C':'CMS','AN0250-C':'CMS','AN0251-C':'CMS','AN0252-C':'CMS','AN0253-C':'CMS','AN0254-C':'CMS','AN0255-C':'CMS','AN0256-C':'CMS','AN0258-C':'CMS','AN0259-C':'CMS','AN0260-C':'CMS','AN0261-C':'CMS','AN0262-C':'CMS','AN0263-C':'CMS','AN0264-C':'CMS','AN0266-C':'CMS','AN0267-C':'CMS','AN0268-C':'CMS','AN0269-C':'CMS','AN0270-C':'CMS','AN0272-C':'CMS','AN0275-C':'CMS','AN0276-C':'CMS','AN0277-C':'CMS','AN0280-C':'CMS','AN0282-C':'CMS','AN0283-C':'CMS','AN0284-C':'CMS','AN0285-C':'CMS','AN0286-C':'CMS','AN0287-C':'CMS','AN0288-C':'CMS','AN0290-C':'CMS','AN0291-C':'CMS','AN0292-C':'CMS','AN0294-C':'CMS','AN0295-C':'CMS','AN0296-C':'CMS','AN0297-C':'CMS','AN0298-C':'CMS','AN0299-C':'CMS','AN0300-C':'CMS','AN0301-C':'CMS','AN0303-C':'CMS','AN0304-C':'CMS','AN0305-C':'CMS','AN0307-C':'CMS','AN0308-C':'CMS','AN0309-C':'CMS','AN0310-C':'CMS','AN0312-C':'CMS','AN0313-C':'CMS','AN0314-C':'CMS','AN0315-C':'CMS','AN0317-C':'CMS','AN0318-C':'CMS','AN0319-C':'CMS','AN0321-C':'CMS','AR0007-C':'AOM','AR0008-C':'AOM','AR0009-C':'AOM','AR0010-C':'AOM','AR0011-C':'AOM','AR0012-C':'AOM','AR0014-C':'AOM','AR0015-C':'AOM','AR0017-C':'AOM','AR0019-C':'AOM','AR0020-C':'AOM','AR0021-C':'AOM','AR0022-C':'AOM','AR0023-C':'AOM','AR0024-C':'AOM','AR0026-C':'AOM','AR0027-C':'AOM','AR0034-C':'AOM','AR0035-C':'AOM','AR0042-C':'AOM','AR0043-C':'AOM','AR0045-C':'AOM','AR0047-C':'AOM','AR0049-C':'AOM','AR0050-C':'AOM','AR0051-C':'AOM','AR0053-C':'AOM','AR0054-C':'AOM','AR0057-C':'AOM','AR0059-C':'AOM','AR0061-C':'AOM','AR0062-C':'AOM','AR0063-C':'AOM','AR0065-C':'AOM','AR0066-C':'AOM','AR0069-C':'AOM','AR0070-C':'AOM','AR0071-C':'AOM','AR0072-C':'AOM','AR0073-C':'AOM','AR0074-C':'AOM','AR0075-C':'AOM','AR0076-C':'AOM','AR0078-C':'AOM','AR0079-C':'AOM','AR0080-C':'AOM','AR0081-C':'AOM','AR0083-C':'AOM','AR0084-C':'AOM','AR0086-C':'AOM','AR0087-C':'AOM','AR0089-C':'AOM','AR0090-C':'AOM','AR0092-C':'AOM','AR0093-C':'AOM','AR0095-C':'AOM','AR0096-C':'AOM','AR0098-C':'AOM','AR0099-C':'AOM','AR0100-C':'AOM','AS0001-C':'GAS','AS0002-C':'GAS','AS0003-C':'GAS','AS0004-C':'GAS','AS0006-C':'GAS','AS0007-C':'GAS','AS0008-C':'GAS','AS0009-C':'GAS','AS0010-C':'GAS','AS0011-C':'GAS','AS0012-C':'GAS','AS0013-C':'GAS','AS0014-C':'GAS','AS0015-C':'GAS','AS0016-C':'GAS','AS0017-C':'GAS','AS0018-C':'GAS','AS0019-C':'GAS','AS0020-C':'GAS','AS0021-C':'GAS','AS0022-C':'GAS','AS0024-C':'GAS','AS0026-C':'GAS','AS0028-C':'GAS','AS0030-C':'GAS','AS0032-C':'GAS','AS0033-C':'GAS','AS0034-C':'GAS','AS0035-C':'GAS','AS0036-C':'GAS','AS0037-C':'GAS','AS0039-C':'GAS','AS0042-C':'GAS','AS0044-C':'GAS','AS0045-C':'GAS','AS0047-C':'GAS','AS0049-C':'GAS','AS0052-C':'GAS','AS0053-C':'GAS','AS0054-C':'GAS','AS0055-C':'GAS','AS0056-C':'GAS','AS0058-C':'GAS','AS0059-C':'GAS','AS0064-C':'GAS','AS0065-C':'GAS','AS0066-C':'GAS','AS0068-C':'GAS','AS0069-C':'GAS','AS0070-C':'GAS','AS0071-C':'GAS','AS0072-C':'GAS','AS0073-C':'GAS','AS0074-C':'GAS','AS0076-C':'GAS','AS0077-C':'GAS','AV0001-C':'GNS','AV0002-C':'GNS','AV0003-C':'GNS','AV0004-C':'GNS','AV0005-C':'GNS','AV0007-C':'GNS','AV0008-C':'GNS','AV0009-C':'GNS','AV0010-C':'GNS','AV0011-C':'GNS','AV0012-C':'GNS','AV0013-C':'GNS','AV0014-C':'GNS','AV0015-C':'GNS','AV0018-C':'GNS','AV0024-C':'GNS','AV0026-C':'GNS','AV0027-C':'GNS','AV0029-C':'GNS','AV0030-C':'GNS','AV0031-C':'GNS','AV0032-C':'GNS','AV0033-C':'GNS','AV0034-C':'GNS','AV0035-C':'GNS','AV0036-C':'GNS','AV0039-C':'GNS','AV0041-C':'GNS','AV0044-C':'GNS','AV0045-C':'GNS','AV0047-C':'GNS'};
var cols = {
'BFS': 'rgb(51,51,255)',
'BFM': 'rgb(255,77,77)',
'UGS': 'rgb(51,153,179)',
'GWA': 'rgb(230,128,0)',
'KES': 'rgb(0,204,0)',
'CMS': 'rgb(204,51,204)',
'AOM': 'rgb(0,0,179)',
'GAS': 'rgb(179,0,0)',
'GNS': 'rgb(0,128,0)'
}
var _links = [];
var _nodes = [];
var load = function(newick) {
var newick = Newick.parse(newick);
var newickNodes = [];
function buildNewickNodes(node, callback) {
newickNodes.push(node);
if (node.children) {
for (var i = 0; i < node.children.length; i++) {
buildNewickNodes(node.children[i])
}
}
}
var leaf_nodes = [];
buildNewickNodes(newick);
var countItems = function (branch) {
var cnt = 0;
if (branch.children)
$.each(branch.children, function (idx, child) {
cnt += countItems(child);
});
else {
leaf_nodes.push(branch);
cnt += 1;
}
branch.itemCount = cnt;
return cnt;
};
countItems(newick);
String.prototype.hashCode = function() {
var hash = 0, i, chr, len;
if (this.length == 0) return hash;
for (i = 0, len = this.length; i < len; i++) {
chr = this.charCodeAt(i);
hash = ((hash << 5) - hash) + chr;
hash |= 0; // Convert to 32bit integer
}
return hash;
};
var rndIter = function(val) {
for (var i=0; i<5; i++)
val = (val * 9301 + 49297) % 233280;
return val;
};
$.each(leaf_nodes, function(i, node) {
node.rndIndex = rndIter(node.name.hashCode());
node.col = cols[population[node.name]]
});
var byProperty = function (prop) {
return function (a, b) {
if (typeof a[prop] == "number") {
return (a[prop] - b[prop]);
} else {
return ((a[prop] < b[prop]) ? -1 : ((a[prop] > b[prop]) ? 1 : 0));
}
};
};
var calcAvIndex = function(branch) {
var cnt = 0;
var vl = 0;
if (branch.children)
$.each(branch.children, function(idx, child) {
var rs = calcAvIndex(child);
vl += rs[0];
cnt += rs[1];
});
if (branch.rndIndex) {
cnt = 1;
vl = branch.rndIndex;
}
branch.avIndex = vl/cnt;
if (branch.children)
branch.children.sort(byProperty('avIndex'));
return [vl, cnt];
};
calcAvIndex(newick);
var actualAnglesMap = {};
var angularSpread = function (branch, ang1, ang2, parentPosX, parentPosY, parentAngle) {
branch.relativeAngle = (ang1 + ang2) / 2;
branch.absoluteAngle = parentAngle + branch.relativeAngle;
if (!branch.children)
actualAnglesMap[branch.name] = branch.absoluteAngle;
branch.posX = parentPosX + (branch.distance || 0) * Math.cos(branch.absoluteAngle);
branch.posY = parentPosY + (branch.distance || 0) * Math.sin(branch.absoluteAngle);
branch.pointingLeft = Math.cos(branch.absoluteAngle) < 0;
var cnt = 0;
var angW = ang2 - ang1;
if (branch.children)
$.each(branch.children, function (idx, child) {
var subang1 = -angW / 2 + cnt * 1.0 / branch.itemCount * angW;
cnt += child.itemCount;
var subang2 = -angW / 2 + cnt * 1.0 / branch.itemCount * angW;
angularSpread(child, subang1, subang2, branch.posX, branch.posY, branch.absoluteAngle);
});
};
angularSpread(newick, 0, 2 * Math.PI, 0, 0, 0);
var links = [];
var nodes = [];
var add_path = function (branch, path) {
path = path.slice();
path.push((branch.posX * scale).toFixed(4) + ',' + (branch.posY * scale).toFixed(4));
if (!branch.children) {
links.push({
name: branch.name,
path: path,
col: branch.col
});
nodes.push({name: branch.name,
pos: [(branch.posX * scale).toFixed(4), (branch.posY * scale).toFixed(4)],
col: branch.col
});
}
else
$.each(branch.children, function (idx, child) {
add_path(child, path);
});
};
add_path(newick, []);
for (var j = 0; j < links.length; j++)
links[j].path = string_path(links[j].path);
_links.push(links);
_nodes.push(nodes);
};
function string_path(path) {
var out = 'M0,0';
for (var i=0;i<(70-path.length);i++) {
out += 'L0,0';
}
for (i=0;i<path.length;i++) {
out += 'L' + path[i];
}
return out;
}
function tweenFunc() {
return function (d, i, a) {
var b = d.path;
var regex_a = /[-+]?(?:\d+\.?\d*|\.?\d+)(?:[eE][-+]?\d+)?/g
var regex_b = /[-+]?(?:\d+\.?\d*|\.?\d+)(?:[eE][-+]?\d+)?/g
var a_numbers = [];
var b_numbers = [];
var num_a, num_b;
while ((num_a = regex_a.exec(a)) && (num_b = regex_b.exec(b))) {
a_numbers.push(parseFloat(num_a[0]));
b_numbers.push(parseFloat(num_b[0]));
}
var a_polar = [];
//Skip first 2 as they are 'M'
for (var i = 2; i < a_numbers.length;)
{
var x = a_numbers[i++];
var y = a_numbers[i++];
a_polar.push(Math.sqrt(x*x+y*y));
a_polar.push(Math.atan2(y, x));
}
var b_polar = [];
for (i = 2; i < b_numbers.length;)
{
var x = b_numbers[i++];
var y = b_numbers[i++];
b_polar.push(Math.sqrt(x*x+y*y));
b_polar.push(Math.atan2(y, x));
}
//Correct so we don't go all the way around
for (i = 0; i < b_polar.length;i += 2) {
var r1 = a_polar[i];
var r2 = b_polar[i];
var t1 = a_polar[i+1];
var t2 = b_polar[i+1];
if (Math.abs((t2 - Math.PI * 2)-t1) < Math.abs(t2-t1))
b_polar[i+1] = t2 - Math.PI * 2;
if (Math.abs((t2 + Math.PI * 2)-t1) < Math.abs(t2-t1))
b_polar[i+1] = t2 + Math.PI * 2;
//console.log(t1, t2, Math.abs(t2-t1), Math.abs((t2 - Math.PI * 2)-t1), Math.abs((t2 + Math.PI * 2)-t1));
if (!(r1 > 0))
a_polar[i+1] = b_polar[i+1];
if (!(r2 > 0))
b_polar[i+1] = a_polar[i+1];
}
var interps = [];
for (i = 0; i < a_polar.length;i++) {
interps.push(d3.interpolateNumber(a_polar[i], b_polar[i]));
}
return function(t) {
var out = 'M0,0';
for (var i=0;i<interps.length;) {
var r = interps[i++](t);
var theta = interps[i++](t);
out += 'L' + (r*Math.cos(theta)).toFixed(4) +','+ (r*Math.sin(theta)).toFixed(4);
}
return out;
};
};
}
function run() {
$.each(newicks, function (i, newick) {
load(newick);
});
var div = d3.select("#tree")
.style("width", w + "px")
.style("height", w + "px")
.style("-webkit-backface-visibility", "hidden");
var svg = div.append("svg:svg")
.attr("width", w)
.attr("height", w)
.append("svg:g")
.attr("transform", "translate(" + w/2 + "," + w/2 + ")");
var paths = svg.selectAll("path.link")
.data(_links[0], function(d) { return d.name;})
.enter().append("svg:path")
.attr("d", function(d) { return d.path; })
.style('stroke', function(d) { return d.col; });
// var nodes = svg.selectAll("path.link")
// .data(_nodes[0], function(d) { return d.name;})
// .enter().append("svg:circle")
// .attr("cx", function(d) { return d.pos[0]; })
// .attr("cy", function(d) { return d.pos[1]; })
// .attr("r", 3)
// .style('fill', function(d) { return d.col; });
function update(num) {
paths.data(_links[Math.round(num)], function(d) { return d.name;})
.transition()
.duration(2000)
.attrTween("d", tweenFunc());//function(d) { return d.path; });
// nodes.data(_nodes[Math.round(num)], function(d) { return d.name;})
// .transition()
// .duration(2000)
// .attr("cx", function(d) { return d.pos[0]; })
// .attr("cy", function(d) { return d.pos[1]; })
}
d3.select("input[type=range]").on("input", function() {
update(this.value)
});
d3.select(".prev").on("click", function() {
$('.slider').val(parseInt($('.slider').val()) - 1 );
update(parseInt($('.slider').val()));
});
d3.select(".next").on("click", function() {
$('.slider').val(parseInt($('.slider').val()) + 1 );
update(parseInt($('.slider').val()));
});
}
</script>
<style type="text/css" media="screen">
body { font-family: "Helvetica Neue", Helvetica, sans-serif; }
svg path {
fill: none;
stroke: #1f77b4;
opacity: 0.8;
}
svg circle {
stroke: none;
opacity: 0.8;
}
</style>
</head>
<body onload="run()">
<table>
<tr>
<td>
<h2>NJT</h2>
<div id='tree'></div>
<input class="slider" style="position:relative;top:3px;width:500px" type="range" min="0" max="25" value="0">
<button class="prev" style="position:relative;top:3px;">Prev</button>
<button class="next" style="position:relative;top:3px;">Next</button>
</td>
</tr>
</table>
</body>
</html>
Raw
newick.js
/**
* 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",
* children: [
* {name: "A", length: 0.1},
* {name: "B", length: 0.2},
* {
* name: "E",
* length: 0.5,
* children: [
* {name: "C", length: 0.3},
* {name: "D", length: 0.4}
* ]
* }
* ]
* }
*
* Converted to JSON, but with no names or lengths:
* {
* children: [
* {}, {}, {
* children: [{}, {}]
* }
* ]
* }
*/
(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 children
var subtree = {};
tree.children = [subtree];
ancestors.push(tree);
tree = subtree;
break;
case ',': // another branch
var subtree = {};
ancestors[ancestors.length-1].children.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.distance = 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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