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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>JSDoc: Module: tree</title>
<script src="scripts/prettify/prettify.js"> </script>
<script src="scripts/prettify/lang-css.js"> </script>
<!--[if lt IE 9]>
<script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
<link type="text/css" rel="stylesheet" href="styles/prettify-tomorrow.css">
<link type="text/css" rel="stylesheet" href="styles/jsdoc-default.css">
</head>
<body>
<div id="main">
<h1 class="page-title">Module: tree</h1>
<section>
<header>
</header>
<article>
<div class="container-overview">
</div>
<h3 class="subsection-title">Classes</h3>
<dl>
<dt><a href="module-tree.Tree.html">Tree</a></dt>
<dd></dd>
<dt><a href="module-tree-Node.html">Node</a></dt>
<dd></dd>
</dl>
<h3 class="subsection-title">Methods</h3>
<h4 class="name" id="~calculateHeights"><span class="type-signature">(inner) </span>calculateHeights<span class="signature">()</span><span class="type-signature"></span></h4>
<div class="description">
A private recursive function that calculates the height of each node (with the most
diverged tip from the root having height given by origin).
</div>
<dl class="details">
<dt class="tag-source">Source:</dt>
<dd class="tag-source"><ul class="dummy"><li>
<a href="tree.js.html">tree.js</a>, <a href="tree.js.html#line1136">line 1136</a>
</li></ul></dd>
</dl>
<h4 class="name" id="~calculateLengths"><span class="type-signature">(inner) </span>calculateLengths<span class="signature">()</span><span class="type-signature"></span></h4>
<div class="description">
A private recursive function that calculates the length of the branch below each node
</div>
<dl class="details">
<dt class="tag-source">Source:</dt>
<dd class="tag-source"><ul class="dummy"><li>
<a href="tree.js.html">tree.js</a>, <a href="tree.js.html#line1147">line 1147</a>
</li></ul></dd>
</dl>
<h4 class="name" id="~fitchParsimony"><span class="type-signature">(inner) </span>fitchParsimony<span class="signature">(name, node)</span><span class="type-signature"> → {*}</span></h4>
<div class="description">
A private recursive function that uses the Fitch algorithm to assign
states to nodes using parsimony. An acctrans or deltrans algorithm can
then be used to reconstruct internal node states.
</div>
<h5>Parameters:</h5>
<table class="params">
<thead>
<tr>
<th>Name</th>
<th>Type</th>
<th class="last">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td class="name"><code>name</code></td>
<td class="type">
</td>
<td class="description last"></td>
</tr>
<tr>
<td class="name"><code>node</code></td>
<td class="type">
</td>
<td class="description last"></td>
</tr>
</tbody>
</table>
<dl class="details">
<dt class="tag-source">Source:</dt>
<dd class="tag-source"><ul class="dummy"><li>
<a href="tree.js.html">tree.js</a>, <a href="tree.js.html#line1166">line 1166</a>
</li></ul></dd>
</dl>
<h5>Returns:</h5>
<dl>
<dt>
Type
</dt>
<dd>
<span class="param-type">*</span>
</dd>
</dl>
<h4 class="name" id="~orderNodes"><span class="type-signature">(inner) </span>orderNodes<span class="signature">(node, ordering, callback)</span><span class="type-signature"> → {number}</span></h4>
<div class="description">
A private recursive function that rotates nodes to give an ordering provided
by a function.
</div>
<h5>Parameters:</h5>
<table class="params">
<thead>
<tr>
<th>Name</th>
<th>Type</th>
<th>Default</th>
<th class="last">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td class="name"><code>node</code></td>
<td class="type">
</td>
<td class="default">
</td>
<td class="description last"></td>
</tr>
<tr>
<td class="name"><code>ordering</code></td>
<td class="type">
</td>
<td class="default">
</td>
<td class="description last">function that takes (a,number of tips form a, b, number of tips from b) and sorts a and be by the output.</td>
</tr>
<tr>
<td class="name"><code>callback</code></td>
<td class="type">
</td>
<td class="default">
null
</td>
<td class="description last">an optional callback that is called each rotate</td>
</tr>
</tbody>
</table>
<dl class="details">
<dt class="tag-source">Source:</dt>
<dd class="tag-source"><ul class="dummy"><li>
<a href="tree.js.html">tree.js</a>, <a href="tree.js.html#line1109">line 1109</a>
</li></ul></dd>
</dl>
<h5>Returns:</h5>
<dl>
<dt>
Type
</dt>
<dd>
<span class="param-type">number</span>
</dd>
</dl>
<h4 class="name" id="~setUpNodes"><span class="type-signature">(inner) </span>setUpNodes<span class="signature">(node)</span><span class="type-signature"></span></h4>
<div class="description">
A private function that sets up the tree by traversing from the root Node and sets all heights and lenghts
</div>
<h5>Parameters:</h5>
<table class="params">
<thead>
<tr>
<th>Name</th>
<th>Type</th>
<th class="last">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td class="name"><code>node</code></td>
<td class="type">
</td>
<td class="description last"></td>
</tr>
</tbody>
</table>
<dl class="details">
<dt class="tag-source">Source:</dt>
<dd class="tag-source"><ul class="dummy"><li>
<a href="tree.js.html">tree.js</a>, <a href="tree.js.html#line1228">line 1228</a>
</li></ul></dd>
</dl>
</article>
</section>
</div>
<nav>
<h2><a href="index.html">Home</a></h2><h3>Modules</h3><ul><li><a href="module-bauble.html">bauble</a></li><li><a href="module-figtree.html">figtree</a></li><li><a href="module-tree.html">tree</a></li></ul><h3>Classes</h3><ul><li><a href="Axis.html">Axis</a></li><li><a href="BaubleManager.html">BaubleManager</a></li><li><a href="CircleBauble.html">CircleBauble</a></li><li><a href="Decoration.html">Decoration</a></li><li><a href="Label.html">Label</a></li><li><a href="Legend.html">Legend</a></li><li><a href="module-bauble.Bauble.html">Bauble</a></li><li><a href="module-figtree.FigTree.html">FigTree</a></li><li><a href="module-tree.Tree.html">Tree</a></li><li><a href="module-tree-Node.html">Node</a></li><li><a href="ScaleBar.html">ScaleBar</a></li></ul><h3>Global</h3><ul><li><a href="global.html#branch">branch</a></li><li><a href="global.html#branchLabel">branchLabel</a></li><li><a href="global.html#branchPathGenerator">branchPathGenerator</a></li><li><a href="global.html#circle">circle</a></li><li><a href="global.html#dateToDecimal">dateToDecimal</a></li><li><a href="global.html#decimalToDate">decimalToDate</a></li><li><a href="global.html#equalAngleLayout">equalAngleLayout</a></li><li><a href="global.html#internalNodeLabel">internalNodeLabel</a></li><li><a href="global.html#label">label</a></li><li><a href="global.html#leapYear">leapYear</a></li><li><a href="global.html#leastSquares">leastSquares</a></li><li><a href="global.html#legend">legend</a></li><li><a href="global.html#makeEdges">makeEdges</a></li><li><a href="global.html#makeVertexFromNode">makeVertexFromNode</a></li><li><a href="global.html#rectangle">rectangle</a></li><li><a href="global.html#rectangularHilightedLayout">rectangularHilightedLayout</a></li><li><a href="global.html#scaleBar">scaleBar</a></li><li><a href="global.html#tipLabel">tipLabel</a></li></ul>
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Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 3.6.3</a> on Sat Mar 21 2020 11:15:18 GMT+0000 (Greenwich Mean Time)
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