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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>JSDoc: Module: layout</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: layout</h1>
<section>
<header>
</header>
<article>
<div class="container-overview">
</div>
<h3 class="subsection-title">Members</h3>
<h4 class="name" id=".equalAngleLayout"><span class="type-signature">(static, constant) </span>equalAngleLayout<span class="type-signature"></span></h4>
<div class="description">
The equal angle layout. This function returns a layout function. It take and optional internal node, which if provided acts
as the starting node and fixes the order nodes are visited. This means the tree not update. The root position will
still change in response to rerooting.
</div>
<dl class="details">
<dt class="tag-source">Source:</dt>
<dd class="tag-source"><ul class="dummy"><li>
<a href="layout_equaleanglelayout.f.js.html">layout/equaleanglelayout.f.js</a>, <a href="layout_equaleanglelayout.f.js.html#line86">line 86</a>
</li></ul></dd>
</dl>
<h3 class="subsection-title">Methods</h3>
<h4 class="name" id=".makeEdges"><span class="type-signature">(static) </span>makeEdges<span class="signature">(vertices)</span><span class="type-signature"> → {*}</span></h4>
<div class="description">
Makes edges from an array of vertices.
Edge {
v0: parent vertex,
v1: target vertex,
key: vertex.key,
id:vertex.id,
classes:vertex.classes,
x:x position,
y:y.position,
textLabel:{ label postions
x:,
y: -6,
alignmentBaseline: "bottom",
textAnchor:"middle",
},
</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>vertices</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="layout_layoutHelpers.js.html">layout/layoutHelpers.js</a>, <a href="layout_layoutHelpers.js.html#line114">line 114</a>
</li></ul></dd>
</dl>
<h5>Returns:</h5>
<dl>
<dt>
Type
</dt>
<dd>
<span class="param-type">*</span>
</dd>
</dl>
<h4 class="name" id=".makeVertexFromNode"><span class="type-signature">(static) </span>makeVertexFromNode<span class="signature">(node)</span><span class="type-signature"></span></h4>
<div class="description">
Makes a vertex from a node in a tree.
anatomy of a vertex
{
name:node.name,
length:node.length,
height:node.height,
divergence:node.divergence,
level:node.level,
label:node.label,
annotations:node.annotations,
key: node.id,
id:node.id,
parent:node.parent?node.parent.id:null,
children:node.children?node.children.map(child=>child.id):null,
degree: (node.children ? node.children.length + 1 : 1),// the number of edges (including stem)
textLabel:{
labelBelow:labelBelow,
x:leftLabel?"-6":"12",
y:leftLabel?(labelBelow ? "-8": "8" ):"0",
alignmentBaseline: leftLabel?(labelBelow ? "bottom": "hanging" ):"middle",
textAnchor:leftLabel?"end":"start",
},
classes: getVertexClassesFromNode(node),
[p.node]:node,
};
</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="layout_layoutHelpers.js.html">layout/layoutHelpers.js</a>, <a href="layout_layoutHelpers.js.html#line63">line 63</a>
</li></ul></dd>
</dl>
<h5>Returns:</h5>
<div class="param-desc">
vertex
</div>
<h4 class="name" id="~leastSquares"><span class="type-signature">(inner) </span>leastSquares<span class="signature">(data)</span><span class="type-signature"> → {Object}</span></h4>
<div class="description">
returns slope, intercept and r-square of the line
</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>data</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="layout_rootToTipLayout.js.html">layout/rootToTipLayout.js</a>, <a href="layout_rootToTipLayout.js.html#line64">line 64</a>
</li></ul></dd>
</dl>
<h5>Returns:</h5>
<dl>
<dt>
Type
</dt>
<dd>
<span class="param-type">Object</span>
</dd>
</dl>
</article>
</section>
<section>
<header>
</header>
<article>
<div class="container-overview">
</div>
<h3 class="subsection-title">Members</h3>
<h4 class="name" id=".equalAngleLayout"><span class="type-signature">(static, constant) </span>equalAngleLayout<span class="type-signature"></span></h4>
<div class="description">
The equal angle layout. This function returns a layout function. It take and optional internal node, which if provided acts
as the starting node and fixes the order nodes are visited. This means the tree not update. The root position will
still change in response to rerooting.
</div>
<dl class="details">
<dt class="tag-source">Source:</dt>
<dd class="tag-source"><ul class="dummy"><li>
<a href="layout_equaleanglelayout.f.js.html">layout/equaleanglelayout.f.js</a>, <a href="layout_equaleanglelayout.f.js.html#line86">line 86</a>
</li></ul></dd>
</dl>
<h3 class="subsection-title">Methods</h3>
<h4 class="name" id=".makeEdges"><span class="type-signature">(static) </span>makeEdges<span class="signature">(vertices)</span><span class="type-signature"> → {*}</span></h4>
<div class="description">
Makes edges from an array of vertices.
Edge {
v0: parent vertex,
v1: target vertex,
key: vertex.key,
id:vertex.id,
classes:vertex.classes,
x:x position,
y:y.position,
textLabel:{ label postions
x:,
y: -6,
alignmentBaseline: "bottom",
textAnchor:"middle",
},
</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>vertices</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="layout_layoutHelpers.js.html">layout/layoutHelpers.js</a>, <a href="layout_layoutHelpers.js.html#line114">line 114</a>
</li></ul></dd>
</dl>
<h5>Returns:</h5>
<dl>
<dt>
Type
</dt>
<dd>
<span class="param-type">*</span>
</dd>
</dl>
<h4 class="name" id=".makeVertexFromNode"><span class="type-signature">(static) </span>makeVertexFromNode<span class="signature">(node)</span><span class="type-signature"></span></h4>
<div class="description">
Makes a vertex from a node in a tree.
anatomy of a vertex
{
name:node.name,
length:node.length,
height:node.height,
divergence:node.divergence,
level:node.level,
label:node.label,
annotations:node.annotations,
key: node.id,
id:node.id,
parent:node.parent?node.parent.id:null,
children:node.children?node.children.map(child=>child.id):null,
degree: (node.children ? node.children.length + 1 : 1),// the number of edges (including stem)
textLabel:{
labelBelow:labelBelow,
x:leftLabel?"-6":"12",
y:leftLabel?(labelBelow ? "-8": "8" ):"0",
alignmentBaseline: leftLabel?(labelBelow ? "bottom": "hanging" ):"middle",
textAnchor:leftLabel?"end":"start",
},
classes: getVertexClassesFromNode(node),
[p.node]:node,
};
</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">