doc/global.html

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    <title>JSDoc: Global</title>

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    <h1 class="page-title">Global</h1>

    
<section>

<header>
    
        <h2></h2>
        
    
</header>

<article>
    <div class="container-overview">
    
        
<dl class="details">

    
</dl>


    </div>

    
        <h3 class="subsection-title">Members</h3>

        
<h4 class="name" id="equalAngleLayout"><span class="type-signature">(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#line85">line 85</a>
    </li></ul></dd>
    

</dl>


<h4 class="name" id="rectangularHilightedLayout"><span class="type-signature">(constant) </span>rectangularHilightedLayout<span class="type-signature"></span></h4>


<div class="description">
    This layout highlights parts of the tree and compresses others. The layout factory takes a predicate function that is called
on each node and returns true or false. true == more space around node.
</div>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="layout_rectangularHilightedLayout.js.html">layout/rectangularHilightedLayout.js</a>, <a href="layout_rectangularHilightedLayout.js.html#line59">line 59</a>
    </li></ul></dd>
    

</dl>


        <h3 class="subsection-title">Methods</h3>

        
    <h4 class="name" id="branch"><span class="type-signature"></span>branch<span class="signature">()</span><span class="type-signature"> &rarr; {<a href="BaubleManager.html">BaubleManager</a>|*}</span></h4>
    

<div class="description">
    branch is a helper function that returns a new branch instance.
</div>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="baubles_branch.js.html">baubles/branch.js</a>, <a href="baubles_branch.js.html#line214">line 214</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type"><a href="BaubleManager.html">BaubleManager</a></span>
|

<span class="param-type">*</span>


    </dd>
</dl>

    
    <h4 class="name" id="branchLabel"><span class="type-signature"></span>branchLabel<span class="signature">(text)</span><span class="type-signature"> &rarr; {Bauble|*|null|undefined}</span></h4>
    

<div class="description">
    Helper function that puts label in the middle of a curveStepBefore branch
</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>text</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="baubles_label.js.html">baubles/label.js</a>, <a href="baubles_label.js.html#line106">line 106</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">Bauble</span>
|

<span class="param-type">*</span>
|

<span class="param-type">null</span>
|

<span class="param-type">undefined</span>


    </dd>
</dl>

    
    <h4 class="name" id="branchPathGenerator"><span class="type-signature"></span>branchPathGenerator<span class="signature">(scales, branchCurve)</span><span class="type-signature"> &rarr; {function}</span></h4>
    

<div class="description">
    Generates a line() function that takes an edge and it's index and returns a line for d3 path element. It is called
by the figtree class as
const branchPath = this.layout.branchPathGenerator(this.scales())
newBranches.append("path")
 .attr("class", "branch-path")
 .attr("d", (e,i) => branchPath(e,i));
</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>scales</code></td>
            

            <td class="type">
            
            </td>

            
            <td class="description last"></td>
        </tr>

    
        <tr>
            
                <td class="name"><code>branchCurve</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="baubles_branch.js.html">baubles/branch.js</a>, <a href="baubles_branch.js.html#line178">line 178</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">function</span>


    </dd>
</dl>

    
    <h4 class="name" id="circle"><span class="type-signature"></span>circle<span class="signature">()</span><span class="type-signature"> &rarr; {<a href="CircleBauble.html">CircleBauble</a>}</span></h4>
    

<div class="description">
    helper function returns a new instance of a circle bauble.
</div>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="baubles_circlebauble.js.html">baubles/circlebauble.js</a>, <a href="baubles_circlebauble.js.html#line161">line 161</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type"><a href="CircleBauble.html">CircleBauble</a></span>


    </dd>
</dl>

    
    <h4 class="name" id="dateToDecimal"><span class="type-signature"></span>dateToDecimal<span class="signature">(date)</span><span class="type-signature"> &rarr; {number}</span></h4>
    

<div class="description">
    A function that converts a date into a decimal.
</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>date</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="utilities.js.html">utilities.js</a>, <a href="utilities.js.html#line53">line 53</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="decimalToDate"><span class="type-signature"></span>decimalToDate<span class="signature">(decimalDate)</span><span class="type-signature"> &rarr; {Date}</span></h4>
    

<div class="description">
    A function which converts a decimal float into a date object
</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>decimalDate</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="utilities.js.html">utilities.js</a>, <a href="utilities.js.html#line40">line 40</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">Date</span>


    </dd>
</dl>

    
    <h4 class="name" id="internalNodeLabel"><span class="type-signature"></span>internalNodeLabel<span class="signature">(text)</span><span class="type-signature"> &rarr; {*}</span></h4>
    

<div class="description">
    Helper function filters label to just work on internal nodes
</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>text</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="baubles_label.js.html">baubles/label.js</a>, <a href="baubles_label.js.html#line96">line 96</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">*</span>


    </dd>
</dl>

    
    <h4 class="name" id="label"><span class="type-signature"></span>label<span class="signature">(text)</span><span class="type-signature"> &rarr; {*}</span></h4>
    

<div class="description">
    Helper function for making labels. Sets position and alignment based on
vertex or edge object.
</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>text</code></td>
            

            <td class="type">
            
            </td>

            
            <td class="description last">text to be displayed</td>
        </tr>

    
    </tbody>
</table>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="baubles_label.js.html">baubles/label.js</a>, <a href="baubles_label.js.html#line70">line 70</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">*</span>


    </dd>
</dl>

    
    <h4 class="name" id="leapYear"><span class="type-signature"></span>leapYear<span class="signature">(year)</span><span class="type-signature"> &rarr; {boolean}</span></h4>
    

<div class="description">
    Helper function to determine if the provided year is a leap year
</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>year</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="utilities.js.html">utilities.js</a>, <a href="utilities.js.html#line31">line 31</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">boolean</span>


    </dd>
</dl>

    
    <h4 class="name" id="leastSquares"><span class="type-signature"></span>leastSquares<span class="signature">(data)</span><span class="type-signature"> &rarr; {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#line63">line 63</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">Object</span>


    </dd>
</dl>

    
    <h4 class="name" id="legend"><span class="type-signature"></span>legend<span class="signature">()</span><span class="type-signature"> &rarr; {<a href="Legend.html">Legend</a>}</span></h4>
    

<div class="description">
    helper function that returns a new legend instance
</div>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="decoration_legend.js.html">decoration/legend.js</a>, <a href="decoration_legend.js.html#line156">line 156</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type"><a href="Legend.html">Legend</a></span>


    </dd>
</dl>

    
    <h4 class="name" id="makeEdges"><span class="type-signature"></span>makeEdges<span class="signature">(vertices)</span><span class="type-signature"> &rarr; {*}</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#line113">line 113</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"></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#line62">line 62</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<div class="param-desc">
    vertex
</div>


    <h4 class="name" id="rectangle"><span class="type-signature"></span>rectangle<span class="signature">()</span><span class="type-signature"> &rarr; {<a href="RectangularBauble.html">RectangularBauble</a>}</span></h4>
    

<div class="description">
    A helper function that returns a new rectangular bauble
</div>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="baubles_rectanglebauble.js.html">baubles/rectanglebauble.js</a>, <a href="baubles_rectanglebauble.js.html#line146">line 146</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type"><a href="RectangularBauble.html">RectangularBauble</a></span>


    </dd>
</dl>

    
    <h4 class="name" id="scaleBar"><span class="type-signature"></span>scaleBar<span class="signature">()</span><span class="type-signature"> &rarr; {<a href="ScaleBar.html">ScaleBar</a>}</span></h4>
    

<div class="description">
    Helper function that returns a new scalebar instance.
</div>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="decoration_scaleBar.js.html">decoration/scaleBar.js</a>, <a href="decoration_scaleBar.js.html#line124">line 124</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type"><a href="ScaleBar.html">ScaleBar</a></span>


    </dd>
</dl>

    
    <h4 class="name" id="tipLabel"><span class="type-signature"></span>tipLabel<span class="signature">(text)</span><span class="type-signature"> &rarr; {*}</span></h4>
    

<div class="description">
    Helper function filters label to just work on tips
</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>text</code></td>
            

            <td class="type">
            
            </td>

            
            <td class="description last">string or function for assigning label (will be passed vertex or edge)</td>
        </tr>

    
    </tbody>
</table>


<dl class="details">

    
    <dt class="tag-source">Source:</dt>
    <dd class="tag-source"><ul class="dummy"><li>
        <a href="baubles_label.js.html">baubles/label.js</a>, <a href="baubles_label.js.html#line87">line 87</a>
    </li></ul></dd>
    

</dl>


<h5>Returns:</h5>

        
<dl>
    <dt>
        Type
    </dt>
    <dd>
        
<span class="param-type">*</span>


    </dd>
</dl>

    
</article>

</section>


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