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-rw-r--r--doc/jcgp/backend/population/class-use/Chromosome.html340
-rw-r--r--doc/jcgp/backend/population/class-use/Connection.html301
-rw-r--r--doc/jcgp/backend/population/class-use/Gene.html194
-rw-r--r--doc/jcgp/backend/population/class-use/Input.html187
-rw-r--r--doc/jcgp/backend/population/class-use/MutableElement.html228
-rw-r--r--doc/jcgp/backend/population/class-use/Node.html244
-rw-r--r--doc/jcgp/backend/population/class-use/Output.html202
-rw-r--r--doc/jcgp/backend/population/class-use/Population.html265
8 files changed, 1961 insertions, 0 deletions
diff --git a/doc/jcgp/backend/population/class-use/Chromosome.html b/doc/jcgp/backend/population/class-use/Chromosome.html
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@@ -0,0 +1,340 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!-- NewPage -->
+<html lang="en">
+<head>
+<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:07 BST 2014 -->
+<title>Uses of Class jcgp.backend.population.Chromosome</title>
+<meta name="date" content="2014-05-06">
+<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
+<script type="text/javascript" src="../../../../script.js"></script>
+</head>
+<body>
+<script type="text/javascript"><!--
+ try {
+ if (location.href.indexOf('is-external=true') == -1) {
+ parent.document.title="Uses of Class jcgp.backend.population.Chromosome";
+ }
+ }
+ catch(err) {
+ }
+//-->
+</script>
+<noscript>
+<div>JavaScript is disabled on your browser.</div>
+</noscript>
+<!-- ========= START OF TOP NAVBAR ======= -->
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+<ul class="navList" title="Navigation">
+<li><a href="../../../../overview-summary.html">Overview</a></li>
+<li><a href="../package-summary.html">Package</a></li>
+<li><a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Class</a></li>
+<li class="navBarCell1Rev">Use</li>
+<li><a href="../package-tree.html">Tree</a></li>
+<li><a href="../../../../deprecated-list.html">Deprecated</a></li>
+<li><a href="../../../../index-files/index-1.html">Index</a></li>
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+</ul>
+</div>
+<div class="subNav">
+<ul class="navList">
+<li>Prev</li>
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+<ul class="navList">
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+<li><a href="Chromosome.html" target="_top">No&nbsp;Frames</a></li>
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+<!-- -->
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+<!-- ========= END OF TOP NAVBAR ========= -->
+<div class="header">
+<h2 title="Uses of Class jcgp.backend.population.Chromosome" class="title">Uses of Class<br>jcgp.backend.population.Chromosome</h2>
+</div>
+<div class="classUseContainer">
+<ul class="blockList">
+<li class="blockList">
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.modules.mutator">jcgp.backend.modules.mutator</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.backend.parsers">jcgp.backend.parsers</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.gui.population">jcgp.gui.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<ul class="blockList">
+<li class="blockList"><a name="jcgp.backend.modules.mutator">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> in <a href="../../../../jcgp/backend/modules/mutator/package-summary.html">jcgp.backend.modules.mutator</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/modules/mutator/package-summary.html">jcgp.backend.modules.mutator</a> with parameters of type <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">ProbabilisticMutator.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/ProbabilisticMutator.html#mutate-jcgp.backend.population.Chromosome-">mutate</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>abstract void</code></td>
+<td class="colLast"><span class="typeNameLabel">Mutator.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/Mutator.html#mutate-jcgp.backend.population.Chromosome-">mutate</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</code>
+<div class="block">Applies mutations to the specified chromosome according
+ to the parameter values.</div>
+</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">PointMutator.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/PointMutator.html#mutate-jcgp.backend.population.Chromosome-">mutate</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.backend.parsers">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> in <a href="../../../../jcgp/backend/parsers/package-summary.html">jcgp.backend.parsers</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/parsers/package-summary.html">jcgp.backend.parsers</a> with parameters of type <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>static void</code></td>
+<td class="colLast"><span class="typeNameLabel">ChromosomeParser.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parsers/ChromosomeParser.html#parse-java.io.File-jcgp.backend.population.Chromosome-jcgp.backend.resources.Resources-">parse</a></span>(java.io.File&nbsp;file,
+ <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
+ <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
+<div class="block">Use this method to parse .chr files into a given chromosome.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>static void</code></td>
+<td class="colLast"><span class="typeNameLabel">ChromosomeParser.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parsers/ChromosomeParser.html#save-java.io.File-jcgp.backend.population.Chromosome-jcgp.backend.resources.Resources-">save</a></span>(java.io.File&nbsp;file,
+ <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
+ <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
+<div class="block">Writes a chromosome into the specified .chr file.</div>
+</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.backend.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that return <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Population.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Population.html#get-int-">get</a></span>(int&nbsp;index)</code>
+<div class="block">Returns the indexed chromosome.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Population.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Population.html#getRandomChromosome--">getRandomChromosome</a></span>()</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>boolean</code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#compareActiveGenesTo-jcgp.backend.population.Chromosome-">compareActiveGenesTo</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</code>
+<div class="block">Does the same as <code>compareGenesto()</code> but only looks
+ at the active portion of the chromosome.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>boolean</code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#compareGenesTo-jcgp.backend.population.Chromosome-">compareGenesTo</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</code>
+<div class="block">Performs a deep comparison between this chromosome and the provided one.</div>
+</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>int</code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#compareTo-jcgp.backend.population.Chromosome-">compareTo</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;o)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#copyGenes-jcgp.backend.population.Chromosome-">copyGenes</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</code>
+<div class="block">Creates a deep copy of the specified chromosome in the
+ this instance.</div>
+</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
+<caption><span>Constructors in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colOne" scope="col">Constructor and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#Chromosome-jcgp.backend.population.Chromosome-">Chromosome</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</code>
+<div class="block">Copy constructor.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html#Node-jcgp.backend.population.Chromosome-int-int-int-">Node</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
+ int&nbsp;row,
+ int&nbsp;column,
+ int&nbsp;arity)</code>
+<div class="block">Constructs a new instance of <code>Node</code> with the
+ specified parameters.</div>
+</td>
+</tr>
+<tr class="altColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Output.html#Output-jcgp.backend.population.Chromosome-int-">Output</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
+ int&nbsp;index)</code>
+<div class="block">Makes a new instance of <code>Output</code> with the
+ specified arguments.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Population.html#Population-jcgp.backend.population.Chromosome-jcgp.backend.resources.Resources-">Population</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;parent,
+ <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
+<div class="block">Initialise a population of copies of the given chromosome.</div>
+</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.gui.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">ChromosomePane.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/ChromosomePane.html#updateGenes-jcgp.backend.population.Chromosome-">updateGenes</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chr)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
+<caption><span>Constructors in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colOne" scope="col">Constructor and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/ChromosomePane.html#ChromosomePane-jcgp.backend.population.Chromosome-jcgp.gui.GUI-jcgp.gui.population.PopulationPane-">ChromosomePane</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
+ <a href="../../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui,
+ <a href="../../../../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</a>&nbsp;parent)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+</ul>
+</li>
+</ul>
+</div>
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
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+<!-- -->
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diff --git a/doc/jcgp/backend/population/class-use/Connection.html b/doc/jcgp/backend/population/class-use/Connection.html
new file mode 100644
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+++ b/doc/jcgp/backend/population/class-use/Connection.html
@@ -0,0 +1,301 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!-- NewPage -->
+<html lang="en">
+<head>
+<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:07 BST 2014 -->
+<title>Uses of Interface jcgp.backend.population.Connection</title>
+<meta name="date" content="2014-05-06">
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+<li><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Class</a></li>
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+<div class="header">
+<h2 title="Uses of Interface jcgp.backend.population.Connection" class="title">Uses of Interface<br>jcgp.backend.population.Connection</h2>
+</div>
+<div class="classUseContainer">
+<ul class="blockList">
+<li class="blockList">
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.gui.population">jcgp.gui.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<ul class="blockList">
+<li class="blockList"><a name="jcgp.backend.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
+<caption><span>Classes in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that implement <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Class and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>class&nbsp;</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></span></code>
+<div class="block">This is a chromosome input.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>class&nbsp;</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span></code>
+<div class="block">Nodes make up the main part of the chromosome,
+ where the actual functions are evolved.</div>
+</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that return <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Node.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html#getConnection-int-">getConnection</a></span>(int&nbsp;index)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getRandomConnection--">getRandomConnection</a></span>()</code>
+<div class="block">This method will pick a completely random connection, independently
+ of levels back, including inputs.</div>
+</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getRandomConnection-int-">getRandomConnection</a></span>(int&nbsp;column)</code>
+<div class="block">Returns a random allowed connection respecting levels back.<br>
+ This method may always pick inputs, as they can be picked
+ regardless of the column.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Output.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Output.html#getSource--">getSource</a></span>()</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">Node.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html#initialise-jcgp.backend.function.Function-jcgp.backend.population.Connection...-">initialise</a></span>(<a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;newFunction,
+ <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>...&nbsp;newConnections)</code>
+<div class="block">Initialises the node with the specified values.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">Node.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html#setConnection-int-jcgp.backend.population.Connection-">setConnection</a></span>(int&nbsp;index,
+ <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">Output.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Output.html#setConnection-int-jcgp.backend.population.Connection-">setConnection</a></span>(int&nbsp;index,
+ <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>
+<div class="block">When mutating an output, the index parameter
+ is simply ignored and the output source is
+ set.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">MutableElement.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/MutableElement.html#setConnection-int-jcgp.backend.population.Connection-">setConnection</a></span>(int&nbsp;index,
+ <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>
+<div class="block">This method sets the indexed connection to the specified new connection.</div>
+</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.gui.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a> in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> that return <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">GUINode.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUINode.html#getChangingConnection--">getChangingConnection</a></span>()</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">GUIInput.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIInput.html#getChangingConnection--">getChangingConnection</a></span>()</code>&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">GUIOutput.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIOutput.html#getChangingConnection--">getChangingConnection</a></span>()</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>abstract <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
+<td class="colLast"><span class="typeNameLabel">GUIGene.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIGene.html#getChangingConnection--">getChangingConnection</a></span>()</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">GUINode.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUINode.html#setChangingConnection-jcgp.backend.population.Connection-">setChangingConnection</a></span>(<a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">GUIInput.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIInput.html#setChangingConnection-jcgp.backend.population.Connection-">setChangingConnection</a></span>(<a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">GUIOutput.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIOutput.html#setChangingConnection-jcgp.backend.population.Connection-">setChangingConnection</a></span>(<a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>abstract void</code></td>
+<td class="colLast"><span class="typeNameLabel">GUIGene.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIGene.html#setChangingConnection-jcgp.backend.population.Connection-">setChangingConnection</a></span>(<a href="../../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>&nbsp;</td>
+</tr>
+</tbody>
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diff --git a/doc/jcgp/backend/population/class-use/Gene.html b/doc/jcgp/backend/population/class-use/Gene.html
new file mode 100644
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+++ b/doc/jcgp/backend/population/class-use/Gene.html
@@ -0,0 +1,194 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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+<li><a href="../../../../jcgp/backend/population/Gene.html" title="class in jcgp.backend.population">Class</a></li>
+<li class="navBarCell1Rev">Use</li>
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+<ul class="blockList">
+<li class="blockList">
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/Gene.html" title="class in jcgp.backend.population">Gene</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.gui.population">jcgp.gui.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<ul class="blockList">
+<li class="blockList"><a name="jcgp.backend.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Gene.html" title="class in jcgp.backend.population">Gene</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing subclasses, and an explanation">
+<caption><span>Subclasses of <a href="../../../../jcgp/backend/population/Gene.html" title="class in jcgp.backend.population">Gene</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Class and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>class&nbsp;</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></span></code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>class&nbsp;</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span></code>&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>class&nbsp;</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></span></code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.gui.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Gene.html" title="class in jcgp.backend.population">Gene</a> in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> that return <a href="../../../../jcgp/backend/population/Gene.html" title="class in jcgp.backend.population">Gene</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>abstract <a href="../../../../jcgp/backend/population/Gene.html" title="class in jcgp.backend.population">Gene</a></code></td>
+<td class="colLast"><span class="typeNameLabel">GUIGene.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIGene.html#getGene--">getGene</a></span>()</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
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+<!-- ======= START OF BOTTOM NAVBAR ====== -->
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diff --git a/doc/jcgp/backend/population/class-use/Input.html b/doc/jcgp/backend/population/class-use/Input.html
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+++ b/doc/jcgp/backend/population/class-use/Input.html
@@ -0,0 +1,187 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!-- NewPage -->
+<html lang="en">
+<head>
+<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:07 BST 2014 -->
+<title>Uses of Class jcgp.backend.population.Input</title>
+<meta name="date" content="2014-05-06">
+<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
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+<li><a href="../package-summary.html">Package</a></li>
+<li><a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Class</a></li>
+<li class="navBarCell1Rev">Use</li>
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+<h2 title="Uses of Class jcgp.backend.population.Input" class="title">Uses of Class<br>jcgp.backend.population.Input</h2>
+</div>
+<div class="classUseContainer">
+<ul class="blockList">
+<li class="blockList">
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.gui.population">jcgp.gui.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
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+<li class="blockList"><a name="jcgp.backend.population">
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+<h3>Uses of <a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that return <a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getInput-int-">getInput</a></span>(int&nbsp;index)</code>
+<div class="block">Returns a reference to the indexed input.</div>
+</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.gui.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a> in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
+<caption><span>Constructors in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colOne" scope="col">Constructor and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIInput.html#GUIInput-jcgp.gui.population.ChromosomePane-jcgp.backend.population.Input-">GUIInput</a></span>(<a href="../../../../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">ChromosomePane</a>&nbsp;parentRef,
+ <a href="../../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a>&nbsp;input)</code>&nbsp;</td>
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diff --git a/doc/jcgp/backend/population/class-use/MutableElement.html b/doc/jcgp/backend/population/class-use/MutableElement.html
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index 0000000..77bf35f
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+++ b/doc/jcgp/backend/population/class-use/MutableElement.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!-- NewPage -->
+<html lang="en">
+<head>
+<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:07 BST 2014 -->
+<title>Uses of Interface jcgp.backend.population.MutableElement</title>
+<meta name="date" content="2014-05-06">
+<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
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+ if (location.href.indexOf('is-external=true') == -1) {
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+<li><a href="../package-summary.html">Package</a></li>
+<li><a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">Class</a></li>
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+<div class="header">
+<h2 title="Uses of Interface jcgp.backend.population.MutableElement" class="title">Uses of Interface<br>jcgp.backend.population.MutableElement</h2>
+</div>
+<div class="classUseContainer">
+<ul class="blockList">
+<li class="blockList">
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<ul class="blockList">
+<li class="blockList"><a name="jcgp.backend.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
+<caption><span>Classes in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that implement <a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Class and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>class&nbsp;</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span></code>
+<div class="block">Nodes make up the main part of the chromosome,
+ where the actual functions are evolved.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>class&nbsp;</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></span></code>
+<div class="block">This is a chromosome output.</div>
+</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that return <a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getRandomMutableElement--">getRandomMutableElement</a></span>()</code>
+<div class="block">This method is useful for mutating chromosomes.</div>
+</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> with parameters of type <a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>boolean</code></td>
+<td class="colLast"><span class="typeNameLabel">Node.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html#copyOf-jcgp.backend.population.MutableElement-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a>&nbsp;element)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>boolean</code></td>
+<td class="colLast"><span class="typeNameLabel">Output.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Output.html#copyOf-jcgp.backend.population.MutableElement-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a>&nbsp;m)</code>&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>boolean</code></td>
+<td class="colLast"><span class="typeNameLabel">MutableElement.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/MutableElement.html#copyOf-jcgp.backend.population.MutableElement-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a>&nbsp;element)</code>
+<div class="block">Asserts if the specified element is a copy of the elements
+ this is called on.<br>
+ This method returns true if and only if:
+
+ the elements being compared are not the same instance;
+ the connections of the compared elements are not the same instance;
+ the elements have the same function (in the case of Node);
+ the grid position of the elements themselves are the same;
+ the grid position of all equivalent connections are the same;
+
+ <br><br>
+ The relationship computed by this method is:
+
+ symmetric: a.copyOf(b) == b.copyOf(a);
+ not reflexive: a.copyOf(a) returns false;
+ not transitive: if a.copyOf(b) is true and b.copyOf(c) is true, a.copyOf(c) is
+ not necessarily true since it is possible that a == c.
+ </div>
+</td>
+</tr>
+</tbody>
+</table>
+</li>
+</ul>
+</li>
+</ul>
+</div>
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
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@@ -0,0 +1,244 @@
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+<!-- NewPage -->
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+<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:07 BST 2014 -->
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+<li class="navBarCell1Rev">Use</li>
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+<li class="blockList">
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.gui.population">jcgp.gui.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<ul class="blockList">
+<li class="blockList"><a name="jcgp.backend.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that return <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getNode-int-int-">getNode</a></span>(int&nbsp;row,
+ int&nbsp;column)</code>
+<div class="block">Returns a reference to any node, addressed by row and column.</div>
+</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that return types with arguments of type <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>java.util.ArrayList&lt;<a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&gt;</code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getActiveNodes--">getActiveNodes</a></span>()</code>
+<div class="block">This method computes a list of active nodes (if necessary) and returns it.</div>
+</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Method parameters in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> with type arguments of type <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">Output.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Output.html#getActiveNodes-java.util.ArrayList-">getActiveNodes</a></span>(java.util.ArrayList&lt;<a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&gt;&nbsp;activeNodes)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.gui.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a> in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> that return <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></code></td>
+<td class="colLast"><span class="typeNameLabel">GUINode.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUINode.html#getNode--">getNode</a></span>()</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">GUINode.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUINode.html#setNode-jcgp.backend.population.Node-">setNode</a></span>(<a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&nbsp;newNode)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
+<caption><span>Constructors in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colOne" scope="col">Constructor and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUINode.html#GUINode-jcgp.gui.population.ChromosomePane-jcgp.backend.population.Node-javafx.scene.shape.Line:A-jcgp.gui.GUI-">GUINode</a></span>(<a href="../../../../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">ChromosomePane</a>&nbsp;parentRef,
+ <a href="../../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&nbsp;node,
+ javafx.scene.shape.Line[]&nbsp;connectionLines,
+ <a href="../../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+</ul>
+</li>
+</ul>
+</div>
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
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diff --git a/doc/jcgp/backend/population/class-use/Output.html b/doc/jcgp/backend/population/class-use/Output.html
new file mode 100644
index 0000000..19bd12a
--- /dev/null
+++ b/doc/jcgp/backend/population/class-use/Output.html
@@ -0,0 +1,202 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!-- NewPage -->
+<html lang="en">
+<head>
+<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:07 BST 2014 -->
+<title>Uses of Class jcgp.backend.population.Output</title>
+<meta name="date" content="2014-05-06">
+<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
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+<li class="navBarCell1Rev">Use</li>
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+</div>
+<div class="classUseContainer">
+<ul class="blockList">
+<li class="blockList">
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.gui.population">jcgp.gui.population</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<ul class="blockList">
+<li class="blockList"><a name="jcgp.backend.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a> in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/population/package-summary.html">jcgp.backend.population</a> that return <a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></code></td>
+<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getOutput-int-">getOutput</a></span>(int&nbsp;index)</code>
+<div class="block">Returns a reference to the indexed output.</div>
+</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.gui.population">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a> in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">GUIOutput.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIOutput.html#setOutput-jcgp.backend.population.Output-">setOutput</a></span>(<a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a>&nbsp;newOutput)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing constructors, and an explanation">
+<caption><span>Constructors in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colOne" scope="col">Constructor and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIOutput.html#GUIOutput-jcgp.gui.population.ChromosomePane-jcgp.backend.population.Output-javafx.scene.shape.Line-jcgp.gui.GUI-">GUIOutput</a></span>(<a href="../../../../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">ChromosomePane</a>&nbsp;parentRef,
+ <a href="../../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a>&nbsp;output,
+ javafx.scene.shape.Line&nbsp;line,
+ <a href="../../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
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diff --git a/doc/jcgp/backend/population/class-use/Population.html b/doc/jcgp/backend/population/class-use/Population.html
new file mode 100644
index 0000000..d98d156
--- /dev/null
+++ b/doc/jcgp/backend/population/class-use/Population.html
@@ -0,0 +1,265 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!-- NewPage -->
+<html lang="en">
+<head>
+<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:07 BST 2014 -->
+<title>Uses of Class jcgp.backend.population.Population</title>
+<meta name="date" content="2014-05-06">
+<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
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+<script type="text/javascript"><!--
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+ if (location.href.indexOf('is-external=true') == -1) {
+ parent.document.title="Uses of Class jcgp.backend.population.Population";
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+ }
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+<li><a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Class</a></li>
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+<h2 title="Uses of Class jcgp.backend.population.Population" class="title">Uses of Class<br>jcgp.backend.population.Population</h2>
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+<ul class="blockList">
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+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
+<caption><span>Packages that use <a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Package</th>
+<th class="colLast" scope="col">Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp">jcgp</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a href="#jcgp.backend.modules.es">jcgp.backend.modules.es</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><a href="#jcgp.backend.modules.problem">jcgp.backend.modules.problem</a></td>
+<td class="colLast">&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<ul class="blockList">
+<li class="blockList"><a name="jcgp">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a> in <a href="../../../../jcgp/package-summary.html">jcgp</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/package-summary.html">jcgp</a> that return <a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code><a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a></code></td>
+<td class="colLast"><span class="typeNameLabel">JCGP.</span><code><span class="memberNameLink"><a href="../../../../jcgp/JCGP.html#getPopulation--">getPopulation</a></span>()</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.backend.modules.es">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a> in <a href="../../../../jcgp/backend/modules/es/package-summary.html">jcgp.backend.modules.es</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/modules/es/package-summary.html">jcgp.backend.modules.es</a> with parameters of type <a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">TournamentSelection.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/es/TournamentSelection.html#evolve-jcgp.backend.population.Population-jcgp.backend.modules.mutator.Mutator-">evolve</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population,
+ <a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>&nbsp;mutator)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>abstract void</code></td>
+<td class="colLast"><span class="typeNameLabel">EvolutionaryStrategy.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html#evolve-jcgp.backend.population.Population-jcgp.backend.modules.mutator.Mutator-">evolve</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population,
+ <a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>&nbsp;mutator)</code>
+<div class="block">Performs the selection algorithm and uses the mutator to create
+ the next generation of solutions.</div>
+</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">MuPlusLambda.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/es/MuPlusLambda.html#evolve-jcgp.backend.population.Population-jcgp.backend.modules.mutator.Mutator-">evolve</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population,
+ <a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>&nbsp;mutator)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList"><a name="jcgp.backend.modules.problem">
+<!-- -->
+</a>
+<h3>Uses of <a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a> in <a href="../../../../jcgp/backend/modules/problem/package-summary.html">jcgp.backend.modules.problem</a></h3>
+<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
+<caption><span>Methods in <a href="../../../../jcgp/backend/modules/problem/package-summary.html">jcgp.backend.modules.problem</a> with parameters of type <a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th class="colLast" scope="col">Method and Description</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">SymbolicRegressionProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">evaluate</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population,
+ <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>abstract void</code></td>
+<td class="colLast"><span class="typeNameLabel">Problem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">evaluate</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population,
+ <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
+<div class="block">The most important method of the problem type.</div>
+</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>void</code></td>
+<td class="colLast"><span class="typeNameLabel">DigitalCircuitProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">evaluate</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population,
+ <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>int</code></td>
+<td class="colLast"><span class="typeNameLabel">SymbolicRegressionProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#hasImprovement-jcgp.backend.population.Population-">hasImprovement</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>abstract int</code></td>
+<td class="colLast"><span class="typeNameLabel">Problem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasImprovement-jcgp.backend.population.Population-">hasImprovement</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>
+<div class="block">Used to assert whether a given population has a chromosome that is an improvement over
+ the current best chromosome.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>int</code></td>
+<td class="colLast"><span class="typeNameLabel">DigitalCircuitProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html#hasImprovement-jcgp.backend.population.Population-">hasImprovement</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>&nbsp;</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>int</code></td>
+<td class="colLast"><span class="typeNameLabel">SymbolicRegressionProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#perfectSolutionFound-jcgp.backend.population.Population-">perfectSolutionFound</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>&nbsp;</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>abstract int</code></td>
+<td class="colLast"><span class="typeNameLabel">Problem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#perfectSolutionFound-jcgp.backend.population.Population-">perfectSolutionFound</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>
+<div class="block">Used to assert whether a given population contains a perfect solution
+ to the problem.</div>
+</td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><code>int</code></td>
+<td class="colLast"><span class="typeNameLabel">DigitalCircuitProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html#perfectSolutionFound-jcgp.backend.population.Population-">perfectSolutionFound</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>&nbsp;</td>
+</tr>
+</tbody>
+</table>
+</li>
+</ul>
+</li>
+</ul>
+</div>
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