From 4f26361eb08aa09334d1eea0a124110c20d809ce Mon Sep 17 00:00:00 2001
From: Eduardo Pedroni <e.pedroni91@gmail.com>
Date: Sat, 18 Oct 2014 15:21:45 +0200
Subject: Moved javadocs to a different repository for hosting, updated README

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 doc/jcgp/JCGP.html                                 | 704 -----------------
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 ...avellingSalesmanFunctions.AbsoluteCosineAB.html | 334 --------
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 ...ravellingSalesmanFunctions.BoundedDivision.html | 330 --------
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 ...ingSalesmanFunctions.SquaredMultiplication.html | 329 --------
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 ...avellingSalesmanFunctions.AbsoluteCosineAB.html | 124 ---
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 ...vellingSalesmanFunctions.ScaledExponential.html | 124 ---
 ...avellingSalesmanFunctions.ScaledHypotenuse.html | 124 ---
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 .../modules/problem/DigitalCircuitProblem.html     | 423 ----------
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-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>JCGP</title>
-<meta name="date" content="2014-05-22">
-<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="JCGP";
-        }
-    }
-    catch(err) {
-    }
-//-->
-var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":10,"i7":10,"i8":10,"i9":10,"i10":10,"i11":10,"i12":9,"i13":10,"i14":10,"i15":10,"i16":10,"i17":10,"i18":10,"i19":10,"i20":10};
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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 class="navBarCell1Rev">Class</li>
-<li><a href="class-use/JCGP.html">Use</a></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>
-<li><a href="../help-doc.html">Help</a></li>
-</ul>
-</div>
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp</div>
-<h2 title="Class JCGP" class="title">Class JCGP</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.JCGP</li>
-</ul>
-</li>
-</ul>
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">JCGP</span>
-extends java.lang.Object</pre>
-<div class="block">Top-level JCGP class. This class is the entry point for a CGP experiment. 
- <br><br>
- An instance of JCGP encapsulates the entire experiment. It contains a <code>Resources</code>
- object which can be retrieved via a getter. Modules can be selected using their
- respective setters.
- <br><br>
- The flow of the experiment is controlled using <code>start()</code>, <code>nextGeneration()</code>
- and <code>reset()</code>. Files can be loaded with their respective load methods and
- chromosome configurations can be saved with <code>saveChromosome()</code>. 
- <br><br>
- JCGP supports an extra console in addition to <code>System.console()</code>, so that messages
- can also be printed to a GUI, for example. This extra console can be set with <code>setConsole()</code>, 
- and must implement jcgp.resources.Console.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
-</div>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#JCGP--">JCGP</a></span>()</code>
-<div class="block">Creates a new instance of JCGP.</div>
-</td>
-</tr>
-</table>
-</li>
-</ul>
-<!-- ========== METHOD SUMMARY =========== -->
-<ul class="blockList">
-<li class="blockList"><a name="method.summary">
-<!--   -->
-</a>
-<h3>Method Summary</h3>
-<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code><a href="../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a>[]</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getEvolutionaryStrategies--">getEvolutionaryStrategies</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code><a href="../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getEvolutionaryStrategy--">getEvolutionaryStrategy</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code><a href="../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getMutator--">getMutator</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code><a href="../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>[]</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getMutators--">getMutators</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" 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"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getPopulation--">getPopulation</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code><a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getProblem--">getProblem</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code><a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a>[]</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getProblems--">getProblems</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i7" class="rowColor">
-<td class="colFirst"><code><a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#getResources--">getResources</a></span>()</code>
-<div class="block">Returns a reference to the <code>ModifiableResources</code> used by the
- experiment.</div>
-</td>
-</tr>
-<tr id="i8" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#isFinished--">isFinished</a></span>()</code>
-<div class="block">Returns the experiment's status.</div>
-</td>
-</tr>
-<tr id="i9" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#loadChromosome-java.io.File-int-">loadChromosome</a></span>(java.io.File&nbsp;file,
-              int&nbsp;chromosomeIndex)</code>
-<div class="block">Loads a chromosome from the given file into
- the specified population index.</div>
-</td>
-</tr>
-<tr id="i10" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#loadParameters-java.io.File-">loadParameters</a></span>(java.io.File&nbsp;file)</code>
-<div class="block">When given a .par file, this method loads the parameters into the
- experiment's resources.</div>
-</td>
-</tr>
-<tr id="i11" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#loadProblemData-java.io.File-">loadProblemData</a></span>(java.io.File&nbsp;file)</code>
-<div class="block">Parses a problem data file.</div>
-</td>
-</tr>
-<tr id="i12" class="altColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#main-java.lang.String...-">main</a></span>(java.lang.String...&nbsp;args)</code>
-<div class="block">JCGP main method, this is used to execute JCGP from the command line.</div>
-</td>
-</tr>
-<tr id="i13" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#nextGeneration--">nextGeneration</a></span>()</code>
-<div class="block">Performs one full generational cycle.</div>
-</td>
-</tr>
-<tr id="i14" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#reset--">reset</a></span>()</code>
-<div class="block">Resets the experiment.</div>
-</td>
-</tr>
-<tr id="i15" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#saveChromosome-java.io.File-int-">saveChromosome</a></span>(java.io.File&nbsp;file,
-              int&nbsp;chromosomeIndex)</code>
-<div class="block">Saves a copy of the specified chromosome 
- into the given file.</div>
-</td>
-</tr>
-<tr id="i16" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#setConsole-jcgp.backend.resources.Console-">setConsole</a></span>(<a href="../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a>&nbsp;console)</code>
-<div class="block">Sets an extra console.</div>
-</td>
-</tr>
-<tr id="i17" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#setEvolutionaryStrategy-int-">setEvolutionaryStrategy</a></span>(int&nbsp;index)</code>&nbsp;</td>
-</tr>
-<tr id="i18" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#setMutator-int-">setMutator</a></span>(int&nbsp;index)</code>&nbsp;</td>
-</tr>
-<tr id="i19" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#setProblem-int-">setProblem</a></span>(int&nbsp;index)</code>&nbsp;</td>
-</tr>
-<tr id="i20" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../jcgp/JCGP.html#start--">start</a></span>()</code>
-<div class="block">This method calls <code>nextGeneration()</code> in a loop
- until the experiment is flagged as finished.</div>
-</td>
-</tr>
-</table>
-<ul class="blockList">
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-<!--   -->
-</a>
-<h3>Methods inherited from class&nbsp;java.lang.Object</h3>
-<code>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<div class="details">
-<ul class="blockList">
-<li class="blockList">
-<!-- ========= CONSTRUCTOR DETAIL ======== -->
-<ul class="blockList">
-<li class="blockList"><a name="constructor.detail">
-<!--   -->
-</a>
-<h3>Constructor Detail</h3>
-<a name="JCGP--">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>JCGP</h4>
-<pre>public&nbsp;JCGP()</pre>
-<div class="block">Creates a new instance of JCGP.</div>
-</li>
-</ul>
-</li>
-</ul>
-<!-- ============ METHOD DETAIL ========== -->
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-<li class="blockList"><a name="method.detail">
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-<h3>Method Detail</h3>
-<a name="main-java.lang.String...-">
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-<ul class="blockList">
-<li class="blockList">
-<h4>main</h4>
-<pre>public static&nbsp;void&nbsp;main(java.lang.String...&nbsp;args)</pre>
-<div class="block">JCGP main method, this is used to execute JCGP from the command line. 
- <br><br>
- In this case the program works in the same way as the classic CGP implementation,
- requiring a .par file and an optional problem data file. As in the traditional CGP
- implementation, the program must be compiled with the right problem type selected.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>args</code> - one or more files needed to perform the experiment.</dd>
-</dl>
-</li>
-</ul>
-<a name="getResources--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getResources</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;getResources()</pre>
-<div class="block">Returns a reference to the <code>ModifiableResources</code> used by the
- experiment. <br>
- Use this with care, since changing experiment parameters may
- have unintended effects if not done properly.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a reference to the experiment's resources.</dd>
-</dl>
-</li>
-</ul>
-<a name="getPopulation--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getPopulation</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;getPopulation()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a reference to the experiment's population.</dd>
-</dl>
-</li>
-</ul>
-<a name="getMutators--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getMutators</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>[]&nbsp;getMutators()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a complete list of the experiment's mutators.</dd>
-</dl>
-</li>
-</ul>
-<a name="getMutator--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getMutator</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>&nbsp;getMutator()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the currently selected mutator.</dd>
-</dl>
-</li>
-</ul>
-<a name="getEvolutionaryStrategies--">
-<!--   -->
-</a>
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-<h4>getEvolutionaryStrategies</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a>[]&nbsp;getEvolutionaryStrategies()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a complete list of the experiment's evolutionary strategies.</dd>
-</dl>
-</li>
-</ul>
-<a name="getEvolutionaryStrategy--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getEvolutionaryStrategy</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a>&nbsp;getEvolutionaryStrategy()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the currently selected evolutionary strategy.</dd>
-</dl>
-</li>
-</ul>
-<a name="getProblems--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getProblems</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a>[]&nbsp;getProblems()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a complete list of the experiment's problem types.</dd>
-</dl>
-</li>
-</ul>
-<a name="getProblem--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getProblem</h4>
-<pre>public&nbsp;<a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a>&nbsp;getProblem()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the currently selected problem type.</dd>
-</dl>
-</li>
-</ul>
-<a name="setMutator-int-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>setMutator</h4>
-<pre>public&nbsp;void&nbsp;setMutator(int&nbsp;index)</pre>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the index of the desired mutator.</dd>
-</dl>
-</li>
-</ul>
-<a name="setEvolutionaryStrategy-int-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>setEvolutionaryStrategy</h4>
-<pre>public&nbsp;void&nbsp;setEvolutionaryStrategy(int&nbsp;index)</pre>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the index of the desired evolutionary strategy.</dd>
-</dl>
-</li>
-</ul>
-<a name="setProblem-int-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>setProblem</h4>
-<pre>public&nbsp;void&nbsp;setProblem(int&nbsp;index)</pre>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the index of the desired problem type.</dd>
-</dl>
-</li>
-</ul>
-<a name="nextGeneration--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>nextGeneration</h4>
-<pre>public&nbsp;void&nbsp;nextGeneration()</pre>
-<div class="block">Performs one full generational cycle. More specifically, 
- this method evaluates the current population using the 
- selected problem, and checks whether a solution has been found.
- <br>
- If the experiment is to continue, a new generation is created 
- using the selected evolutionary strategy and mutator.
- <br><br>
- This method also deals with ending runs, in other words, 
- a new population is created at the end of each run automatically.
- When all runs have been performed, this method sets the experiment
- finished flag and does nothing until <code>reset()</code> is called.</div>
-</li>
-</ul>
-<a name="start--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>start</h4>
-<pre>public&nbsp;void&nbsp;start()</pre>
-<div class="block">This method calls <code>nextGeneration()</code> in a loop
- until the experiment is flagged as finished. This is
- performed on the same thread of execution, so this
- method will most likely block for a significant amount
- of time (problem-dependent, but anywhere from seconds to days).
- <br>
- Once the experiment is finished, calling this method does
- nothing until <code>reset()</code> is called.</div>
-</li>
-</ul>
-<a name="reset--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>reset</h4>
-<pre>public&nbsp;void&nbsp;reset()</pre>
-<div class="block">Resets the experiment.
- <br>
- More specifically: this creates a new population, resets
- the current generation and run parameters to 1 and prints
- a complete list of the experiment's parameters.</div>
-</li>
-</ul>
-<a name="loadParameters-java.io.File-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>loadParameters</h4>
-<pre>public&nbsp;void&nbsp;loadParameters(java.io.File&nbsp;file)</pre>
-<div class="block">When given a .par file, this method loads the parameters into the
- experiment's resources. This causes an experiment-wide reset.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the file to parse.</dd>
-</dl>
-</li>
-</ul>
-<a name="loadProblemData-java.io.File-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>loadProblemData</h4>
-<pre>public&nbsp;void&nbsp;loadProblemData(java.io.File&nbsp;file)</pre>
-<div class="block">Parses a problem data file. This is problem-dependent, not
- all problems require a data file.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the file to parse.</dd>
-</dl>
-</li>
-</ul>
-<a name="loadChromosome-java.io.File-int-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>loadChromosome</h4>
-<pre>public&nbsp;void&nbsp;loadChromosome(java.io.File&nbsp;file,
-                           int&nbsp;chromosomeIndex)</pre>
-<div class="block">Loads a chromosome from the given file into
- the specified population index.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the chromosome to parse.</dd>
-<dd><code>chromosomeIndex</code> - the population index into which to parse.</dd>
-</dl>
-</li>
-</ul>
-<a name="saveChromosome-java.io.File-int-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>saveChromosome</h4>
-<pre>public&nbsp;void&nbsp;saveChromosome(java.io.File&nbsp;file,
-                           int&nbsp;chromosomeIndex)</pre>
-<div class="block">Saves a copy of the specified chromosome 
- into the given file.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the target file.</dd>
-<dd><code>chromosomeIndex</code> - the index of the chromosome to save.</dd>
-</dl>
-</li>
-</ul>
-<a name="isFinished--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>isFinished</h4>
-<pre>public&nbsp;boolean&nbsp;isFinished()</pre>
-<div class="block">Returns the experiment's status. When finished, the only
- way to continue is by calling <code>reset()</code>.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if the experiment is finished.</dd>
-</dl>
-</li>
-</ul>
-<a name="setConsole-jcgp.backend.resources.Console-">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>setConsole</h4>
-<pre>public&nbsp;void&nbsp;setConsole(<a href="../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a>&nbsp;console)</pre>
-<div class="block">Sets an extra console. The entire JCGP library prints
- messages to <code>System.console()</code> but also to an 
- additional console, if one is defined. This is used so 
- that messages are printed on a user interface as well, 
- or written directly to a file, for example.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>console</code> - the extra console to be used.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
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-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
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-<td class="colFirst"><code>java.lang.String</code></td>
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-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../jcgp/backend/function/Function.html#run-java.lang.Object...-">Function</a></code></span></div>
-<div class="block">Executes the function.</div>
-<dl>
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-<dd><code><a href="../../../jcgp/backend/function/Function.html#run-java.lang.Object...-">run</a></code>&nbsp;in class&nbsp;<code><a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a></code></dd>
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diff --git a/doc/jcgp/backend/function/DigitalCircuitFunctions.html b/doc/jcgp/backend/function/DigitalCircuitFunctions.html
deleted file mode 100644
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-<title>DigitalCircuitFunctions</title>
-<meta name="date" content="2014-05-22">
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-</ul>
-</div>
-<div class="subNav">
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.function</div>
-<h2 title="Class DigitalCircuitFunctions" class="title">Class DigitalCircuitFunctions</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">jcgp.backend.function.FunctionSet</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.function.DigitalCircuitFunctions</li>
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-<pre>public class <span class="typeNameLabel">DigitalCircuitFunctions</span>
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-<div class="block">This class contains all digital circuit functions
- (defined as unsigned integer functions in the classic
- CGP implementation) defined in static nested classes.
- <br>
- This is the function set used by <code>DigitalCircuitProblem</code>.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html" title="class in jcgp.backend.modules.problem"><code>DigitalCircuitProblem</code></a></dd>
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-<caption><span>Nested Classes</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
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-<div class="block">ANDs inputs together.</div>
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-<tr class="rowColor">
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-<div class="block">ANDs inputs together with one input inverted.</div>
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-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.AndNotB</a></span></code>
-<div class="block">ANDs inputs together with one input inverted.</div>
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-<div class="block">Outputs a constant 1, has no inputs.</div>
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-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<div class="block">Works as a multiplexer.</div>
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-<tr class="rowColor">
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux3.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux3</a></span></code>
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux4.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux4</a></span></code>
-<div class="block">Works as a multiplexer.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<div class="block">Inverts input, equivalent to inverter logic gate.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.NotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.NotB</a></span></code>
-<div class="block">Inverts input, equivalent to inverter logic gate.</div>
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-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Or.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Or</a></span></code>
-<div class="block">ORs inputs together.</div>
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-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.OrNotA</a></span></code>
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-<div class="block">Connects one node to another with no function.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.html#DigitalCircuitFunctions--">DigitalCircuitFunctions</a></span>()</code>
-<div class="block">Creates a new instance of <code>DigitalCircuitFunctions</code>.</div>
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-<code><a href="../../../jcgp/backend/function/FunctionSet.html#disableFunction-int-">disableFunction</a>, <a href="../../../jcgp/backend/function/FunctionSet.html#enableFunction-int-">enableFunction</a>, <a href="../../../jcgp/backend/function/FunctionSet.html#getAllowedFunction-int-">getAllowedFunction</a>, <a href="../../../jcgp/backend/function/FunctionSet.html#getAllowedFunctionCount--">getAllowedFunctionCount</a>, <a href="../../../jcgp/backend/function/FunctionSet.html#getFunction-int-">getFunction</a>, <a href="../../../jcgp/backend/function/FunctionSet.html#getMaxArity--">getMaxArity</a>, <a href="../../../jcgp/backend/function/FunctionSet.html#getTotalFunctionCount--">getTotalFunctionCount</a>, <a href="../../../jcgp/backend/function/FunctionSet.html#isEnabled-jcgp.backend.function.Function-">isEnabled</a></code></li>
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diff --git a/doc/jcgp/backend/function/Function.html b/doc/jcgp/backend/function/Function.html
deleted file mode 100644
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--- a/doc/jcgp/backend/function/Function.html
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-<div class="header">
-<div class="subTitle">jcgp.backend.function</div>
-<h2 title="Class Function" class="title">Class Function</h2>
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-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
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href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux2.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux2</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux3.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux3</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux4.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux4</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Nand.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Nand</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Nor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Nor</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.NotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.NotA</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.NotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.NotB</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Or.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Or</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.OrNotA</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.OrNotB</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.WireA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.WireA</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.WireB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.WireB</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Xnor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Xnor</a>, <a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Xor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Xor</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Absolute.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Absolute</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Addition.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Addition</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Cosine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Cosine</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.CosineAB.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.CosineAB</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Division.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Division</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Exponential.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Exponential</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicCosine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicCosine</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicSine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicSine</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicTangent.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicTangent</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Hypotenuse.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Hypotenuse</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.LogBaseTen.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.LogBaseTen</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Multiplication.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Multiplication</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.NaturalLog.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.NaturalLog</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Power.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Power</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Reciprocal.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Reciprocal</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Sine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Sine</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.SineAB.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.SineAB</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.SquareRoot.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.SquareRoot</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Subtraction.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Subtraction</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Tangent.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Tangent</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteCosineAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteCosineAB</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteSineAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteSineAB</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.BoundedDivision.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.BoundedDivision</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Cube.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Cube</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Multiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Multiplication</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledAddition.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledAddition</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledExponential.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledExponential</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledHypotenuse.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledHypotenuse</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Square.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Square</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquaredMultiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquaredMultiplication</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquareRoot.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquareRoot</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SymmetricSubtraction.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SymmetricSubtraction</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public abstract class <span class="typeNameLabel">Function</span>
-extends java.lang.Object</pre>
-<div class="block">Function is a callback wrapper. 
- <br><br>
- A concrete implementation of Function overrides <code>run()</code> to perform
- any arbitrary operation on the arguments specified. It must also override
- <code>getArity()</code> to return the function arity.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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-<td class="colFirst"><code>abstract int</code></td>
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-<td class="colFirst"><code>abstract java.lang.Object</code></td>
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-</ul>
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-<li><a href="#method.summary">Method</a></li>
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-<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
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diff --git a/doc/jcgp/backend/function/FunctionSet.html b/doc/jcgp/backend/function/FunctionSet.html
deleted file mode 100644
index 92ee84e..0000000
--- a/doc/jcgp/backend/function/FunctionSet.html
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-<title>FunctionSet</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../script.js"></script>
-</head>
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-<script type="text/javascript"><!--
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-</ul>
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-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.function</div>
-<h2 title="Class FunctionSet" class="title">Class FunctionSet</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
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-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.html" title="class in jcgp.backend.function">DigitalCircuitFunctions</a>, <a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions</a>, <a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions</a></dd>
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-<pre>public abstract class <span class="typeNameLabel">FunctionSet</span>
-extends java.lang.Object</pre>
-<div class="block">FunctionSet encapsulates a group of functions. This is done to
- simplify the implementation of problem types.
- <br><br>
- FunctionSet contains a variety of useful methods for acquiring general
- information, such as the maximum arity across all functions and the total
- number of functions.
- <br><br>
- In addition, FunctionSet offers the ability to enable and disable functions.
- Accessing the functions through <code>getAllowedFunction()</code> will return
- allowed functions only, providing an easy way to control which functions
- can be used in mutations.
- <br><br>
- An implementation of FunctionSet must simply use its constructor to set
- the name field and use <code>registerFunctions()</code> to add the required
- functions.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<div class="block">Returns a function from the complete collection,
- enabled or disabled alike.</div>
-</td>
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-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/FunctionSet.html#getMaxArity--">getMaxArity</a></span>()</code>
-<div class="block">Computes and returns the maximum arity out of
- all enabled functions.</div>
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/FunctionSet.html#getTotalFunctionCount--">getTotalFunctionCount</a></span>()</code>&nbsp;</td>
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/FunctionSet.html#isEnabled-jcgp.backend.function.Function-">isEnabled</a></span>(<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;function)</code>
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-<div class="block">Returns an allowed function. This throws an
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-<div class="block">Returns a function from the complete collection,
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- index is beyond the count of allowed functions.</div>
-<dl>
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-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the problem's current maximum arity.</dd>
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-<dl>
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-<dl>
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-<div class="block">Checks if a specified function is enabled. If the function
- does not belong in the FunctionSet, this returns false.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>function</code> - the function to check.</dd>
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-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
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diff --git a/doc/jcgp/backend/function/SymbolicRegressionFunctions.Absolute.html b/doc/jcgp/backend/function/SymbolicRegressionFunctions.Absolute.html
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-<div class="subTitle">jcgp.backend.function</div>
-<h2 title="Class SymbolicRegressionFunctions.Absolute" class="title">Class SymbolicRegressionFunctions.Absolute</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">jcgp.backend.function.Function</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.function.SymbolicRegressionFunctions.Absolute</li>
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-<pre>public static class <span class="typeNameLabel">SymbolicRegressionFunctions.Absolute</span>
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-<div class="block">Absolute returns the positive value of input 0.</div>
-<dl>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><code>Math</code></dd>
-</dl>
-</li>
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-<div class="header">
-<div class="subTitle">jcgp.backend.function</div>
-<h2 title="Class SymbolicRegressionFunctions" class="title">Class SymbolicRegressionFunctions</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">jcgp.backend.function.FunctionSet</a></li>
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-<li>jcgp.backend.function.SymbolicRegressionFunctions</li>
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-<pre>public class <span class="typeNameLabel">SymbolicRegressionFunctions</span>
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-<div class="block">This class contains all symbolic regression functions
- (defined as double functions in the classic CGP implementation)
- in static nested classes.
- <br>
- This is the function set used by SymbolicRegressionProblem.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem"><code>SymbolicRegressionProblem</code></a></dd>
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-<th class="colFirst" scope="col">Modifier and Type</th>
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-<div class="block">Cosine function, in radians.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Division.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Division</a></span></code>
-<div class="block">Protected division, returns the quotient of input 0 (the dividend) and input 1 (the divisor).</div>
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-<div class="block">Returns the hyperbolic cosine of input 0.</div>
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-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicSine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicSine</a></span></code>
-<div class="block">Returns the hyperbolic sine of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicTangent.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicTangent</a></span></code>
-<div class="block">Returns the hyperbolic tangent of input 0.</div>
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-<div class="block">Hypotenuse function.</div>
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-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.LogBaseTen.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.LogBaseTen</a></span></code>
-<div class="block">Protected log base 10 function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Multiplication.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Multiplication</a></span></code>
-<div class="block">Multiplication returns the product of inputs 0 and 1.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<div class="block">Protected natural log function.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Power.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Power</a></span></code>
-<div class="block">Power function.</div>
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-<div class="block">Protected reciprocal function, returns (1 / input 0).</div>
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-<div class="block">Sine function, in radians.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.SineAB.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.SineAB</a></span></code>
-<div class="block">Sine of sum.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<div class="block">Protected square root function, returns the square root of the absolute
- value of input 0.</div>
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-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<div class="block">Subtraction returns the difference between inputs 0 and 1.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<div class="block">Protected tangent function, in radians.</div>
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-<div class="block">Cosine of sum. Returns the absolute value of the cosine 
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-<div class="block">Hyperbolic tangent of sum. Returns the absolute value of the sine 
- of the sum of inputs 0 and 1, in radians.</div>
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diff --git a/doc/jcgp/backend/function/TravellingSalesmanFunctions.html b/doc/jcgp/backend/function/TravellingSalesmanFunctions.html
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-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.function</div>
-<h2 title="Class TravellingSalesmanFunctions" class="title">Class TravellingSalesmanFunctions</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">jcgp.backend.function.FunctionSet</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.function.TravellingSalesmanFunctions</li>
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-</li>
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-</ul>
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-<pre>public class <span class="typeNameLabel">TravellingSalesmanFunctions</span>
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-<div class="block">This class contains all travelling salesman functions in static nested classes.
- <br>
- This is the function set to be used by TravellingSalesmanProblem.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteCosineAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteCosineAB</a></span></code>
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-<div class="block">Sine of sum.</div>
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-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.BoundedDivision.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.BoundedDivision</a></span></code>
-<div class="block">Bounded division, returns the quotient of the two inputs where the larger
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-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
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-<div class="block">Cube function, returns the value of input 0 cubed.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Multiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Multiplication</a></span></code>
-<div class="block">Multiplication returns the product of inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledAddition.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledAddition</a></span></code>
-<div class="block">Scaled addition returns the sum of inputs 0 and 1 scaled
- to the range 0 &lt; x &gt; 1.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledExponential.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledExponential</a></span></code>
-<div class="block">Scaled exponential function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledHypotenuse.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledHypotenuse</a></span></code>
-<div class="block">Scaled hypotenuse function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Square.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Square</a></span></code>
-<div class="block">Square function, returns the square of the
- value of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquaredMultiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquaredMultiplication</a></span></code>
-<div class="block">Multiplication returns the product of inputs 0 and 1, squared.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquareRoot.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquareRoot</a></span></code>
-<div class="block">Protected square root function, returns the square root of the absolute
- value of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SymmetricSubtraction.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SymmetricSubtraction</a></span></code>
-<div class="block">Symmetric subtraction returns the absolute difference between inputs 0 and 1,
- scaled to the range 0 &lt;; x &gt; 1.</div>
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-<div class="subTitle">jcgp.backend.function</div>
-<h2 title="Class UnsignedInteger" class="title">Class UnsignedInteger</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
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-<pre>public class <span class="typeNameLabel">UnsignedInteger</span>
-extends java.lang.Object</pre>
-<div class="block">Integer wrapper type for unsigned integer values. 
- <br><br>
- Java offers no support for unsigned types save from 
- unsigned conversion methods. This class uses those methods
- to simulate the unsigned int data type, useful for circuit 
- truth table encodings.
- <br><br>
- When a string representation of an unsigned integer is parsed
- using Integer.parseUnsignedInt(), an Integer is created using
- all 32 bits for unsigned magnitude. The integer however is still
- signed and will behave as such for all arithmetic operations.
- Bitwise operations can still be performed as they work at the bit
- level, making this data type particularly suitable for circuit design. 
- <br><br>
- TODO in the unlikely event that unsigned integers are natively 
- implemented in Java, they should be used instead of this class.
- <br><br>
- Why are unsigned integers not supported?<br>
- http://stackoverflow.com/questions/430346/why-doesnt-java-support-unsigned-ints</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><code>Integer</code></dd>
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/function/UnsignedInteger.html#UnsignedInteger-java.lang.String-">UnsignedInteger</a></span>(java.lang.String&nbsp;i)</code>
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-<dd><code>toString</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.ConstantOne.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.ConstantOne.html
deleted file mode 100644
index e16fe98..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.ConstantOne.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.ConstantZero.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.ConstantZero.html
deleted file mode 100644
index 2159801..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.ConstantZero.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux1.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux1.html
deleted file mode 100644
index f0a7094..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux1.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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-<meta name="date" content="2014-05-22">
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-            parent.document.title="Uses of Class jcgp.backend.function.DigitalCircuitFunctions.Mux1";
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux2.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux2.html
deleted file mode 100644
index 246a2c6..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux2.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
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-<meta name="date" content="2014-05-22">
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux3.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux3.html
deleted file mode 100644
index e09f782..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux3.html
+++ /dev/null
@@ -1,124 +0,0 @@
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-<!-- NewPage -->
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux4.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux4.html
deleted file mode 100644
index 9b7ad3f..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Mux4.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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-<meta name="date" content="2014-05-22">
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-            parent.document.title="Uses of Class jcgp.backend.function.DigitalCircuitFunctions.Mux4";
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Nand.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Nand.html
deleted file mode 100644
index b0ca5b6..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Nand.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Nor.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Nor.html
deleted file mode 100644
index 6591c48..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Nor.html
+++ /dev/null
@@ -1,124 +0,0 @@
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.NotA.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.NotA.html
deleted file mode 100644
index b702a97..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.NotA.html
+++ /dev/null
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deleted file mode 100644
index cd0a4b4..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.NotB.html
+++ /dev/null
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Or.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Or.html
deleted file mode 100644
index 092269f..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Or.html
+++ /dev/null
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deleted file mode 100644
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--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.OrNotA.html
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.OrNotB.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.OrNotB.html
deleted file mode 100644
index 8331fcf..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.OrNotB.html
+++ /dev/null
@@ -1,124 +0,0 @@
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.WireA.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.WireA.html
deleted file mode 100644
index e7496da..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.WireA.html
+++ /dev/null
@@ -1,124 +0,0 @@
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.WireB.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.WireB.html
deleted file mode 100644
index 55046af..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.WireB.html
+++ /dev/null
@@ -1,124 +0,0 @@
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-<!-- NewPage -->
-<html lang="en">
-<head>
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-<meta name="date" content="2014-05-22">
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Xnor.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Xnor.html
deleted file mode 100644
index a7f202d..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Xnor.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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diff --git a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Xor.html b/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Xor.html
deleted file mode 100644
index c7290d1..0000000
--- a/doc/jcgp/backend/function/class-use/DigitalCircuitFunctions.Xor.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<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/function/Function.html" title="class in jcgp.backend.function">Function</a> in <a href="../../../../jcgp/backend/function/package-summary.html">jcgp.backend.function</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<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>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.And.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.And</a></span></code>
-<div class="block">ANDs inputs together.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.AndNotA</a></span></code>
-<div class="block">ANDs inputs together with one input inverted.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.AndNotB</a></span></code>
-<div class="block">ANDs inputs together with one input inverted.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantOne.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.ConstantOne</a></span></code>
-<div class="block">Outputs a constant 1, has no inputs.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantZero.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.ConstantZero</a></span></code>
-<div class="block">Outputs a constant 0, has no inputs.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux1.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux1</a></span></code>
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux2.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux2</a></span></code>
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux3.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux3</a></span></code>
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux4.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux4</a></span></code>
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Nand.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Nand</a></span></code>
-<div class="block">NANDs inputs together.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Nor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Nor</a></span></code>
-<div class="block">NORs inputs together.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.NotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.NotA</a></span></code>
-<div class="block">Inverts input, equivalent to inverter logic gate.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.NotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.NotB</a></span></code>
-<div class="block">Inverts input, equivalent to inverter logic gate.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Or.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Or</a></span></code>
-<div class="block">ORs inputs together.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.OrNotA</a></span></code>
-<div class="block">ORs inputs together with one inverted input.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.OrNotB</a></span></code>
-<div class="block">ORs inputs together with one inverted input.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.WireA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.WireA</a></span></code>
-<div class="block">Connects one node to another with no function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.WireB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.WireB</a></span></code>
-<div class="block">Connects one node to another with no function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Xnor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Xnor</a></span></code>
-<div class="block">XNORs inputs together.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Xor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Xor</a></span></code>
-<div class="block">XORs inputs together.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Absolute.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Absolute</a></span></code>
-<div class="block">Absolute returns the positive value of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Addition.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Addition</a></span></code>
-<div class="block">Addition returns the sum of inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Cosine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Cosine</a></span></code>
-<div class="block">Cosine function, in radians.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.CosineAB.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.CosineAB</a></span></code>
-<div class="block">Cosine of sum.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Division.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Division</a></span></code>
-<div class="block">Protected division, returns the quotient of input 0 (the dividend) and input 1 (the divisor).</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Exponential.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Exponential</a></span></code>
-<div class="block">Exponential function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicCosine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicCosine</a></span></code>
-<div class="block">Returns the hyperbolic cosine of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicSine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicSine</a></span></code>
-<div class="block">Returns the hyperbolic sine of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicTangent.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicTangent</a></span></code>
-<div class="block">Returns the hyperbolic tangent of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Hypotenuse.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Hypotenuse</a></span></code>
-<div class="block">Hypotenuse function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.LogBaseTen.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.LogBaseTen</a></span></code>
-<div class="block">Protected log base 10 function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Multiplication.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Multiplication</a></span></code>
-<div class="block">Multiplication returns the product of inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.NaturalLog.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.NaturalLog</a></span></code>
-<div class="block">Protected natural log function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Power.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Power</a></span></code>
-<div class="block">Power function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Reciprocal.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Reciprocal</a></span></code>
-<div class="block">Protected reciprocal function, returns (1 / input 0).</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Sine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Sine</a></span></code>
-<div class="block">Sine function, in radians.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.SineAB.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.SineAB</a></span></code>
-<div class="block">Sine of sum.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.SquareRoot.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.SquareRoot</a></span></code>
-<div class="block">Protected square root function, returns the square root of the absolute
- value of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Subtraction.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Subtraction</a></span></code>
-<div class="block">Subtraction returns the difference between inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.Tangent.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Tangent</a></span></code>
-<div class="block">Protected tangent function, in radians.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteCosineAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteCosineAB</a></span></code>
-<div class="block">Cosine of sum.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB</a></span></code>
-<div class="block">Hyperbolic tangent of sum.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteSineAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteSineAB</a></span></code>
-<div class="block">Sine of sum.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.BoundedDivision.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.BoundedDivision</a></span></code>
-<div class="block">Bounded division, returns the quotient of the two inputs where the larger
- is the denominator.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.Cube.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Cube</a></span></code>
-<div class="block">Cube function, returns the value of input 0 cubed.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.Multiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Multiplication</a></span></code>
-<div class="block">Multiplication returns the product of inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledAddition.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledAddition</a></span></code>
-<div class="block">Scaled addition returns the sum of inputs 0 and 1 scaled
- to the range 0 &lt; x &gt; 1.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledExponential.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledExponential</a></span></code>
-<div class="block">Scaled exponential function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledHypotenuse.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledHypotenuse</a></span></code>
-<div class="block">Scaled hypotenuse function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.Square.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Square</a></span></code>
-<div class="block">Square function, returns the square of the
- value of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.SquaredMultiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquaredMultiplication</a></span></code>
-<div class="block">Multiplication returns the product of inputs 0 and 1, squared.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.SquareRoot.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquareRoot</a></span></code>
-<div class="block">Protected square root function, returns the square root of the absolute
- value of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.SymmetricSubtraction.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SymmetricSubtraction</a></span></code>
-<div class="block">Symmetric subtraction returns the absolute difference between inputs 0 and 1,
- scaled to the range 0 &lt;; x &gt; 1.</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/function/package-summary.html">jcgp.backend.function</a> that return <a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</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/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><span class="typeNameLabel">FunctionSet.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/FunctionSet.html#getAllowedFunction-int-">getAllowedFunction</a></span>(int&nbsp;index)</code>
-<div class="block">Returns an allowed function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><span class="typeNameLabel">FunctionSet.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/FunctionSet.html#getFunction-int-">getFunction</a></span>(int&nbsp;index)</code>
-<div class="block">Returns a function from the complete collection,
- enabled or disabled alike.</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/function/package-summary.html">jcgp.backend.function</a> with parameters of type <a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</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">FunctionSet.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/FunctionSet.html#isEnabled-jcgp.backend.function.Function-">isEnabled</a></span>(<a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;function)</code>
-<div class="block">Checks if a specified function is enabled.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.population">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</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/function/Function.html" title="class in jcgp.backend.function">Function</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/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Node.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Node.html#getFunction--">getFunction</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/function/Function.html" title="class in jcgp.backend.function">Function</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#setFunction-jcgp.backend.function.Function-">setFunction</a></span>(<a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;newFunction)</code>
-<div class="block">Sets the node function.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.resources">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a> in <a href="../../../../jcgp/backend/resources/package-summary.html">jcgp.backend.resources</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/resources/package-summary.html">jcgp.backend.resources</a> that return <a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</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/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Resources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/Resources.html#getFunction-int-">getFunction</a></span>(int&nbsp;index)</code>
-<div class="block">Gets the indexed function out of the
- complete set of functions.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Resources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/Resources.html#getRandomFunction--">getRandomFunction</a></span>()</code>
-<div class="block">Gets a random allowed function from the problem function set.</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/resources/package-summary.html">jcgp.backend.resources</a> with parameters of type <a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</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>int</code></td>
-<td class="colLast"><span class="typeNameLabel">Resources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/Resources.html#getFunctionIndex-jcgp.backend.function.Function-">getFunctionIndex</a></span>(<a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;function)</code>
-<div class="block">Returns the index of a specified function.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.gui.population">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</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/function/Function.html" title="class in jcgp.backend.function">Function</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#setFunction-jcgp.backend.function.Function-">setFunction</a></span>(<a href="../../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;function)</code>&nbsp;</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
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-<li class="navBarCell1Rev">Use</li>
-<li><a href="../package-tree.html">Tree</a></li>
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diff --git a/doc/jcgp/backend/function/class-use/FunctionSet.html b/doc/jcgp/backend/function/class-use/FunctionSet.html
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index e34d80d..0000000
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-<caption><span>Packages that use <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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.function">jcgp.backend.function</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.backend.modules.problem">jcgp.backend.modules.problem</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.backend.parsers">jcgp.backend.parsers</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.backend.resources">jcgp.backend.resources</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="altColor">
-<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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-<h3>Uses of <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a> in <a href="../../../../jcgp/backend/function/package-summary.html">jcgp.backend.function</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/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a> in <a href="../../../../jcgp/backend/function/package-summary.html">jcgp.backend.function</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/function/DigitalCircuitFunctions.html" title="class in jcgp.backend.function">DigitalCircuitFunctions</a></span></code>
-<div class="block">This class contains all digital circuit functions
- (defined as unsigned integer functions in the classic
- CGP implementation) defined in static nested classes.</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/function/SymbolicRegressionFunctions.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions</a></span></code>
-<div class="block">This class contains all symbolic regression functions
- (defined as double functions in the classic CGP implementation)
- in static nested classes.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions</a></span></code>
-<div class="block">This class contains all travelling salesman functions in static nested classes.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.modules.problem">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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> that return <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Problem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#getFunctionSet--">getFunctionSet</a></span>()</code>&nbsp;</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.parsers">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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">FunctionParser.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parsers/FunctionParser.html#parse-java.io.File-jcgp.backend.function.FunctionSet-jcgp.backend.resources.Resources-">parse</a></span>(java.io.File&nbsp;file,
-     <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a>&nbsp;functionSet,
-     <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Reads the specified file and attempts to enable 
- and disable the functions in the FunctionSet 
- accordingly.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.resources">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a> in <a href="../../../../jcgp/backend/resources/package-summary.html">jcgp.backend.resources</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/resources/package-summary.html">jcgp.backend.resources</a> that return <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Resources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/Resources.html#getFunctionSet--">getFunctionSet</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/resources/package-summary.html">jcgp.backend.resources</a> with parameters of type <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#setFunctionSet-jcgp.backend.function.FunctionSet-">setFunctionSet</a></span>(<a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a>&nbsp;functionSet)</code>
-<div class="block">Update the current function set.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.gui.population">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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">FunctionSelector.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/FunctionSelector.html#remakeFunctions-jcgp.backend.function.FunctionSet-">remakeFunctions</a></span>(<a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a>&nbsp;fs)</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/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</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/FunctionSelector.html#FunctionSelector-jcgp.backend.function.FunctionSet-">FunctionSelector</a></span>(<a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a>&nbsp;functionSet)</code>&nbsp;</td>
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diff --git a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Absolute.html b/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Absolute.html
deleted file mode 100644
index 72126c1..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Absolute.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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diff --git a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Addition.html b/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Addition.html
deleted file mode 100644
index ed8f30d..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Addition.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
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-<meta name="date" content="2014-05-22">
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
index 0aa8ebb..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.HyperbolicSine.html
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deleted file mode 100644
index 1e98999..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.HyperbolicTangent.html
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@@ -1,124 +0,0 @@
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deleted file mode 100644
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--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.NaturalLog.html
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@@ -1,124 +0,0 @@
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deleted file mode 100644
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+++ /dev/null
@@ -1,124 +0,0 @@
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diff --git a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Sine.html b/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Sine.html
deleted file mode 100644
index 23e66c6..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Sine.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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diff --git a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.SineAB.html b/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.SineAB.html
deleted file mode 100644
index b57ee8c..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.SineAB.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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diff --git a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.SquareRoot.html b/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.SquareRoot.html
deleted file mode 100644
index 3a5fb36..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.SquareRoot.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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diff --git a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Subtraction.html b/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Subtraction.html
deleted file mode 100644
index e7aa673..0000000
--- a/doc/jcgp/backend/function/class-use/SymbolicRegressionFunctions.Subtraction.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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deleted file mode 100644
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--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.AbsoluteCosineAB.html
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deleted file mode 100644
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deleted file mode 100644
index d3b01cc..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.AbsoluteSineAB.html
+++ /dev/null
@@ -1,124 +0,0 @@
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.BoundedDivision.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.BoundedDivision.html
deleted file mode 100644
index 8a56857..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.BoundedDivision.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.Cube.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.Cube.html
deleted file mode 100644
index 7474f4f..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.Cube.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.Multiplication.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.Multiplication.html
deleted file mode 100644
index 6c98a61..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.Multiplication.html
+++ /dev/null
@@ -1,124 +0,0 @@
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deleted file mode 100644
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deleted file mode 100644
index 210751c..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.ScaledExponential.html
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.ScaledHypotenuse.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.ScaledHypotenuse.html
deleted file mode 100644
index 36053b2..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.ScaledHypotenuse.html
+++ /dev/null
@@ -1,124 +0,0 @@
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--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.Square.html
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SquareRoot.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SquareRoot.html
deleted file mode 100644
index 5b17018..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SquareRoot.html
+++ /dev/null
@@ -1,124 +0,0 @@
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SquaredMultiplication.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SquaredMultiplication.html
deleted file mode 100644
index a0d4e22..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SquaredMultiplication.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SymmetricSubtraction.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SymmetricSubtraction.html
deleted file mode 100644
index 22d3ee5..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.SymmetricSubtraction.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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diff --git a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.html b/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.html
deleted file mode 100644
index 66768f4..0000000
--- a/doc/jcgp/backend/function/class-use/TravellingSalesmanFunctions.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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diff --git a/doc/jcgp/backend/function/class-use/UnsignedInteger.html b/doc/jcgp/backend/function/class-use/UnsignedInteger.html
deleted file mode 100644
index 28a317a..0000000
--- a/doc/jcgp/backend/function/class-use/UnsignedInteger.html
+++ /dev/null
@@ -1,263 +0,0 @@
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-<caption><span>Packages that use <a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
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-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.backend.function">jcgp.backend.function</a></td>
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-<td class="colFirst"><a href="#jcgp.backend.modules.problem">jcgp.backend.modules.problem</a></td>
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-<h3>Uses of <a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a> in <a href="../../../../jcgp/backend/function/package-summary.html">jcgp.backend.function</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/function/package-summary.html">jcgp.backend.function</a> that return <a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</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/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.ConstantZero.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantZero.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.ConstantOne.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantOne.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.WireA.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.WireA.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.WireB.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.WireB.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.NotA.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.NotA.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.NotB.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.NotB.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.And.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.And.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.AndNotA.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotA.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.AndNotB.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotB.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Nor.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Nor.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Xor.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Xor.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Xnor.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Xnor.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Or.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Or.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.OrNotA.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotA.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.OrNotB.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotB.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Nand.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Nand.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Mux1.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux1.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Mux2.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux2.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Mux3.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux3.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitFunctions.Mux4.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.Mux4.html#run-java.lang.Object...-">run</a></span>(java.lang.Object...&nbsp;args)</code>&nbsp;</td>
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-</li>
-<li class="blockList"><a name="jcgp.backend.modules.problem">
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-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</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> that return types with arguments of type <a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</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/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;<a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a>&gt;</code></td>
-<td class="colLast"><span class="typeNameLabel">DigitalCircuitProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html#parseTestCase-java.lang.String:A-java.lang.String:A-">parseTestCase</a></span>(java.lang.String[]&nbsp;inputs,
-             java.lang.String[]&nbsp;outputs)</code>&nbsp;</td>
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diff --git a/doc/jcgp/backend/function/package-frame.html b/doc/jcgp/backend/function/package-frame.html
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-<li><a href="DigitalCircuitFunctions.AndNotA.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.AndNotA</a></li>
-<li><a href="DigitalCircuitFunctions.AndNotB.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.AndNotB</a></li>
-<li><a href="DigitalCircuitFunctions.ConstantOne.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.ConstantOne</a></li>
-<li><a href="DigitalCircuitFunctions.ConstantZero.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.ConstantZero</a></li>
-<li><a href="DigitalCircuitFunctions.Mux1.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.Mux1</a></li>
-<li><a href="DigitalCircuitFunctions.Mux2.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.Mux2</a></li>
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-<li><a href="DigitalCircuitFunctions.Mux4.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.Mux4</a></li>
-<li><a href="DigitalCircuitFunctions.Nand.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.Nand</a></li>
-<li><a href="DigitalCircuitFunctions.Nor.html" title="class in jcgp.backend.function" target="classFrame">DigitalCircuitFunctions.Nor</a></li>
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-<li><a href="SymbolicRegressionFunctions.Cosine.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.Cosine</a></li>
-<li><a href="SymbolicRegressionFunctions.CosineAB.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.CosineAB</a></li>
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-<li><a href="SymbolicRegressionFunctions.Multiplication.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.Multiplication</a></li>
-<li><a href="SymbolicRegressionFunctions.NaturalLog.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.NaturalLog</a></li>
-<li><a href="SymbolicRegressionFunctions.Power.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.Power</a></li>
-<li><a href="SymbolicRegressionFunctions.Reciprocal.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.Reciprocal</a></li>
-<li><a href="SymbolicRegressionFunctions.Sine.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.Sine</a></li>
-<li><a href="SymbolicRegressionFunctions.SineAB.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.SineAB</a></li>
-<li><a href="SymbolicRegressionFunctions.SquareRoot.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.SquareRoot</a></li>
-<li><a href="SymbolicRegressionFunctions.Subtraction.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.Subtraction</a></li>
-<li><a href="SymbolicRegressionFunctions.Tangent.html" title="class in jcgp.backend.function" target="classFrame">SymbolicRegressionFunctions.Tangent</a></li>
-<li><a href="TravellingSalesmanFunctions.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions</a></li>
-<li><a href="TravellingSalesmanFunctions.AbsoluteCosineAB.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.AbsoluteCosineAB</a></li>
-<li><a href="TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB</a></li>
-<li><a href="TravellingSalesmanFunctions.AbsoluteSineAB.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.AbsoluteSineAB</a></li>
-<li><a href="TravellingSalesmanFunctions.BoundedDivision.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.BoundedDivision</a></li>
-<li><a href="TravellingSalesmanFunctions.Cube.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.Cube</a></li>
-<li><a href="TravellingSalesmanFunctions.Multiplication.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.Multiplication</a></li>
-<li><a href="TravellingSalesmanFunctions.ScaledAddition.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.ScaledAddition</a></li>
-<li><a href="TravellingSalesmanFunctions.ScaledExponential.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.ScaledExponential</a></li>
-<li><a href="TravellingSalesmanFunctions.ScaledHypotenuse.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.ScaledHypotenuse</a></li>
-<li><a href="TravellingSalesmanFunctions.Square.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.Square</a></li>
-<li><a href="TravellingSalesmanFunctions.SquaredMultiplication.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.SquaredMultiplication</a></li>
-<li><a href="TravellingSalesmanFunctions.SquareRoot.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.SquareRoot</a></li>
-<li><a href="TravellingSalesmanFunctions.SymmetricSubtraction.html" title="class in jcgp.backend.function" target="classFrame">TravellingSalesmanFunctions.SymmetricSubtraction</a></li>
-<li><a href="UnsignedInteger.html" title="class in jcgp.backend.function" target="classFrame">UnsignedInteger</a></li>
-</ul>
-</div>
-</body>
-</html>
diff --git a/doc/jcgp/backend/function/package-summary.html b/doc/jcgp/backend/function/package-summary.html
deleted file mode 100644
index f66491e..0000000
--- a/doc/jcgp/backend/function/package-summary.html
+++ /dev/null
@@ -1,502 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
-<head>
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-<title>jcgp.backend.function</title>
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-            parent.document.title="jcgp.backend.function";
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-<ul class="navList" title="Navigation">
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-<li class="navBarCell1Rev">Package</li>
-<li>Class</li>
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-<li><a href="../../../jcgp/package-summary.html">Prev&nbsp;Package</a></li>
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-<div class="header">
-<h1 title="Package" class="title">Package&nbsp;jcgp.backend.function</h1>
-</div>
-<div class="contentContainer">
-<ul class="blockList">
-<li class="blockList">
-<table class="typeSummary" border="0" cellpadding="3" cellspacing="0" summary="Class Summary table, listing classes, and an explanation">
-<caption><span>Class Summary</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Class</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.html" title="class in jcgp.backend.function">DigitalCircuitFunctions</a></td>
-<td class="colLast">
-<div class="block">This class contains all digital circuit functions
- (defined as unsigned integer functions in the classic
- CGP implementation) defined in static nested classes.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.And.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.And</a></td>
-<td class="colLast">
-<div class="block">ANDs inputs together.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.AndNotA</a></td>
-<td class="colLast">
-<div class="block">ANDs inputs together with one input inverted.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.AndNotB</a></td>
-<td class="colLast">
-<div class="block">ANDs inputs together with one input inverted.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantOne.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.ConstantOne</a></td>
-<td class="colLast">
-<div class="block">Outputs a constant 1, has no inputs.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantZero.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.ConstantZero</a></td>
-<td class="colLast">
-<div class="block">Outputs a constant 0, has no inputs.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux1.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux1</a></td>
-<td class="colLast">
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux2.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux2</a></td>
-<td class="colLast">
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux3.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux3</a></td>
-<td class="colLast">
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux4.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Mux4</a></td>
-<td class="colLast">
-<div class="block">Works as a multiplexer.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Nand.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Nand</a></td>
-<td class="colLast">
-<div class="block">NANDs inputs together.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Nor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Nor</a></td>
-<td class="colLast">
-<div class="block">NORs inputs together.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.NotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.NotA</a></td>
-<td class="colLast">
-<div class="block">Inverts input, equivalent to inverter logic gate.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.NotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.NotB</a></td>
-<td class="colLast">
-<div class="block">Inverts input, equivalent to inverter logic gate.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Or.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Or</a></td>
-<td class="colLast">
-<div class="block">ORs inputs together.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.OrNotA</a></td>
-<td class="colLast">
-<div class="block">ORs inputs together with one inverted input.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.OrNotB</a></td>
-<td class="colLast">
-<div class="block">ORs inputs together with one inverted input.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.WireA.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.WireA</a></td>
-<td class="colLast">
-<div class="block">Connects one node to another with no function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.WireB.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.WireB</a></td>
-<td class="colLast">
-<div class="block">Connects one node to another with no function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Xnor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Xnor</a></td>
-<td class="colLast">
-<div class="block">XNORs inputs together.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Xor.html" title="class in jcgp.backend.function">DigitalCircuitFunctions.Xor</a></td>
-<td class="colLast">
-<div class="block">XORs inputs together.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a></td>
-<td class="colLast">
-<div class="block">Function is a callback wrapper.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a></td>
-<td class="colLast">
-<div class="block">FunctionSet encapsulates a group of functions.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions</a></td>
-<td class="colLast">
-<div class="block">This class contains all symbolic regression functions
- (defined as double functions in the classic CGP implementation)
- in static nested classes.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Absolute.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Absolute</a></td>
-<td class="colLast">
-<div class="block">Absolute returns the positive value of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Addition.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Addition</a></td>
-<td class="colLast">
-<div class="block">Addition returns the sum of inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Cosine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Cosine</a></td>
-<td class="colLast">
-<div class="block">Cosine function, in radians.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.CosineAB.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.CosineAB</a></td>
-<td class="colLast">
-<div class="block">Cosine of sum.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Division.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Division</a></td>
-<td class="colLast">
-<div class="block">Protected division, returns the quotient of input 0 (the dividend) and input 1 (the divisor).</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Exponential.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Exponential</a></td>
-<td class="colLast">
-<div class="block">Exponential function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicCosine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicCosine</a></td>
-<td class="colLast">
-<div class="block">Returns the hyperbolic cosine of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicSine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicSine</a></td>
-<td class="colLast">
-<div class="block">Returns the hyperbolic sine of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicTangent.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.HyperbolicTangent</a></td>
-<td class="colLast">
-<div class="block">Returns the hyperbolic tangent of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Hypotenuse.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Hypotenuse</a></td>
-<td class="colLast">
-<div class="block">Hypotenuse function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.LogBaseTen.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.LogBaseTen</a></td>
-<td class="colLast">
-<div class="block">Protected log base 10 function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Multiplication.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Multiplication</a></td>
-<td class="colLast">
-<div class="block">Multiplication returns the product of inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.NaturalLog.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.NaturalLog</a></td>
-<td class="colLast">
-<div class="block">Protected natural log function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Power.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Power</a></td>
-<td class="colLast">
-<div class="block">Power function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Reciprocal.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Reciprocal</a></td>
-<td class="colLast">
-<div class="block">Protected reciprocal function, returns (1 / input 0).</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Sine.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Sine</a></td>
-<td class="colLast">
-<div class="block">Sine function, in radians.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.SineAB.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.SineAB</a></td>
-<td class="colLast">
-<div class="block">Sine of sum.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.SquareRoot.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.SquareRoot</a></td>
-<td class="colLast">
-<div class="block">Protected square root function, returns the square root of the absolute
- value of input 0.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Subtraction.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Subtraction</a></td>
-<td class="colLast">
-<div class="block">Subtraction returns the difference between inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Tangent.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Tangent</a></td>
-<td class="colLast">
-<div class="block">Protected tangent function, in radians.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions</a></td>
-<td class="colLast">
-<div class="block">This class contains all travelling salesman functions in static nested classes.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteCosineAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteCosineAB</a></td>
-<td class="colLast">
-<div class="block">Cosine of sum.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB</a></td>
-<td class="colLast">
-<div class="block">Hyperbolic tangent of sum.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteSineAB.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.AbsoluteSineAB</a></td>
-<td class="colLast">
-<div class="block">Sine of sum.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.BoundedDivision.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.BoundedDivision</a></td>
-<td class="colLast">
-<div class="block">Bounded division, returns the quotient of the two inputs where the larger
- is the denominator.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Cube.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Cube</a></td>
-<td class="colLast">
-<div class="block">Cube function, returns the value of input 0 cubed.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Multiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Multiplication</a></td>
-<td class="colLast">
-<div class="block">Multiplication returns the product of inputs 0 and 1.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledAddition.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledAddition</a></td>
-<td class="colLast">
-<div class="block">Scaled addition returns the sum of inputs 0 and 1 scaled
- to the range 0 &lt; x &gt; 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledExponential.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledExponential</a></td>
-<td class="colLast">
-<div class="block">Scaled exponential function.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledHypotenuse.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.ScaledHypotenuse</a></td>
-<td class="colLast">
-<div class="block">Scaled hypotenuse function.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Square.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.Square</a></td>
-<td class="colLast">
-<div class="block">Square function, returns the square of the
- value of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquaredMultiplication.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquaredMultiplication</a></td>
-<td class="colLast">
-<div class="block">Multiplication returns the product of inputs 0 and 1, squared.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquareRoot.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SquareRoot</a></td>
-<td class="colLast">
-<div class="block">Protected square root function, returns the square root of the absolute
- value of input 0.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SymmetricSubtraction.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.SymmetricSubtraction</a></td>
-<td class="colLast">
-<div class="block">Symmetric subtraction returns the absolute difference between inputs 0 and 1,
- scaled to the range 0 &lt;; x &gt; 1.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></td>
-<td class="colLast">
-<div class="block">Integer wrapper type for unsigned integer values.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
-</a>
-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
-<a name="navbar.bottom.firstrow">
-<!--   -->
-</a>
-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li class="navBarCell1Rev">Package</li>
-<li>Class</li>
-<li><a href="package-use.html">Use</a></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>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/package-summary.html">Prev&nbsp;Package</a></li>
-<li><a href="../../../jcgp/backend/modules/package-summary.html">Next&nbsp;Package</a></li>
-</ul>
-<ul class="navList">
-<li><a href="../../../index.html?jcgp/backend/function/package-summary.html" target="_top">Frames</a></li>
-<li><a href="package-summary.html" target="_top">No&nbsp;Frames</a></li>
-</ul>
-<ul class="navList" id="allclasses_navbar_bottom">
-<li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
-</ul>
-<div>
-<script type="text/javascript"><!--
-  allClassesLink = document.getElementById("allclasses_navbar_bottom");
-  if(window==top) {
-    allClassesLink.style.display = "block";
-  }
-  else {
-    allClassesLink.style.display = "none";
-  }
-  //-->
-</script>
-</div>
-<a name="skip.navbar.bottom">
-<!--   -->
-</a></div>
-<!-- ======== END OF BOTTOM NAVBAR ======= -->
-</body>
-</html>
diff --git a/doc/jcgp/backend/function/package-tree.html b/doc/jcgp/backend/function/package-tree.html
deleted file mode 100644
index 97c625d..0000000
--- a/doc/jcgp/backend/function/package-tree.html
+++ /dev/null
@@ -1,201 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>jcgp.backend.function Class Hierarchy</title>
-<meta name="date" content="2014-05-22">
-<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="jcgp.backend.function Class Hierarchy";
-        }
-    }
-    catch(err) {
-    }
-//-->
-</script>
-<noscript>
-<div>JavaScript is disabled on your browser.</div>
-</noscript>
-<!-- ========= START OF TOP NAVBAR ======= -->
-<div class="topNav"><a name="navbar.top">
-<!--   -->
-</a>
-<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
-<a name="navbar.top.firstrow">
-<!--   -->
-</a>
-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li><a href="package-summary.html">Package</a></li>
-<li>Class</li>
-<li>Use</li>
-<li class="navBarCell1Rev">Tree</li>
-<li><a href="../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/package-tree.html">Prev</a></li>
-<li><a href="../../../jcgp/backend/modules/package-tree.html">Next</a></li>
-</ul>
-<ul class="navList">
-<li><a href="../../../index.html?jcgp/backend/function/package-tree.html" target="_top">Frames</a></li>
-<li><a href="package-tree.html" target="_top">No&nbsp;Frames</a></li>
-</ul>
-<ul class="navList" id="allclasses_navbar_top">
-<li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
-</ul>
-<div>
-<script type="text/javascript"><!--
-  allClassesLink = document.getElementById("allclasses_navbar_top");
-  if(window==top) {
-    allClassesLink.style.display = "block";
-  }
-  else {
-    allClassesLink.style.display = "none";
-  }
-  //-->
-</script>
-</div>
-<a name="skip.navbar.top">
-<!--   -->
-</a></div>
-<!-- ========= END OF TOP NAVBAR ========= -->
-<div class="header">
-<h1 class="title">Hierarchy For Package jcgp.backend.function</h1>
-<span class="packageHierarchyLabel">Package Hierarchies:</span>
-<ul class="horizontal">
-<li><a href="../../../overview-tree.html">All Packages</a></li>
-</ul>
-</div>
-<div class="contentContainer">
-<h2 title="Class Hierarchy">Class Hierarchy</h2>
-<ul>
-<li type="circle">java.lang.Object
-<ul>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function"><span class="typeNameLink">Function</span></a>
-<ul>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.And.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.And</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotA.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.AndNotA</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.AndNotB.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.AndNotB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantOne.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.ConstantOne</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.ConstantZero.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.ConstantZero</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux1.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Mux1</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux2.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Mux2</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux3.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Mux3</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Mux4.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Mux4</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Nand.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Nand</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Nor.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Nor</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.NotA.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.NotA</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.NotB.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.NotB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Or.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Or</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotA.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.OrNotA</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.OrNotB.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.OrNotB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.WireA.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.WireA</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.WireB.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.WireB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Xnor.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Xnor</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.Xor.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions.Xor</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Absolute.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Absolute</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Addition.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Addition</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Cosine.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Cosine</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.CosineAB.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.CosineAB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Division.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Division</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Exponential.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Exponential</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicCosine.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.HyperbolicCosine</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicSine.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.HyperbolicSine</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.HyperbolicTangent.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.HyperbolicTangent</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Hypotenuse.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Hypotenuse</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.LogBaseTen.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.LogBaseTen</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Multiplication.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Multiplication</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.NaturalLog.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.NaturalLog</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Power.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Power</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Reciprocal.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Reciprocal</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Sine.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Sine</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.SineAB.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.SineAB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.SquareRoot.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.SquareRoot</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Subtraction.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Subtraction</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.Tangent.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions.Tangent</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteCosineAB.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.AbsoluteCosineAB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.AbsoluteHyperbolicTangentAB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.AbsoluteSineAB.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.AbsoluteSineAB</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.BoundedDivision.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.BoundedDivision</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Cube.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.Cube</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Multiplication.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.Multiplication</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledAddition.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.ScaledAddition</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledExponential.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.ScaledExponential</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.ScaledHypotenuse.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.ScaledHypotenuse</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.Square.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.Square</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquaredMultiplication.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.SquaredMultiplication</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SquareRoot.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.SquareRoot</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.SymmetricSubtraction.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions.SymmetricSubtraction</span></a></li>
-</ul>
-</li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function"><span class="typeNameLink">FunctionSet</span></a>
-<ul>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/DigitalCircuitFunctions.html" title="class in jcgp.backend.function"><span class="typeNameLink">DigitalCircuitFunctions</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/SymbolicRegressionFunctions.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions</span></a></li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/TravellingSalesmanFunctions.html" title="class in jcgp.backend.function"><span class="typeNameLink">TravellingSalesmanFunctions</span></a></li>
-</ul>
-</li>
-<li type="circle">jcgp.backend.function.<a href="../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function"><span class="typeNameLink">UnsignedInteger</span></a></li>
-</ul>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
-</a>
-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
-<a name="navbar.bottom.firstrow">
-<!--   -->
-</a>
-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li><a href="package-summary.html">Package</a></li>
-<li>Class</li>
-<li>Use</li>
-<li class="navBarCell1Rev">Tree</li>
-<li><a href="../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/package-tree.html">Prev</a></li>
-<li><a href="../../../jcgp/backend/modules/package-tree.html">Next</a></li>
-</ul>
-<ul class="navList">
-<li><a href="../../../index.html?jcgp/backend/function/package-tree.html" target="_top">Frames</a></li>
-<li><a href="package-tree.html" target="_top">No&nbsp;Frames</a></li>
-</ul>
-<ul class="navList" id="allclasses_navbar_bottom">
-<li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
-</ul>
-<div>
-<script type="text/javascript"><!--
-  allClassesLink = document.getElementById("allclasses_navbar_bottom");
-  if(window==top) {
-    allClassesLink.style.display = "block";
-  }
-  else {
-    allClassesLink.style.display = "none";
-  }
-  //-->
-</script>
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-<a name="skip.navbar.bottom">
-<!--   -->
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-</html>
diff --git a/doc/jcgp/backend/function/package-use.html b/doc/jcgp/backend/function/package-use.html
deleted file mode 100644
index c5fb03c..0000000
--- a/doc/jcgp/backend/function/package-use.html
+++ /dev/null
@@ -1,289 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Package jcgp.backend.function</title>
-<meta name="date" content="2014-05-22">
-<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 Package jcgp.backend.function";
-        }
-    }
-    catch(err) {
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-<tr>
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-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/function/class-use/Function.html#jcgp.backend.function">Function</a>
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-<td class="colOne"><a href="../../../jcgp/backend/function/class-use/FunctionSet.html#jcgp.backend.function">FunctionSet</a>
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-<td class="colOne"><a href="../../../jcgp/backend/function/class-use/UnsignedInteger.html#jcgp.backend.function">UnsignedInteger</a>
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diff --git a/doc/jcgp/backend/modules/Module.html b/doc/jcgp/backend/modules/Module.html
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-<h2 title="Class Module" class="title">Class Module</h2>
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diff --git a/doc/jcgp/backend/modules/class-use/Module.html b/doc/jcgp/backend/modules/class-use/Module.html
deleted file mode 100644
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-<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.es">jcgp.backend.modules.es</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.backend.modules.mutator">jcgp.backend.modules.mutator</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>
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-<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/modules/Module.html" title="class in jcgp.backend.modules">Module</a> in <a href="../../../../jcgp/backend/modules/es/package-summary.html">jcgp.backend.modules.es</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/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></span></code>
-<div class="block">This class specifies the characteristics of an evolutionary strategy.</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/modules/es/MuPlusLambda.html" title="class in jcgp.backend.modules.es">MuPlusLambda</a></span></code>
-<div class="block">(μ + λ)-ES
- <br><br>
- This strategy selects the μ fittest chromosomes from the population.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/es/TournamentSelection.html" title="class in jcgp.backend.modules.es">TournamentSelection</a></span></code>
-<div class="block">Tournament selection
- <br><br>
- This strategy generates a new population by selecting a specified number
- of chromosomes from the original population and selecting the fittest out
- of the isolated subset (the tournament).</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.modules.mutator">
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-<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/modules/mutator/FixedPointMutator.html" title="class in jcgp.backend.modules.mutator">FixedPointMutator</a></span></code>
-<div class="block">Fixed point mutator
- <br><br>
- This operator uses the point mutator 
- algorithm to mutate a user-defined fixed
- number of genes.</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/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a></span></code>
-<div class="block">This class specifies the basic characteristics of a mutation operator.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/PercentPointMutator.html" title="class in jcgp.backend.modules.mutator">PercentPointMutator</a></span></code>
-<div class="block">Percent point mutator
- <br><br>
- This operator calculates how many genes to mutate based on the mutation rate
- parameter.</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/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">PointMutator</a></span></code>
-<div class="block">Point mutator
- <br><br>
- In point mutation, a number of random genes
- is picked and mutated until all required
- mutations have been performed.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/ProbabilisticMutator.html" title="class in jcgp.backend.modules.mutator">ProbabilisticMutator</a></span></code>
-<div class="block">Probabilistic mutator
- <br><br>
- This operator iterates through every mutable gene in the chromosome and 
- decides whether to mutate each of them individually.</div>
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-<div class="block">Defines the general behaviour of a CGP problem.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem">SymbolicRegressionProblem</a></span></code>
-<div class="block">Symbolic regression functions
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- Using this problem type, regression problems can be solved.</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/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;T&gt;</span></code>
-<div class="block">Abstract model for a problem that uses test cases.</div>
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diff --git a/doc/jcgp/backend/modules/es/EvolutionaryStrategy.html b/doc/jcgp/backend/modules/es/EvolutionaryStrategy.html
deleted file mode 100644
index 3469469..0000000
--- a/doc/jcgp/backend/modules/es/EvolutionaryStrategy.html
+++ /dev/null
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:32 BST 2014 -->
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-<div class="subTitle">jcgp.backend.modules.es</div>
-<h2 title="Class EvolutionaryStrategy" class="title">Class EvolutionaryStrategy</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.modules.es.EvolutionaryStrategy</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../../jcgp/backend/modules/es/MuPlusLambda.html" title="class in jcgp.backend.modules.es">MuPlusLambda</a>, <a href="../../../../jcgp/backend/modules/es/TournamentSelection.html" title="class in jcgp.backend.modules.es">TournamentSelection</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public abstract class <span class="typeNameLabel">EvolutionaryStrategy</span>
-extends <a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">Module</a></pre>
-<div class="block">This class specifies the characteristics of an evolutionary strategy. The evolutionary
- strategy's job is to generate the next population of solutions. In JCGP this is done by modifying
- the provided population object rather than creating a new one. 
- <br><br>
- A typical implementation of EvolutionaryStratey iterates through the chromosomes
- in the population and selects the individual(s) to be promoted. It then uses
- <code>mutator.mutate()</code> to generically mutate the promoted individual(s). Parameter-dependent
- strategies can be implemented by accessing the parameters via the resources
- argument.
- <br><br>
- Parameters may be specified to control the implemented strategy. Any parameters
- registered with <code>registerParameters()</code> should be displayed by the user interface,
- if it is being used. See <a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules"><code>Module</code></a> for more information. 
- <br><br>
- It is advisable to use <code>Resources.reportln()</code> and <code>Resources.report()</code>
- to print any relevant information. Note that reportln() and report() are affected
- by the report interval base parameter. Use <code>Resources.println()</code> and
- <code>Resources.print()</code> to print information regardless of the current generation.
- See <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources"><code>Resources</code></a> for more information.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules"><code>Module</code></a></dd>
-</dl>
-</li>
-</ul>
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-<h3>Method Summary</h3>
-<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t3" class="tableTab"><span><a href="javascript:show(4);">Abstract Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>abstract void</code></td>
-<td class="colLast"><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>
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-</table>
-<ul class="blockList">
-<li class="blockList"><a name="methods.inherited.from.class.jcgp.backend.modules.Module">
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-</a>
-<h3>Methods inherited from class&nbsp;jcgp.backend.modules.<a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">Module</a></h3>
-<code><a href="../../../../jcgp/backend/modules/Module.html#getLocalParameters--">getLocalParameters</a>, <a href="../../../../jcgp/backend/modules/Module.html#toString--">toString</a></code></li>
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-</a>
-<h3>Methods inherited from class&nbsp;java.lang.Object</h3>
-<code>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</code></li>
-</ul>
-</li>
-</ul>
-</li>
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-<!-- ============ METHOD DETAIL ========== -->
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-<div class="header">
-<div class="subTitle">jcgp.backend.modules.es</div>
-<h2 title="Class MuPlusLambda" class="title">Class MuPlusLambda</h2>
-</div>
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-<li>java.lang.Object</li>
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-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">jcgp.backend.modules.es.EvolutionaryStrategy</a></li>
-<li>
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-<li>jcgp.backend.modules.es.MuPlusLambda</li>
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-<pre>public class <span class="typeNameLabel">MuPlusLambda</span>
-extends <a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></pre>
-<div class="block">(μ + λ)-ES
- <br><br>
- This strategy selects the μ fittest chromosomes from the population.
- The promoted individuals are copied into the new population and mutated
- λ times, but also carried forward unchanged. The total population size
- is μ + λ. 
- <br><br>
- Two integer parameters are used to control this strategy: parents
- and offspring. They are constrained in that they must always add up to
- the population size, and must never be smaller than 1.
- <br>
- One additional parameter, report, controls whether a detailed log of the
- algorithm's operation is to be printed or not. Reports respect the report
- interval base parameter.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es"><code>EvolutionaryStrategy</code></a></dd>
-</dl>
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-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/es/MuPlusLambda.html#MuPlusLambda-jcgp.backend.resources.Resources-">MuPlusLambda</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Creates a new instance of MuPlusLambda.</div>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
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-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
-<div class="block">Performs the selection algorithm and uses the mutator to create
- the next generation of solutions.</div>
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-<code><a href="../../../../jcgp/backend/modules/Module.html#getLocalParameters--">getLocalParameters</a>, <a href="../../../../jcgp/backend/modules/Module.html#toString--">toString</a></code></li>
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-<pre>public&nbsp;MuPlusLambda(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Creates a new instance of MuPlusLambda.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
-</dl>
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-<pre>public&nbsp;void&nbsp;evolve(<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)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html#evolve-jcgp.backend.population.Population-jcgp.backend.modules.mutator.Mutator-">EvolutionaryStrategy</a></code></span></div>
-<div class="block">Performs the selection algorithm and uses the mutator to create
- the next generation of solutions.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html#evolve-jcgp.backend.population.Population-jcgp.backend.modules.mutator.Mutator-">evolve</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to evolve.</dd>
-<dd><code>mutator</code> - the mutator with which to mutate the promoted individuals.</dd>
-</dl>
-</li>
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diff --git a/doc/jcgp/backend/modules/es/TournamentSelection.html b/doc/jcgp/backend/modules/es/TournamentSelection.html
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-<h2 title="Class TournamentSelection" class="title">Class TournamentSelection</h2>
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-<pre>public class <span class="typeNameLabel">TournamentSelection</span>
-extends <a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></pre>
-<div class="block">Tournament selection
- <br><br>
- This strategy generates a new population by selecting a specified number
- of chromosomes from the original population and selecting the fittest out
- of the isolated subset (the tournament). The selected individual is mutated
- using the specified mutator. This process is repeated until the new population
- is complete.
- <br><br>
- One integer parameter is used to control this strategy: tournament
- size. This must always be greater than 0 and smaller than or equal to the
- population size. Setting it to equal population size results in the same
- chromosome being selected for every tournament, and setting it to 1 leads
- to an effectively random search.
- <br>
- One additional parameter, report, controls whether a detailed log of the
- algorithm's operation is to be printed or not. Reports respect the report
- interval base parameter.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es"><code>EvolutionaryStrategy</code></a></dd>
-</dl>
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-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/es/TournamentSelection.html#TournamentSelection-jcgp.backend.resources.Resources-">TournamentSelection</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Creates a new instance of TournamentSelection.</div>
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-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
-<div class="block">Performs the selection algorithm and uses the mutator to create
- the next generation of solutions.</div>
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-<code><a href="../../../../jcgp/backend/modules/Module.html#getLocalParameters--">getLocalParameters</a>, <a href="../../../../jcgp/backend/modules/Module.html#toString--">toString</a></code></li>
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-<h4>TournamentSelection</h4>
-<pre>public&nbsp;TournamentSelection(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Creates a new instance of TournamentSelection.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
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-<pre>public&nbsp;void&nbsp;evolve(<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)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html#evolve-jcgp.backend.population.Population-jcgp.backend.modules.mutator.Mutator-">EvolutionaryStrategy</a></code></span></div>
-<div class="block">Performs the selection algorithm and uses the mutator to create
- the next generation of solutions.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html#evolve-jcgp.backend.population.Population-jcgp.backend.modules.mutator.Mutator-">evolve</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to evolve.</dd>
-<dd><code>mutator</code> - the mutator with which to mutate the promoted individuals.</dd>
-</dl>
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-<tr>
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-<td class="colFirst"><a href="#jcgp">jcgp</a></td>
-<td class="colLast">&nbsp;</td>
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-<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/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Modifier and Type</th>
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-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a>[]</code></td>
-<td class="colLast"><span class="typeNameLabel">JCGP.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/JCGP.html#getEvolutionaryStrategies--">getEvolutionaryStrategies</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es">EvolutionaryStrategy</a></code></td>
-<td class="colLast"><span class="typeNameLabel">JCGP.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/JCGP.html#getEvolutionaryStrategy--">getEvolutionaryStrategy</a></span>()</code>&nbsp;</td>
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-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/es/MuPlusLambda.html" title="class in jcgp.backend.modules.es">MuPlusLambda</a></span></code>
-<div class="block">(μ + λ)-ES
- <br><br>
- This strategy selects the μ fittest chromosomes from the population.</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/modules/es/TournamentSelection.html" title="class in jcgp.backend.modules.es">TournamentSelection</a></span></code>
-<div class="block">Tournament selection
- <br><br>
- This strategy generates a new population by selecting a specified number
- of chromosomes from the original population and selecting the fittest out
- of the isolated subset (the tournament).</div>
-</td>
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diff --git a/doc/jcgp/backend/modules/mutator/FixedPointMutator.html b/doc/jcgp/backend/modules/mutator/FixedPointMutator.html
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-<div class="subTitle">jcgp.backend.modules.mutator</div>
-<h2 title="Class FixedPointMutator" class="title">Class FixedPointMutator</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">jcgp.backend.modules.mutator.Mutator</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">jcgp.backend.modules.mutator.PointMutator</a></li>
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-extends <a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">PointMutator</a></pre>
-<div class="block">Fixed point mutator
- <br><br>
- This operator uses the point mutator 
- algorithm to mutate a user-defined fixed
- number of genes.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator"><code>PointMutator</code></a></dd>
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-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/FixedPointMutator.html#FixedPointMutator-jcgp.backend.resources.Resources-">FixedPointMutator</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
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-<pre>public&nbsp;FixedPointMutator(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Creates a new instance of FixedPointMutator.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
-</dl>
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diff --git a/doc/jcgp/backend/modules/mutator/Mutator.html b/doc/jcgp/backend/modules/mutator/Mutator.html
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:30 BST 2014 -->
-<title>Mutator</title>
-<meta name="date" content="2014-05-22">
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-</ul>
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-<li>Detail:&nbsp;</li>
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.modules.mutator</div>
-<h2 title="Class Mutator" class="title">Class Mutator</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.modules.mutator.Mutator</li>
-</ul>
-</li>
-</ul>
-</li>
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-<div class="description">
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-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">PointMutator</a>, <a href="../../../../jcgp/backend/modules/mutator/ProbabilisticMutator.html" title="class in jcgp.backend.modules.mutator">ProbabilisticMutator</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public abstract class <span class="typeNameLabel">Mutator</span>
-extends <a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">Module</a></pre>
-<div class="block">This class specifies the basic characteristics of a mutation operator. Its job is 
- to modify the connections and functions of the chromosome according to the operator's
- parameters.
- <br><br>
- Parameters may be specified to control the implemented mutation. Any parameters
- registered with <code>registerParameters()</code> should be displayed by the user interface,
- if it is being used. See <a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules"><code>Module</code></a> for more information. 
- <br><br>
- It is advisable to use <code>Resources.reportln()</code> and <code>Resources.report()</code>
- to print any relevant information. Note that reportln() and report() are affected
- by the report interval base parameter. Use <code>Resources.println()</code> and
- <code>Resources.print()</code> to print information regardless of the current generation.
- See <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources"><code>Resources</code></a> for more information.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>abstract void</code></td>
-<td class="colLast"><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>
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-<div class="block">Applies mutations to the specified chromosome according
- to the parameter values.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>chromosome</code> - the chromosome to mutate.</dd>
-</dl>
-</li>
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-<div class="header">
-<div class="subTitle">jcgp.backend.modules.mutator</div>
-<h2 title="Class PercentPointMutator" class="title">Class PercentPointMutator</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">jcgp.backend.modules.mutator.Mutator</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">jcgp.backend.modules.mutator.PointMutator</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.modules.mutator.PercentPointMutator</li>
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-<pre>public class <span class="typeNameLabel">PercentPointMutator</span>
-extends <a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">PointMutator</a></pre>
-<div class="block">Percent point mutator
- <br><br>
- This operator calculates how many genes to mutate based on the mutation rate
- parameter. The total number of genes is computed from the number of nodes, 
- the arity and the number of outputs. It then uses the point mutation 
- algorithm to perform the required number of mutations.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator"><code>PointMutator</code></a></dd>
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-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/PercentPointMutator.html#PercentPointMutator-jcgp.backend.resources.Resources-">PercentPointMutator</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Creates a new instance of PercentPointMutator.</div>
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-<pre>public&nbsp;PercentPointMutator(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Creates a new instance of PercentPointMutator.</div>
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-</dl>
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diff --git a/doc/jcgp/backend/modules/mutator/PointMutator.html b/doc/jcgp/backend/modules/mutator/PointMutator.html
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-<meta name="date" content="2014-05-22">
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-<h2 title="Class PointMutator" class="title">Class PointMutator</h2>
-</div>
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-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
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-<li>jcgp.backend.modules.mutator.PointMutator</li>
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-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../../jcgp/backend/modules/mutator/FixedPointMutator.html" title="class in jcgp.backend.modules.mutator">FixedPointMutator</a>, <a href="../../../../jcgp/backend/modules/mutator/PercentPointMutator.html" title="class in jcgp.backend.modules.mutator">PercentPointMutator</a></dd>
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-<pre>public abstract class <span class="typeNameLabel">PointMutator</span>
-extends <a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a></pre>
-<div class="block">Point mutator
- <br><br>
- In point mutation, a number of random genes
- is picked and mutated until all required
- mutations have been performed. The actual number
- of genes to be mutated can be defined in any
- arbitrary way.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
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- to the parameter values.</div>
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-<div class="block">Applies mutations to the specified chromosome according
- to the parameter values.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/mutator/Mutator.html#mutate-jcgp.backend.population.Chromosome-">mutate</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a></code></dd>
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-<dd><code>chromosome</code> - the chromosome to mutate.</dd>
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-<h2 title="Class ProbabilisticMutator" class="title">Class ProbabilisticMutator</h2>
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-<div class="block">Probabilistic mutator
- <br><br>
- This operator iterates through every mutable gene in the chromosome and 
- decides whether to mutate each of them individually. 
- The decision is made based on the difference between the mutation probability
- and a randomly generated double between 0 and 100.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator"><code>Mutator</code></a></dd>
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/ProbabilisticMutator.html#ProbabilisticMutator-jcgp.backend.resources.Resources-">ProbabilisticMutator</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
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-<div class="block">Creates a new instance of ProbabilisticMutator.</div>
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diff --git a/doc/jcgp/backend/modules/mutator/class-use/Mutator.html b/doc/jcgp/backend/modules/mutator/class-use/Mutator.html
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-<tr>
-<th class="colFirst" scope="col">Package</th>
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-</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.mutator">jcgp.backend.modules.mutator</a></td>
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-<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/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<td class="colLast"><span class="typeNameLabel">JCGP.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/JCGP.html#getMutator--">getMutator</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code>void</code></td>
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-<td class="colFirst"><code>abstract void</code></td>
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-      <a href="../../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>&nbsp;mutator)</code>
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-      <a href="../../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a>&nbsp;mutator)</code>&nbsp;</td>
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-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Class and Description</th>
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/mutator/FixedPointMutator.html" title="class in jcgp.backend.modules.mutator">FixedPointMutator</a></span></code>
-<div class="block">Fixed point mutator
- <br><br>
- This operator uses the point mutator 
- algorithm to mutate a user-defined fixed
- number of genes.</div>
-</td>
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-<tr class="rowColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/mutator/PercentPointMutator.html" title="class in jcgp.backend.modules.mutator">PercentPointMutator</a></span></code>
-<div class="block">Percent point mutator
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- This operator calculates how many genes to mutate based on the mutation rate
- parameter.</div>
-</td>
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-<tr class="altColor">
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">PointMutator</a></span></code>
-<div class="block">Point mutator
- <br><br>
- In point mutation, a number of random genes
- is picked and mutated until all required
- mutations have been performed.</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/modules/mutator/ProbabilisticMutator.html" title="class in jcgp.backend.modules.mutator">ProbabilisticMutator</a></span></code>
-<div class="block">Probabilistic mutator
- <br><br>
- This operator iterates through every mutable gene in the chromosome and 
- decides whether to mutate each of them individually.</div>
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diff --git a/doc/jcgp/backend/modules/mutator/class-use/PercentPointMutator.html b/doc/jcgp/backend/modules/mutator/class-use/PercentPointMutator.html
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-<tr>
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-<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/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">PointMutator</a> in <a href="../../../../../jcgp/backend/modules/mutator/package-summary.html">jcgp.backend.modules.mutator</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/modules/mutator/FixedPointMutator.html" title="class in jcgp.backend.modules.mutator">FixedPointMutator</a></span></code>
-<div class="block">Fixed point mutator
- <br><br>
- This operator uses the point mutator 
- algorithm to mutate a user-defined fixed
- number of genes.</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/modules/mutator/PercentPointMutator.html" title="class in jcgp.backend.modules.mutator">PercentPointMutator</a></span></code>
-<div class="block">Percent point mutator
- <br><br>
- This operator calculates how many genes to mutate based on the mutation rate
- parameter.</div>
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-<tr>
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-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../../jcgp/backend/modules/mutator/FixedPointMutator.html" title="class in jcgp.backend.modules.mutator">FixedPointMutator</a></td>
-<td class="colLast">
-<div class="block">Fixed point mutator
- <br><br>
- This operator uses the point mutator 
- algorithm to mutate a user-defined fixed
- number of genes.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator">Mutator</a></td>
-<td class="colLast">
-<div class="block">This class specifies the basic characteristics of a mutation operator.</div>
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-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../../jcgp/backend/modules/mutator/PercentPointMutator.html" title="class in jcgp.backend.modules.mutator">PercentPointMutator</a></td>
-<td class="colLast">
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- <br><br>
- This operator calculates how many genes to mutate based on the mutation rate
- parameter.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../../jcgp/backend/modules/mutator/PointMutator.html" title="class in jcgp.backend.modules.mutator">PointMutator</a></td>
-<td class="colLast">
-<div class="block">Point mutator
- <br><br>
- In point mutation, a number of random genes
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-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../../jcgp/backend/modules/mutator/ProbabilisticMutator.html" title="class in jcgp.backend.modules.mutator">ProbabilisticMutator</a></td>
-<td class="colLast">
-<div class="block">Probabilistic mutator
- <br><br>
- This operator iterates through every mutable gene in the chromosome and 
- decides whether to mutate each of them individually.</div>
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-</tr>
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-<tr class="altColor">
-<td class="colOne"><a href="../../../../jcgp/backend/modules/mutator/class-use/Mutator.html#jcgp">Mutator</a>
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-<li><a href="package-use.html">Use</a></li>
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-<tr>
-<th class="colFirst" scope="col">Class</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">Module</a></td>
-<td class="colLast">
-<div class="block">This class defines the expected behaviour of a module.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
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-<ul class="navList" title="Navigation">
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-<li class="navBarCell1Rev">Package</li>
-<li>Class</li>
-<li><a href="package-use.html">Use</a></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>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/backend/function/package-summary.html">Prev&nbsp;Package</a></li>
-<li><a href="../../../jcgp/backend/modules/es/package-summary.html">Next&nbsp;Package</a></li>
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-<li><a href="../../../index.html?jcgp/backend/modules/package-summary.html" target="_top">Frames</a></li>
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diff --git a/doc/jcgp/backend/modules/problem/BestFitness.html b/doc/jcgp/backend/modules/problem/BestFitness.html
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-<div class="subTitle">jcgp.backend.modules.problem</div>
-<h2 title="Enum BestFitness" class="title">Enum BestFitness</h2>
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-<pre>public enum <span class="typeNameLabel">BestFitness</span>
-extends java.lang.Enum&lt;<a href="../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a>&gt;</pre>
-<div class="block">Enum type to allow problems to indicate their fitness
- orientation.
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- <code>BestFitness.HIGH</code> means high fitness values are
- better than low. Conversely, <code>BestFitness.LOW</code>
- signals that low fitness values indicate better fitness
- than high values.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/BestFitness.html#values--">values</a></span>()</code>
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-<h2 title="Class DigitalCircuitProblem" class="title">Class DigitalCircuitProblem</h2>
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-<li>java.lang.Object</li>
-<li>
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-<li>
-<ul class="inheritance">
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-<li>
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-<div class="block">Digital circuit problem
- <br><br>
- Using this problem type, digital logic circuits can be evolved.
- <code>parseData()</code> must be used to load the desired circuit
- truth table in the standard CGP .plu format.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/function/DigitalCircuitFunctions.html" title="class in jcgp.backend.function"><code>DigitalCircuitFunctions</code></a></dd>
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-<td class="colFirst"><code>void</code></td>
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-<div class="block">The most important method of the problem type.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</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>
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-<td class="colFirst"><code><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;<a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a>&gt;</code></td>
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-<pre>public&nbsp;DigitalCircuitProblem(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Construct a new instance of DigitalCircuitProblem.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
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-<pre>public&nbsp;void&nbsp;evaluate(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-">Problem</a></code></span></div>
-<div class="block">The most important method of the problem type. This is called once
- per generation, when the new population has been generated.
- <br><br>
- The basic functionality of this method is to loop through all chromosomes
- in the population and decode them according to the problem type. The
- fitness of each chromosome is then calculated using the problem data
- or otherwise (subjective problem types such as art generation might
- leave fitness evaluations up to the user) and assigned to the appropriate
- chromosome. 
- <br><br>
- In addition, realisations of this method should update the value of 
- bestFitness as appropriate, since the value of this parameter is displayed
- if a GUI is in use.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-">evaluate</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to be evaluated.</dd>
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-<pre>public&nbsp;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;<a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a>&gt;&nbsp;parseTestCase(java.lang.String[]&nbsp;inputs,
-                                                               java.lang.String[]&nbsp;outputs)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#parseTestCase-java.lang.String:A-java.lang.String:A-">TestCaseProblem</a></code></span></div>
-<div class="block">This method is used internally by <code>addTestCase()</code> in order
- to appropriately parse strings into the right data type for the 
- test cases. Since the data type is problem-dependent, subclasses must 
- implement this method. This method must return a built <code>TestCase</code>
- object from the arguments given.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>inputs</code> - the inputs represented as strings.</dd>
-<dd><code>outputs</code> - the outputs represented as strings.</dd>
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-<dd>the parsed test case.</dd>
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-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasPerfectSolution-jcgp.backend.population.Population-">Problem</a></code></span></div>
-<div class="block">Used to assert whether a given population contains a perfect solution
- to the problem. It is up to the problem to define what qualifies
- a perfect solution, as some problems (subject ones such as music and
- art evolution, for example) might not have perfect solutions at all.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to search through for a perfect chromosome.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the perfect solution index, if one exits, -1 if no perfect solution was found.</dd>
-</dl>
-</li>
-</ul>
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-</ul>
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-<div class="subTitle">jcgp.backend.modules.problem</div>
-<h2 title="Class Problem" class="title">Class Problem</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.modules.problem.Problem</li>
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-</dl>
-<hr>
-<br>
-<pre>public abstract class <span class="typeNameLabel">Problem</span>
-extends <a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">Module</a></pre>
-<div class="block">Defines the general behaviour of a CGP problem. The primary function of <code>Problem</code> 
- is to evaluate a population and assign a fitness value to each chromosome. 
- <br>
- Problems are free to define whether better fitness means a higher or lower fitness value.
- In some problem types, it is more convenient to treat fitness 0 as the best possible value.
- This can be done by changing the fitness orientation to <code>BestFitness.HIGH</code> or <code>BestFitness.LOW</code> as appropriate.
- Fitness orientation is set to high by default.
- <br><br>
- When extending this class, the constructor should call a few methods in order to
- properly construct the problem type: <code>setFunctionSet()</code>, <code>setFileExtension()</code> and <code>setFitnessOrientation()</code>,
- with the respective arguments. As with all subclasses of <code>Module</code>, <code>setName()</code> and
- <code>registerParameters()</code> should be used where appropriate as well.
- <br><br>
- It is advisable to use <code>Resources.reportln()</code> and <code>Resources.report()</code>
- to print any relevant information. Note that reportln() and report() are affected
- by the report interval base parameter. Use <code>Resources.println()</code> and
- <code>Resources.print()</code> to print information regardless of the current generation.
- See <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources"><code>Resources</code></a> for more information.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules"><code>Module</code></a></dd>
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-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>abstract void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-">evaluate</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>
-<div class="block">The most important method of the problem type.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#getBestFitness--">getBestFitness</a></span>()</code>&nbsp;</td>
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-<tr id="i2" class="altColor">
-<td class="colFirst"><code>java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#getFileExtension--">getFileExtension</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code><a href="../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#getFitnessOrientation--">getFitnessOrientation</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#getFunctionSet--">getFunctionSet</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>abstract int</code></td>
-<td class="colLast"><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 id="i6" class="altColor">
-<td class="colFirst"><code>abstract int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</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 id="i7" class="rowColor">
-<td class="colFirst"><code>abstract void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></span>(java.io.File&nbsp;file,
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-<div class="block">Parses the specified file and uses the parsed data to
- set up the problem type instance appropriately.</div>
-</td>
-</tr>
-<tr id="i8" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/Problem.html#reset--">reset</a></span>()</code>
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-<div class="block">The most important method of the problem type. This is called once
- per generation, when the new population has been generated.
- <br><br>
- The basic functionality of this method is to loop through all chromosomes
- in the population and decode them according to the problem type. The
- fitness of each chromosome is then calculated using the problem data
- or otherwise (subjective problem types such as art generation might
- leave fitness evaluations up to the user) and assigned to the appropriate
- chromosome. 
- <br><br>
- In addition, realisations of this method should update the value of 
- bestFitness as appropriate, since the value of this parameter is displayed
- if a GUI is in use.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to be evaluated.</dd>
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-<div class="block">Used to assert whether a given population contains a perfect solution
- to the problem. It is up to the problem to define what qualifies
- a perfect solution, as some problems (subject ones such as music and
- art evolution, for example) might not have perfect solutions at all.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to search through for a perfect chromosome.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the perfect solution index, if one exits, -1 if no perfect solution was found.</dd>
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-<div class="block">Used to assert whether a given population has a chromosome that is an improvement over 
- the current best chromosome. A typical implementation of this method
- will simply compare chromosome fitness values, though the problem type
- is free to implement this in any way.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population potentially containing a fitter chromosome.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the index of the first chromosome in the population that is an improvement, -1 if none is found.</dd>
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-<div class="block">Parses the specified file and uses the parsed data to
- set up the problem type instance appropriately. Any necessary
- resource changes can be performed using the provided <code>ModifiableResources</code>
- instance.
- <br><br>
- In addition, realisations of this method should update the value of
- maxFitness where appropriate, as this may be displayed to the user
- if a GUI is in use.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the data file to parse.</dd>
-<dd><code>resources</code> - a modifiable reference to the experiment's resources.</dd>
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-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the FunctionSet object used by this problem type.</dd>
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-</li>
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-<!--   -->
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-<pre>public&nbsp;java.lang.String&nbsp;getFileExtension()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the file extension accepted by this problem type for problem data files.</dd>
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-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the fitness orientation of this particular problem.</dd>
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-</li>
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-<pre>public&nbsp;double&nbsp;getBestFitness()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the current best fitness, in other words, the fitness
- value of the fittest chromosome in the current generation.</dd>
-</dl>
-</li>
-</ul>
-<a name="reset--">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>reset</h4>
-<pre>public&nbsp;void&nbsp;reset()</pre>
-<div class="block">Resets the bestFitness parameter.</div>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
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-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
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-<h2 title="Class SymbolicRegressionProblem" class="title">Class SymbolicRegressionProblem</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">jcgp.backend.modules.problem.Problem</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">jcgp.backend.modules.problem.TestCaseProblem</a>&lt;java.lang.Double&gt;</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.modules.problem.SymbolicRegressionProblem</li>
-</ul>
-</li>
-</ul>
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-<pre>public class <span class="typeNameLabel">SymbolicRegressionProblem</span>
-extends <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;java.lang.Double&gt;</pre>
-<div class="block">Symbolic regression functions
- <br><br>
- Using this problem type, regression problems can be solved.
- <code>parseData()</code> must be used to load the desired function
- data in the standard CGP .dat format.
- <br><br>
- This problem uses quite a few parameters:
- <ul>
- <li>Error threshold: the maximum difference allowed between an
- evolved output and the equivalent output from the problem data.
- Outputs within the error threshold will be considered correct.
- This is only used if hits is enabled.</li>
- <li>Perfection threshold: if the fitness is calculated without
- using the hits method, it is a decimal value. A solution is
- considered perfect when the difference between its fitness and
- the maximum possible fitness is within the perfection threshold.</li>
- <li>Hits-based fitness: increment the fitness by 1 whenever the
- chromosome output is within the error threshold.</li></ul></div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/function/SymbolicRegressionFunctions.html" title="class in jcgp.backend.function"><code>SymbolicRegressionFunctions</code></a></dd>
-</dl>
-</li>
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-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#SymbolicRegressionProblem-jcgp.backend.resources.Resources-">SymbolicRegressionProblem</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Creates a new instance of SymbolicRegressionProblem.</div>
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-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#evaluate-jcgp.backend.population.Population-">evaluate</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</code>
-<div class="block">The most important method of the problem type.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</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 id="i2" class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;java.lang.Double&gt;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#parseTestCase-java.lang.String:A-java.lang.String:A-">parseTestCase</a></span>(java.lang.String[]&nbsp;inputs,
-             java.lang.String[]&nbsp;outputs)</code>
-<div class="block">This method is used internally by <code>addTestCase()</code> in order
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-<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#getBestFitness--">getBestFitness</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFileExtension--">getFileExtension</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFitnessOrientation--">getFitnessOrientation</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFunctionSet--">getFunctionSet</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#reset--">reset</a></code></li>
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-<h4>SymbolicRegressionProblem</h4>
-<pre>public&nbsp;SymbolicRegressionProblem(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Creates a new instance of SymbolicRegressionProblem.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-<!-- ============ METHOD DETAIL ========== -->
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-<h3>Method Detail</h3>
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-<h4>evaluate</h4>
-<pre>public&nbsp;void&nbsp;evaluate(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-">Problem</a></code></span></div>
-<div class="block">The most important method of the problem type. This is called once
- per generation, when the new population has been generated.
- <br><br>
- The basic functionality of this method is to loop through all chromosomes
- in the population and decode them according to the problem type. The
- fitness of each chromosome is then calculated using the problem data
- or otherwise (subjective problem types such as art generation might
- leave fitness evaluations up to the user) and assigned to the appropriate
- chromosome. 
- <br><br>
- In addition, realisations of this method should update the value of 
- bestFitness as appropriate, since the value of this parameter is displayed
- if a GUI is in use.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-">evaluate</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to be evaluated.</dd>
-</dl>
-</li>
-</ul>
-<a name="parseTestCase-java.lang.String:A-java.lang.String:A-">
-<!--   -->
-</a>
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-<h4>parseTestCase</h4>
-<pre>public&nbsp;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;java.lang.Double&gt;&nbsp;parseTestCase(java.lang.String[]&nbsp;inputs,
-                                                                java.lang.String[]&nbsp;outputs)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#parseTestCase-java.lang.String:A-java.lang.String:A-">TestCaseProblem</a></code></span></div>
-<div class="block">This method is used internally by <code>addTestCase()</code> in order
- to appropriately parse strings into the right data type for the 
- test cases. Since the data type is problem-dependent, subclasses must 
- implement this method. This method must return a built <code>TestCase</code>
- object from the arguments given.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>inputs</code> - the inputs represented as strings.</dd>
-<dd><code>outputs</code> - the outputs represented as strings.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the parsed test case.</dd>
-</dl>
-</li>
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-<!--   -->
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-<h4>hasPerfectSolution</h4>
-<pre>public&nbsp;int&nbsp;hasPerfectSolution(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasPerfectSolution-jcgp.backend.population.Population-">Problem</a></code></span></div>
-<div class="block">Used to assert whether a given population contains a perfect solution
- to the problem. It is up to the problem to define what qualifies
- a perfect solution, as some problems (subject ones such as music and
- art evolution, for example) might not have perfect solutions at all.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to search through for a perfect chromosome.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the perfect solution index, if one exits, -1 if no perfect solution was found.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
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-<dt><span class="paramLabel">Type Parameters:</span></dt>
-<dd><code>U</code> - the data type of the test case.</dd>
-</dl>
-<dl>
-<dt>Enclosing class:</dt>
-<dd><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="type parameter in TestCaseProblem">T</a>&gt;</dd>
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-<hr>
-<br>
-<pre>public static class <span class="typeNameLabel">TestCaseProblem.TestCase&lt;U&gt;</span>
-extends java.lang.Object</pre>
-<div class="block">Basic data type for encapsulating test cases, it simply
- contains arrays of inputs and outputs and associated getters.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-</li>
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-                <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="type parameter in TestCaseProblem.TestCase">U</a>[]&nbsp;outputs)</pre>
-<div class="block">Creates a new test case, inputs and outputs
- must be specified upon instantiation.</div>
-<dl>
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diff --git a/doc/jcgp/backend/modules/problem/TestCaseProblem.html b/doc/jcgp/backend/modules/problem/TestCaseProblem.html
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-<div class="header">
-<div class="subTitle">jcgp.backend.modules.problem</div>
-<h2 title="Class TestCaseProblem" class="title">Class TestCaseProblem&lt;T&gt;</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">jcgp.backend.modules.problem.Problem</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.modules.problem.TestCaseProblem&lt;T&gt;</li>
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-<dd><code>T</code> - the data type to be used by the TestCaseProblem.</dd>
-</dl>
-<dl>
-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html" title="class in jcgp.backend.modules.problem">DigitalCircuitProblem</a>, <a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem">SymbolicRegressionProblem</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public abstract class <span class="typeNameLabel">TestCaseProblem&lt;T&gt;</span>
-extends <a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></pre>
-<div class="block">Abstract model for a problem that uses test cases. A test case
- problem is any problem that compares the chromosome output to
- an expected output taken from a table of input-output mappings.
- <br><br>
- This class defines a basic data type for storing test cases, 
- TestCase, and provides core functionality to add and manipulate
- test cases in the problem. A subclass of <code>TestCaseProblem</code>
- must simply override <code>parseTestCase()</code> to convert parsed
- problem data strings into the required data type (T).</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem"><code>Problem</code></a></dd>
-</dl>
-</li>
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-<caption><span>Nested Classes</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>
-<tr class="altColor">
-<td class="colFirst"><code>static class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="type parameter in TestCaseProblem.TestCase">U</a>&gt;</span></code>
-<div class="block">Basic data type for encapsulating test cases, it simply
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#addTestCase-java.lang.String:A-java.lang.String:A-">addTestCase</a></span>(java.lang.String[]&nbsp;inputs,
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-<div class="block">Adds test cases to the problem instance as they get parsed from a 
- problem data file.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#clearTestCases--">clearTestCases</a></span>()</code>
-<div class="block">Remove all test cases.</div>
-</td>
-</tr>
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-<td class="colFirst"><code>javafx.collections.ObservableList&lt;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="type parameter in TestCaseProblem">T</a>&gt;&gt;</code></td>
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-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.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 id="i4" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></span>(java.io.File&nbsp;file,
-                <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</code>
-<div class="block">Parses the specified file and uses the parsed data to
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-<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-">evaluate</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getBestFitness--">getBestFitness</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFileExtension--">getFileExtension</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFitnessOrientation--">getFitnessOrientation</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFunctionSet--">getFunctionSet</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#reset--">reset</a></code></li>
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-<code><a href="../../../../jcgp/backend/modules/Module.html#getLocalParameters--">getLocalParameters</a>, <a href="../../../../jcgp/backend/modules/Module.html#toString--">toString</a></code></li>
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-<h4>getTestCases</h4>
-<pre>public&nbsp;javafx.collections.ObservableList&lt;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="type parameter in TestCaseProblem">T</a>&gt;&gt;&nbsp;getTestCases()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a list containing the test cases.</dd>
-</dl>
-</li>
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-<pre>public final&nbsp;void&nbsp;addTestCase(java.lang.String[]&nbsp;inputs,
-                              java.lang.String[]&nbsp;outputs)</pre>
-<div class="block">Adds test cases to the problem instance as they get parsed from a 
- problem data file. This template method uses <code>parseTestCase</code>, which
- must be implemented by subclasses.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>inputs</code> - the inputs represented as strings.</dd>
-<dd><code>outputs</code> - the outputs represented as strings.</dd>
-</dl>
-</li>
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-<pre>public&nbsp;void&nbsp;clearTestCases()</pre>
-<div class="block">Remove all test cases.</div>
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-<h4>parseProblemData</h4>
-<pre>public&nbsp;void&nbsp;parseProblemData(java.io.File&nbsp;file,
-                             <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">Problem</a></code></span></div>
-<div class="block">Parses the specified file and uses the parsed data to
- set up the problem type instance appropriately. Any necessary
- resource changes can be performed using the provided <code>ModifiableResources</code>
- instance.
- <br><br>
- In addition, realisations of this method should update the value of
- maxFitness where appropriate, as this may be displayed to the user
- if a GUI is in use.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the data file to parse.</dd>
-<dd><code>resources</code> - a modifiable reference to the experiment's resources.</dd>
-</dl>
-</li>
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-<!--   -->
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-<h4>hasImprovement</h4>
-<pre>public&nbsp;int&nbsp;hasImprovement(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasImprovement-jcgp.backend.population.Population-">Problem</a></code></span></div>
-<div class="block">Used to assert whether a given population has a chromosome that is an improvement over 
- the current best chromosome. A typical implementation of this method
- will simply compare chromosome fitness values, though the problem type
- is free to implement this in any way.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#hasImprovement-jcgp.backend.population.Population-">hasImprovement</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population potentially containing a fitter chromosome.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the index of the first chromosome in the population that is an improvement, -1 if none is found.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
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diff --git a/doc/jcgp/backend/modules/problem/TravellingSalesmanProblem.html b/doc/jcgp/backend/modules/problem/TravellingSalesmanProblem.html
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-<div class="subTitle">jcgp.backend.modules.problem</div>
-<h2 title="Class TravellingSalesmanProblem" class="title">Class TravellingSalesmanProblem</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules">jcgp.backend.modules.Module</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">jcgp.backend.modules.problem.Problem</a></li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.modules.problem.TravellingSalesmanProblem</li>
-</ul>
-</li>
-</ul>
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-<pre>public class <span class="typeNameLabel">TravellingSalesmanProblem</span>
-extends <a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></pre>
-<div class="block">Travelling salesman problem
- <br><br>
- Using this problem type, travelling salesman tours can be evolved.
- <code>parseData()</code> must be used to load the desired city
- coordinates in the standard .tsp format.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/function/TravellingSalesmanFunctions.html" title="class in jcgp.backend.function"><code>TravellingSalesmanFunctions</code></a></dd>
-</dl>
-</li>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TravellingSalesmanProblem.html#TravellingSalesmanProblem-jcgp.backend.resources.Resources-">TravellingSalesmanProblem</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Construct a new instance of TravellingSalesmanProblem.</div>
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-</table>
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-<!-- ========== METHOD SUMMARY =========== -->
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TravellingSalesmanProblem.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 id="i1" class="rowColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TravellingSalesmanProblem.html#isImprovement-jcgp.backend.population.Chromosome-">isImprovement</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;fittest)</code>
-<div class="block">Used to assert whether a given chromosome is an improvement over 
- the current best chromosome.</div>
-</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TravellingSalesmanProblem.html#isPerfectSolution-jcgp.backend.population.Chromosome-">isPerfectSolution</a></span>(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;fittest)</code>
-<div class="block">Used to assert whether a given chromosome is a perfect solution
- to the problem.</div>
-</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TravellingSalesmanProblem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></span>(java.io.File&nbsp;file,
-                <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</code>
-<div class="block">Parses the specified file and uses the parsed data to
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-<h3>Methods inherited from class&nbsp;jcgp.backend.modules.problem.<a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></h3>
-<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#getBestFitness--">getBestFitness</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFileExtension--">getFileExtension</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#getFunctionSet--">getFunctionSet</a>, <a href="../../../../jcgp/backend/modules/problem/Problem.html#reset--">reset</a></code></li>
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-<pre>public&nbsp;TravellingSalesmanProblem(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Construct a new instance of TravellingSalesmanProblem.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
-</dl>
-</li>
-</ul>
-</li>
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-<!-- ============ METHOD DETAIL ========== -->
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-<h4>evaluate</h4>
-<pre>public&nbsp;void&nbsp;evaluate(<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)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">Problem</a></code></span></div>
-<div class="block">The most important method of the problem type. This is called once
- per generation, when the new population has been generated.
- <br><br>
- The basic functionality of this method is to loop through all chromosomes
- in the population and decode them according to the problem type. The
- fitness of each chromosome is then calculated using the problem data
- or otherwise (subjective problem types such as art generation might
- leave fitness evaluations up to the user) and assigned to the appropriate
- chromosome. 
- <br><br>
- In addition, realisations of this method should update the value of 
- bestFitness as appropriate, since the value of this parameter is displayed
- if a GUI is in use.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">evaluate</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>population</code> - the population to be evaluated.</dd>
-<dd><code>resources</code> - parameters and utilities for optional reference.</dd>
-</dl>
-</li>
-</ul>
-<a name="isPerfectSolution-jcgp.backend.population.Chromosome-">
-<!--   -->
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-<h4>isPerfectSolution</h4>
-<pre>public&nbsp;boolean&nbsp;isPerfectSolution(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;fittest)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#isPerfectSolution-jcgp.backend.population.Chromosome-">Problem</a></code></span></div>
-<div class="block">Used to assert whether a given chromosome is a perfect solution
- to the problem. It is up to the problem to define what qualifies
- a perfect solution, as some problems (subject ones such as music and
- art evolution, for example) might not have perfect solutions at all.
- <br><br>
- Note that if this method returns true, the experiment will move on
- to the next run, or finish if no more runs are left.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#isPerfectSolution-jcgp.backend.population.Chromosome-">isPerfectSolution</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>fittest</code> - the potentially perfect chromosome.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if the argument is a perfect solution.</dd>
-</dl>
-</li>
-</ul>
-<a name="parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>parseProblemData</h4>
-<pre>public&nbsp;void&nbsp;parseProblemData(java.io.File&nbsp;file,
-                             <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">Problem</a></code></span></div>
-<div class="block">Parses the specified file and uses the parsed data to
- set up the problem type instance appropriately. Any necessary
- resource changes can be performed using the provided <code>ModifiableResources</code>
- instance.
- <br><br>
- In addition, realisations of this method should update the value of
- maxFitness where appropriate, as this may be displayed to the user
- if a GUI is in use.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the data file to parse.</dd>
-<dd><code>resources</code> - a modifiable reference to the experiment's resources.</dd>
-</dl>
-</li>
-</ul>
-<a name="isImprovement-jcgp.backend.population.Chromosome-">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>isImprovement</h4>
-<pre>public&nbsp;boolean&nbsp;isImprovement(<a href="../../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;fittest)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html#isImprovement-jcgp.backend.population.Chromosome-">Problem</a></code></span></div>
-<div class="block">Used to assert whether a given chromosome is an improvement over 
- the current best chromosome. A typical implementation of this method
- will simply compare chromosome fitness values, though the problem type
- is free to implement this in any way.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../../jcgp/backend/modules/problem/Problem.html#isImprovement-jcgp.backend.population.Chromosome-">isImprovement</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>fittest</code> - the potentially fitter chromosome.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if the argument is fitter than the currently fittest chromosome.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
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diff --git a/doc/jcgp/backend/modules/problem/class-use/BestFitness.html b/doc/jcgp/backend/modules/problem/class-use/BestFitness.html
deleted file mode 100644
index b267c70..0000000
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+++ /dev/null
@@ -1,212 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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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/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</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.problem">jcgp.backend.modules.problem</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.backend.resources">jcgp.backend.resources</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.problem">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</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> that return <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</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/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Problem.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/problem/Problem.html#getFitnessOrientation--">getFitnessOrientation</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a></code></td>
-<td class="colLast"><span class="typeNameLabel">BestFitness.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/problem/BestFitness.html#valueOf-java.lang.String-">valueOf</a></span>(java.lang.String&nbsp;name)</code>
-<div class="block">Returns the enum constant of this type with the specified name.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a>[]</code></td>
-<td class="colLast"><span class="typeNameLabel">BestFitness.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/problem/BestFitness.html#values--">values</a></span>()</code>
-<div class="block">Returns an array containing the constants of this enum type, in
-the order they are declared.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.resources">
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-<h3>Uses of <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a> in <a href="../../../../../jcgp/backend/resources/package-summary.html">jcgp.backend.resources</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/resources/package-summary.html">jcgp.backend.resources</a> that return <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</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/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Resources.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/resources/Resources.html#fitnessOrientation--">fitnessOrientation</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/resources/package-summary.html">jcgp.backend.resources</a> with parameters of type <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</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">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/resources/ModifiableResources.html#setFitnessOrientation-jcgp.backend.modules.problem.BestFitness-">setFitnessOrientation</a></span>(<a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a>&nbsp;newOrientation)</code>&nbsp;</td>
-</tr>
-</tbody>
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diff --git a/doc/jcgp/backend/modules/problem/class-use/DigitalCircuitProblem.html b/doc/jcgp/backend/modules/problem/class-use/DigitalCircuitProblem.html
deleted file mode 100644
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-<caption><span>Methods in <a href="../../../../../jcgp/package-summary.html">jcgp</a> that return <a href="../../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Package</th>
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-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.backend.modules.problem">jcgp.backend.modules.problem</a></td>
-<td class="colLast">&nbsp;</td>
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-<td class="colFirst"><a href="#jcgp.backend.parsers">jcgp.backend.parsers</a></td>
-<td class="colLast">&nbsp;</td>
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-<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/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a> in <a href="../../../../../jcgp/backend/modules/problem/package-summary.html">jcgp.backend.modules.problem</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<div class="block">Digital circuit problem
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-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem">SymbolicRegressionProblem</a></span></code>
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-<td class="colFirst"><code>static void</code></td>
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diff --git a/doc/jcgp/backend/modules/problem/class-use/TravellingSalesmanProblem.html b/doc/jcgp/backend/modules/problem/class-use/TravellingSalesmanProblem.html
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-<td class="colFirst"><a href="../../../../jcgp/backend/modules/problem/DigitalCircuitProblem.html" title="class in jcgp.backend.modules.problem">DigitalCircuitProblem</a></td>
-<td class="colLast">
-<div class="block">Digital circuit problem
- <br><br>
- Using this problem type, digital logic circuits can be evolved.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></td>
-<td class="colLast">
-<div class="block">Defines the general behaviour of a CGP problem.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem">SymbolicRegressionProblem</a></td>
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-<div class="block">Symbolic regression functions
- <br><br>
- Using this problem type, regression problems can be solved.</div>
-</td>
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-<td class="colFirst"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;T&gt;</td>
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-<div class="block">Abstract model for a problem that uses test cases.</div>
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-<td class="colFirst"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;U&gt;</td>
-<td class="colLast">
-<div class="block">Basic data type for encapsulating test cases, it simply
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-<th class="colLast" scope="col">Description</th>
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-<td class="colFirst"><a href="../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a></td>
-<td class="colLast">
-<div class="block">Enum type to allow problems to indicate their fitness
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diff --git a/doc/jcgp/backend/modules/problem/package-tree.html b/doc/jcgp/backend/modules/problem/package-tree.html
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-<li type="circle">java.lang.Object
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diff --git a/doc/jcgp/backend/parameters/BooleanParameter.html b/doc/jcgp/backend/parameters/BooleanParameter.html
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-<h2 title="Class BooleanParameter" class="title">Class BooleanParameter</h2>
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- required this method can be anonymously overridden on an instance-to-instance
- basis.</div>
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- new value, so that the user can be informed if any parameters
- are currently set to invalid values.</div>
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diff --git a/doc/jcgp/backend/parameters/DoubleParameter.html b/doc/jcgp/backend/parameters/DoubleParameter.html
deleted file mode 100644
index a70dda0..0000000
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-<div class="subTitle">jcgp.backend.parameters</div>
-<h2 title="Class DoubleParameter" class="title">Class DoubleParameter</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">jcgp.backend.parameters.Parameter</a>&lt;java.lang.Number&gt;</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.parameters.DoubleParameter</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../jcgp/backend/parameters/monitors/DoubleMonitor.html" title="class in jcgp.backend.parameters.monitors">DoubleMonitor</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">DoubleParameter</span>
-extends <a href="../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</a>&lt;java.lang.Number&gt;</pre>
-<div class="block">Parameter subclass for the double type. Most of the
- functionality is already implemented in <code>Parameter</code>, 
- leaving only construction and type definition to the
- subclasses.
- <br><br>
- This class contains three constructors, two of which are public.
- One assumes the parameter is not critical and only takes a name
- and initial value, while the other allows the critical flag
- to be set as well. The third constructor is protected and allows
- the monitor flag to be set as well, allowing subclasses of this class
- to be used as monitors. See <a href="../../../jcgp/backend/parameters/monitors/DoubleMonitor.html" title="class in jcgp.backend.parameters.monitors"><code>DoubleMonitor</code></a> for an example
- of this usage.
- <br><br>
- The validate method is overridden here and left blank since not all
- parameters actually require validation, but where validation is
- required this method can be anonymously overridden on an instance-to-instance
- basis.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
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-<!-- =========== PROPERTY SUMMARY =========== -->
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-<code><a href="../../../jcgp/backend/parameters/Parameter.html#valueProperty">valueProperty</a></code></li>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parameters/DoubleParameter.html#DoubleParameter-double-java.lang.String-">DoubleParameter</a></span>(double&nbsp;value,
-               java.lang.String&nbsp;name)</code>
-<div class="block">Creates a new instance of this class, assuming the parameter
- is not critical.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parameters/DoubleParameter.html#DoubleParameter-double-java.lang.String-boolean-">DoubleParameter</a></span>(double&nbsp;value,
-               java.lang.String&nbsp;name,
-               boolean&nbsp;critical)</code>
-<div class="block">Creates a new instance of this class.</div>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>java.lang.Double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parameters/DoubleParameter.html#get--">get</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parameters/DoubleParameter.html#validate-java.lang.Number-">validate</a></span>(java.lang.Number&nbsp;newValue)</code>
-<div class="block">This is a callback method which gets called whenever changes
- to parameters (not only its own instance) are made.</div>
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-</a>
-<h3>Methods inherited from class&nbsp;jcgp.backend.parameters.<a href="../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</a></h3>
-<code><a href="../../../jcgp/backend/parameters/Parameter.html#getStatus--">getStatus</a>, <a href="../../../jcgp/backend/parameters/Parameter.html#isCritical--">isCritical</a>, <a href="../../../jcgp/backend/parameters/Parameter.html#isMonitor--">isMonitor</a>, <a href="../../../jcgp/backend/parameters/Parameter.html#set-T-">set</a>, <a href="../../../jcgp/backend/parameters/Parameter.html#toString--">toString</a>, <a href="../../../jcgp/backend/parameters/Parameter.html#valueProperty--">valueProperty</a></code></li>
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-<code>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</code></li>
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-<h4>DoubleParameter</h4>
-<pre>public&nbsp;DoubleParameter(double&nbsp;value,
-                       java.lang.String&nbsp;name)</pre>
-<div class="block">Creates a new instance of this class, assuming the parameter
- is not critical.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>value</code> - the initial value for this parameter.</dd>
-<dd><code>name</code> - the name of this parameter, for GUI display.</dd>
-</dl>
-</li>
-</ul>
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-<!--   -->
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-<pre>public&nbsp;DoubleParameter(double&nbsp;value,
-                       java.lang.String&nbsp;name,
-                       boolean&nbsp;critical)</pre>
-<div class="block">Creates a new instance of this class.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>value</code> - the initial value for this parameter.</dd>
-<dd><code>name</code> - the name of this parameter, for GUI display.</dd>
-<dd><code>critical</code> - true if the parameter is critical.</dd>
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-<h4>get</h4>
-<pre>public&nbsp;java.lang.Double&nbsp;get()</pre>
-<dl>
-<dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
-<dd><code><a href="../../../jcgp/backend/parameters/Parameter.html#get--">get</a></code>&nbsp;in class&nbsp;<code><a href="../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</a>&lt;java.lang.Number&gt;</code></dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the parameter's current value.</dd>
-</dl>
-</li>
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-<a name="validate-java.lang.Number-">
-<!--   -->
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-<h4>validate</h4>
-<pre>public&nbsp;void&nbsp;validate(java.lang.Number&nbsp;newValue)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../jcgp/backend/parameters/Parameter.html#validate-T-">Parameter</a></code></span></div>
-<div class="block">This is a callback method which gets called whenever changes
- to parameters (not only its own instance) are made. This method
- is intended to set the <code>status</code> field according to the
- new value, so that the user can be informed if any parameters
- are currently set to invalid values.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../jcgp/backend/parameters/Parameter.html#validate-T-">validate</a></code>&nbsp;in class&nbsp;<code><a href="../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</a>&lt;java.lang.Number&gt;</code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>newValue</code> - the new value.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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diff --git a/doc/jcgp/backend/parameters/IntegerParameter.html b/doc/jcgp/backend/parameters/IntegerParameter.html
deleted file mode 100644
index 90dad47..0000000
--- a/doc/jcgp/backend/parameters/IntegerParameter.html
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-<head>
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-<meta name="date" content="2014-05-22">
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-<script type="text/javascript" src="../../../script.js"></script>
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-        if (location.href.indexOf('is-external=true') == -1) {
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-<dd><a href="../../../jcgp/backend/parameters/monitors/IntegerMonitor.html" title="class in jcgp.backend.parameters.monitors">IntegerMonitor</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">IntegerParameter</span>
-extends <a href="../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</a>&lt;java.lang.Number&gt;</pre>
-<div class="block">Parameter subclass for the double type. Most of the
- functionality is already implemented in <code>Parameter</code>, 
- leaving only construction and type definition to the
- subclasses.
- <br><br>
- This class contains three constructors, two of which are public.
- One assumes the parameter is not critical and only takes a name
- and initial value, while the other allows the critical flag
- to be set as well. The third constructor is protected and allows
- the monitor flag to be set as well, allowing subclasses of this class
- to be used as monitors. See <a href="../../../jcgp/backend/parameters/monitors/IntegerMonitor.html" title="class in jcgp.backend.parameters.monitors"><code>IntegerMonitor</code></a> for an example
- of this usage.
- <br><br>
- The validate method is overridden here and left blank since not all
- parameters actually require validation, but where validation is
- required this method can be anonymously overridden on an instance-to-instance
- basis.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parameters/IntegerParameter.html#IntegerParameter-int-java.lang.String-">IntegerParameter</a></span>(int&nbsp;value,
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-</td>
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-<td class="colFirst"><code>java.lang.Integer</code></td>
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-<pre>public&nbsp;IntegerParameter(int&nbsp;value,
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-<div class="block">Creates a new instance of this class, assuming the parameter
- is not critical.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>value</code> - the initial value for this parameter.</dd>
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-<div class="block">Creates a new instance of this class.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>value</code> - the initial value for this parameter.</dd>
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- are currently set to invalid values.</div>
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-<h2 title="Class Parameter" class="title">Class Parameter&lt;T&gt;</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
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-<dd><a href="../../../jcgp/backend/parameters/BooleanParameter.html" title="class in jcgp.backend.parameters">BooleanParameter</a>, <a href="../../../jcgp/backend/parameters/DoubleParameter.html" title="class in jcgp.backend.parameters">DoubleParameter</a>, <a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></dd>
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- Parameters are values which control the operation of modules.
- They can be freely modified and accessed by the module in which
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- field. Instead, a different class should be created which constructs
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- and double implementations of parameter (and their associated monitors)
- implement this pattern, refer to them for more details. 
- <br><br>
- The <code>status</code> field holds the current status of the parameter, 
- which should change whenever the parameter value changes.
- In order for this to happen, <code>validate()</code> is called whenever
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- will likely have different validity criteria. The type of status is
- <a href="../../../jcgp/backend/parameters/ParameterStatus.html" title="enum in jcgp.backend.parameters"><code>ParameterStatus</code></a>, an enum type defining all valid states.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../jcgp/backend/modules/Module.html" title="class in jcgp.backend.modules"><code>Module</code></a></dd>
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-<h2 title="Enum ParameterStatus" class="title">Enum ParameterStatus</h2>
-</div>
-<div class="contentContainer">
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-<div class="block">Enum type containing all possible states for parameters.
- <br>
- <ul>
- <li>INVALID: the new parameter value is not valid,
- and the experiment will not be allowed to run.</li>
- <li>WARNING: the new parameter value is technically valid,
- though it might lead to undesirable behaviour.</li>
- <li>WARNING_RESET: the new parameter value is technically valid
- but will require a reset.</li>
- <li>VALID: the new value is valid.</li>
- </ul>
- <br><br>
- The above definitions are final in the sense that they outline
- how parameters are treated by the program depending on their 
- status (e.g. if any parameters are set to WARNING_RESET, a reset 
- will automatically be performed when the experiment is run).
- <br>
- In addition to the status itself, this class includes a field
- to contain details about the current status. If a GUI is in use, 
- the contents of the field should be displayed to the user, as well
- as some visual indication of the status itself. Both the status
- and the message should be updated by each parameter when <code>validate()</code>
- is called.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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diff --git a/doc/jcgp/backend/parameters/class-use/BooleanParameter.html b/doc/jcgp/backend/parameters/class-use/BooleanParameter.html
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index 386d503..0000000
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-<tr>
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-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.backend.parameters.monitors">jcgp.backend.parameters.monitors</a></td>
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-<caption><span>Subclasses of <a href="../../../../jcgp/backend/parameters/BooleanParameter.html" title="class in jcgp.backend.parameters">BooleanParameter</a> in <a href="../../../../jcgp/backend/parameters/monitors/package-summary.html">jcgp.backend.parameters.monitors</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/parameters/monitors/BooleanMonitor.html" title="class in jcgp.backend.parameters.monitors">BooleanMonitor</a></span></code>
-<div class="block">This is a special type of <code>BooleanParameter</code> which 
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-</td>
-</tr>
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-</table>
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diff --git a/doc/jcgp/backend/parameters/class-use/DoubleParameter.html b/doc/jcgp/backend/parameters/class-use/DoubleParameter.html
deleted file mode 100644
index df857bf..0000000
--- a/doc/jcgp/backend/parameters/class-use/DoubleParameter.html
+++ /dev/null
@@ -1,167 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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-<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/parameters/DoubleParameter.html" title="class in jcgp.backend.parameters">DoubleParameter</a> in <a href="../../../../jcgp/backend/parameters/monitors/package-summary.html">jcgp.backend.parameters.monitors</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/parameters/monitors/DoubleMonitor.html" title="class in jcgp.backend.parameters.monitors">DoubleMonitor</a></span></code>
-<div class="block">This is a special type of <code>DoubleParameter</code> which 
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-</tr>
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diff --git a/doc/jcgp/backend/parameters/class-use/IntegerParameter.html b/doc/jcgp/backend/parameters/class-use/IntegerParameter.html
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index 5e94d72..0000000
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-<caption><span>Packages that use <a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
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-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.backend.parameters.monitors">jcgp.backend.parameters.monitors</a></td>
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-<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/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a> in <a href="../../../../jcgp/backend/parameters/monitors/package-summary.html">jcgp.backend.parameters.monitors</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/parameters/monitors/IntegerMonitor.html" title="class in jcgp.backend.parameters.monitors">IntegerMonitor</a></span></code>
-<div class="block">This is a special type of <code>IntegerParameter</code> which 
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-<h3>Uses of <a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a> in <a href="../../../../jcgp/backend/resources/package-summary.html">jcgp.backend.resources</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/resources/package-summary.html">jcgp.backend.resources</a> that return <a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</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/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getArityParameter--">getArityParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getColumnsParameter--">getColumnsParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getCurrentGenerationParameter--">getCurrentGenerationParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getCurrentRunParameter--">getCurrentRunParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getGenerationsParameter--">getGenerationsParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getInputsParameter--">getInputsParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getLevelsBackParameter--">getLevelsBackParameter</a></span>()</code>&nbsp;</td>
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-<tr class="rowColor">
-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getOutputsParameter--">getOutputsParameter</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getRunsParameter--">getRunsParameter</a></span>()</code>&nbsp;</td>
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-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#getSeedParameter--">getSeedParameter</a></span>()</code>&nbsp;</td>
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diff --git a/doc/jcgp/backend/parameters/class-use/Parameter.html b/doc/jcgp/backend/parameters/class-use/Parameter.html
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-<tr>
-<th class="colFirst" scope="col">Package</th>
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-<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/package-summary.html">jcgp.backend.modules</a> that return types with arguments of type <a href="../../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</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/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</a>&lt;?&gt;&gt;</code></td>
-<td class="colLast"><span class="typeNameLabel">Module.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/Module.html#getLocalParameters--">getLocalParameters</a></span>()</code>
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-<td class="colFirst"><code>class&nbsp;</code></td>
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-<td class="colFirst"><code><a href="../../../../jcgp/backend/parameters/ParameterStatus.html" title="enum in jcgp.backend.parameters">ParameterStatus</a></code></td>
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diff --git a/doc/jcgp/backend/parameters/monitors/BooleanMonitor.html b/doc/jcgp/backend/parameters/monitors/BooleanMonitor.html
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-<div class="subTitle">jcgp.backend.parameters.monitors</div>
-<h2 title="Class BooleanMonitor" class="title">Class BooleanMonitor</h2>
-</div>
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-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
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-<pre>public class <span class="typeNameLabel">BooleanMonitor</span>
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-<div class="block">This is a special type of <code>BooleanParameter</code> which 
- cannot be modified in the GUI (if the GUI is in use).</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parameters/monitors/BooleanMonitor.html#BooleanMonitor-boolean-java.lang.String-">BooleanMonitor</a></span>(boolean&nbsp;value,
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- is not critical.</div>
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parameters/monitors/BooleanMonitor.html#BooleanMonitor-boolean-java.lang.String-boolean-">BooleanMonitor</a></span>(boolean&nbsp;value,
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-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parameters/monitors/BooleanMonitor.html#validate-java.lang.Boolean-">validate</a></span>(java.lang.Boolean&nbsp;newValue)</code>
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-<code><a href="../../../../jcgp/backend/parameters/Parameter.html#getStatus--">getStatus</a>, <a href="../../../../jcgp/backend/parameters/Parameter.html#isCritical--">isCritical</a>, <a href="../../../../jcgp/backend/parameters/Parameter.html#isMonitor--">isMonitor</a>, <a href="../../../../jcgp/backend/parameters/Parameter.html#set-T-">set</a>, <a href="../../../../jcgp/backend/parameters/Parameter.html#toString--">toString</a>, <a href="../../../../jcgp/backend/parameters/Parameter.html#valueProperty--">valueProperty</a></code></li>
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- is not critical.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>value</code> - the initial value for this monitor.</dd>
-<dd><code>name</code> - the name of this monitor, for GUI display.</dd>
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-<dd><code>value</code> - the initial value for this monitor.</dd>
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- to parameters (not only its own instance) are made. This method
- is intended to set the <code>status</code> field according to the
- new value, so that the user can be informed if any parameters
- are currently set to invalid values.</div>
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-<dd><code><a href="../../../../jcgp/backend/parameters/BooleanParameter.html#validate-java.lang.Boolean-">validate</a></code>&nbsp;in class&nbsp;<code><a href="../../../../jcgp/backend/parameters/BooleanParameter.html" title="class in jcgp.backend.parameters">BooleanParameter</a></code></dd>
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-<div class="subTitle">jcgp.backend.parameters.monitors</div>
-<h2 title="Class DoubleMonitor" class="title">Class DoubleMonitor</h2>
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diff --git a/doc/jcgp/backend/parameters/monitors/IntegerMonitor.html b/doc/jcgp/backend/parameters/monitors/IntegerMonitor.html
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-<h2 title="Class IntegerMonitor" class="title">Class IntegerMonitor</h2>
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parameters/monitors/IntegerMonitor.html#IntegerMonitor-int-java.lang.String-">IntegerMonitor</a></span>(int&nbsp;value,
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parameters/monitors/IntegerMonitor.html#IntegerMonitor-int-java.lang.String-boolean-">IntegerMonitor</a></span>(int&nbsp;value,
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diff --git a/doc/jcgp/backend/parsers/ChromosomeParser.html b/doc/jcgp/backend/parsers/ChromosomeParser.html
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-<div class="header">
-<div class="subTitle">jcgp.backend.parsers</div>
-<h2 title="Class ChromosomeParser" class="title">Class ChromosomeParser</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
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-<pre>public abstract class <span class="typeNameLabel">ChromosomeParser</span>
-extends java.lang.Object</pre>
-<div class="block">This class contains a method for parsing .chr files and another
- for writing .chr files from given chromosomes.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
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-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parsers/ChromosomeParser.html#ChromosomeParser--">ChromosomeParser</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><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 id="i1" class="rowColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parsers/ChromosomeParser.html#print-jcgp.backend.population.Chromosome-jcgp.backend.resources.Resources-">print</a></span>(<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 to the console in .chr format.</div>
-</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><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>
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-<h4>ChromosomeParser</h4>
-<pre>public&nbsp;ChromosomeParser()</pre>
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-<pre>public static&nbsp;void&nbsp;parse(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)</pre>
-<div class="block">Use this method to parse .chr files into a given chromosome.
- <br><br>
- This is not fully defensive as it doesn't check for number of inputs, 
- doesn't compare rows and columns individually and doesn't account for levels back. It
- is not viable to implement these defensive measures with the chromosome format used 
- by CGP.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the .chr file to parse from.</dd>
-<dd><code>chromosome</code> - the chromosome to configure.</dd>
-<dd><code>resources</code> - the experiment resources.</dd>
-</dl>
-</li>
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-<h4>save</h4>
-<pre>public static&nbsp;void&nbsp;save(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)</pre>
-<div class="block">Writes a chromosome into the specified .chr file.
- <br><br>
- The file is written in the standard .chr format and can
- be read by the original CGP implementation.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the file to write to.</dd>
-<dd><code>chromosome</code> - the chromosome to save.</dd>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
-</dl>
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-<pre>public static&nbsp;void&nbsp;print(<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)</pre>
-<div class="block">Writes a chromosome to the console in .chr format. Note
- that, if using a GUI console, that console must be flushed for the
- output to appear.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>chromosome</code> - the chromosome to save.</dd>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
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- .par file.</div>
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-     <a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a>&nbsp;functionSet,
-     <a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
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-                         <a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Reads the specified file and attempts to enable 
- and disable the functions in the FunctionSet 
- accordingly.
- <br><br>
- Standard CGP .par files do not contain enough information
- to determine if they match the currently selected function set.
- For this reason, the parser assumes the function set is correct
- and treats functions by their index rather than their name. Any
- index outside the bounds of the function set is ignored and a
- warning message is printed once parsing is complete.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the .par file to parse.</dd>
-<dd><code>functionSet</code> - the function set whose functions should be modified.</dd>
-<dd><code>resources</code> - used for printing console messages.</dd>
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-<div class="subTitle">jcgp.backend.parsers</div>
-<h2 title="Class ParameterParser" class="title">Class ParameterParser</h2>
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-extends java.lang.Object</pre>
-<div class="block">Contains a static method for parsing parameters from a
- .par file.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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-     <a href="../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</code>
-<div class="block">Parses the parameters from a specified CGP parameter file and
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-<div class="block">Parses the parameters from a specified CGP parameter file and
- modifies the experiment resources appropriately. 
- <br><br>
- CGP .par files do not follow a very strict convention, so this
- parser does its best to cope with format irregularities. Parsing
- works even if the parameters are in the wrong order, and unknown
- parameters are simply ignored.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the .par file to parse.</dd>
-<dd><code>resources</code> - a reference to the resources object that must be modified.</dd>
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-</li>
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-<li>java.lang.Object</li>
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-<pre>public abstract class <span class="typeNameLabel">TestCaseParser</span>
-extends java.lang.Object</pre>
-<div class="block">Contains a static method for parsing values from a
- CGP problem data file. The actual file extension
- varies from problem to problem, and is therefore
- defined in the experiment's Problem instance.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/parsers/TestCaseParser.html#parse-java.io.File-jcgp.backend.modules.problem.TestCaseProblem-jcgp.backend.resources.ModifiableResources-">parse</a></span>(java.io.File&nbsp;file,
-     <a href="../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;?&gt;&nbsp;problem,
-     <a href="../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</code>
-<div class="block">Sets the number of inputs and outputs in the resources
- to match the given file, and parses each test case
- from the file into the specified problem.</div>
-</td>
-</tr>
-</table>
-<ul class="blockList">
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-<!--   -->
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-<code>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
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-<pre>public&nbsp;TestCaseParser()</pre>
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-<h4>parse</h4>
-<pre>public static&nbsp;void&nbsp;parse(java.io.File&nbsp;file,
-                         <a href="../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;?&gt;&nbsp;problem,
-                         <a href="../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</pre>
-<div class="block">Sets the number of inputs and outputs in the resources
- to match the given file, and parses each test case
- from the file into the specified problem.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>file</code> - the problem file to parse.</dd>
-<dd><code>problem</code> - the problem into which to parse the problem data.</dd>
-<dd><code>resources</code> - a modifiable reference to the experiment's resources</dd>
-</dl>
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deleted file mode 100644
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-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/parsers/ChromosomeParser.html" title="class in jcgp.backend.parsers">ChromosomeParser</a></td>
-<td class="colLast">
-<div class="block">This class contains a method for parsing .chr files and another
- for writing .chr files from given chromosomes.</div>
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-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/parsers/FunctionParser.html" title="class in jcgp.backend.parsers">FunctionParser</a></td>
-<td class="colLast">
-<div class="block">Contains a static method for parsing functions from a
- .par file.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/parsers/ParameterParser.html" title="class in jcgp.backend.parsers">ParameterParser</a></td>
-<td class="colLast">
-<div class="block">Contains a static method for parsing parameters from a
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-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/parsers/TestCaseParser.html" title="class in jcgp.backend.parsers">TestCaseParser</a></td>
-<td class="colLast">
-<div class="block">Contains a static method for parsing values from a
- CGP problem data file.</div>
-</td>
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-<li type="circle">jcgp.backend.parsers.<a href="../../../jcgp/backend/parsers/ChromosomeParser.html" title="class in jcgp.backend.parsers"><span class="typeNameLink">ChromosomeParser</span></a></li>
-<li type="circle">jcgp.backend.parsers.<a href="../../../jcgp/backend/parsers/FunctionParser.html" title="class in jcgp.backend.parsers"><span class="typeNameLink">FunctionParser</span></a></li>
-<li type="circle">jcgp.backend.parsers.<a href="../../../jcgp/backend/parsers/ParameterParser.html" title="class in jcgp.backend.parsers"><span class="typeNameLink">ParameterParser</span></a></li>
-<li type="circle">jcgp.backend.parsers.<a href="../../../jcgp/backend/parsers/TestCaseParser.html" title="class in jcgp.backend.parsers"><span class="typeNameLink">TestCaseParser</span></a></li>
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deleted file mode 100644
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--- a/doc/jcgp/backend/parsers/package-use.html
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diff --git a/doc/jcgp/backend/population/Chromosome.html b/doc/jcgp/backend/population/Chromosome.html
deleted file mode 100644
index bdd49f4..0000000
--- a/doc/jcgp/backend/population/Chromosome.html
+++ /dev/null
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-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.population</div>
-<h2 title="Class Chromosome" class="title">Class Chromosome</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.population.Chromosome</li>
-</ul>
-</li>
-</ul>
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>All Implemented Interfaces:</dt>
-<dd>java.lang.Comparable&lt;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&gt;</dd>
-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">Chromosome</span>
-extends java.lang.Object
-implements java.lang.Comparable&lt;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&gt;</pre>
-<div class="block">This class encapsulates a CGP chromosome.
- <br><br>
- A chromosome contains a matrix of nodes and arrays of inputs and outputs.
- These elements are all interconnected, and actually form the chromosome
- network itself. Individual nodes can be retrieved using <code>getNode()</code>
- which requires the row and column to be specified. The same works for
- inputs and outputs using the associated getters, in which case only the
- index is necessary.
- <br><br>
- In evolutionary computation it is often necessary to make copies of 
- chromosomes; this can be accomplished in JCGP in two ways. The recommended
- way to do this is using <code>copyChromosome()</code> in <code>Population</code>, but alternatively
- it can be done by using the <code>Chromosome</code> copy constructor and specifying the
- object to copy from, or by using the <code>copyGenes()</code> method. 
- <br><br>
- To illustrate this, given two chromosomes, chr1 and chr2, the following code:
- <br><br>
- <code>
- chr1.copyGenes(chr2);
- </code><br><br>
- will modify all of chr1's connections and functions to match those of chr2, without
- creating a new instance. In contrast, 
- <br><br>
- <code>
- chr1 = new Chromosome(chr2);
- </code><br><br>
- creates a new instance of chromosome which is identical to chr2 and assigns it to chr1,
- meaning any old references to chr1 that are not updated will still refer to a chromosome
- that is not identical to chr2. In practice, the most reliable way is to use the copy method
- in <code>Population</code>. Assuming chr1 and chr2 are indexed 1 and 2 in <code>population</code> respectively,
- <br><br>
- population.copyChromosome(2, 1);
- <br><br>
- will copy chr2 into chr1 without creating new instances or requiring access to the underlying
- chromosome array. <code>Chromosome</code> offers a variety of methods to compare chromosomes as well, 
- such as <code>compareGenesTo()</code> and <code>compareActiveGenesTo()</code>. <code>Comparable</code> is implemented
- to compare fitness value, meaning <code>compareTo()</code> returns a value depending the relative fitness
- of the compared chromosomes.
- <br><br>
- In order to set the chromosome's input values for decoding, <code>setInputs()</code> should be used. A few 
- utility methods are provided in order to retrieve random elements from the chromosome, which are used
- internally to initialise with random connections but also externally by mutators when performing 
- mutations.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
-</div>
-<div class="summary">
-<ul class="blockList">
-<li class="blockList">
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->
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-<h3>Constructor Summary</h3>
-<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><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="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#Chromosome-jcgp.backend.resources.Resources-">Chromosome</a></span>(<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Initialise a chromosome with the specified parameters.</div>
-</td>
-</tr>
-</table>
-</li>
-</ul>
-<!-- ========== METHOD SUMMARY =========== -->
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-<li class="blockList"><a name="method.summary">
-<!--   -->
-</a>
-<h3>Method Summary</h3>
-<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><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 id="i1" class="rowColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><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 id="i2" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><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 id="i3" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
-<tr id="i4" 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"><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>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getFitness--">getFitness</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i6" 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"><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>
-<tr id="i7" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></code></td>
-<td class="colLast"><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>
-<tr id="i8" 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"><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>
-<tr id="i9" 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"><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 id="i10" 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"><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 id="i11" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getRandomMutable--">getRandomMutable</a></span>()</code>
-<div class="block">This method is useful for mutating chromosomes.</div>
-</td>
-</tr>
-<tr id="i12" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getResources--">getResources</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i13" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#printNodes--">printNodes</a></span>()</code>
-<div class="block">Iterates through the nodes and prints all connections and functions.</div>
-</td>
-</tr>
-<tr id="i14" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#recomputeActiveNodes--">recomputeActiveNodes</a></span>()</code>
-<div class="block">This causes the list of active nodes to be recomputed lazily (once it is actually requested).</div>
-</td>
-</tr>
-<tr id="i15" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#reinitialiseConnections--">reinitialiseConnections</a></span>()</code>
-<div class="block">Sets random connections and functions across the entire
- chromosome.</div>
-</td>
-</tr>
-<tr id="i16" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#setFitness-double-">setFitness</a></span>(double&nbsp;newFitness)</code>
-<div class="block">Sets the fitness of the chromosome.</div>
-</td>
-</tr>
-<tr id="i17" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#setInputs-java.lang.Object...-">setInputs</a></span>(java.lang.Object...&nbsp;values)</code>
-<div class="block">Loops through the inputs and sets the specified values,
- so that evaluations can be performed.</div>
-</td>
-</tr>
-</table>
-<ul class="blockList">
-<li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
-<!--   -->
-</a>
-<h3>Methods inherited from class&nbsp;java.lang.Object</h3>
-<code>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<div class="details">
-<ul class="blockList">
-<li class="blockList">
-<!-- ========= CONSTRUCTOR DETAIL ======== -->
-<ul class="blockList">
-<li class="blockList"><a name="constructor.detail">
-<!--   -->
-</a>
-<h3>Constructor Detail</h3>
-<a name="Chromosome-jcgp.backend.resources.Resources-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>Chromosome</h4>
-<pre>public&nbsp;Chromosome(<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Initialise a chromosome with the specified parameters. Random valid connections
- are created upon initialisation.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - the experiment's resources.</dd>
-</dl>
-</li>
-</ul>
-<a name="Chromosome-jcgp.backend.population.Chromosome-">
-<!--   -->
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-<ul class="blockListLast">
-<li class="blockList">
-<h4>Chromosome</h4>
-<pre>public&nbsp;Chromosome(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</pre>
-<div class="block">Copy constructor.
- 
- Initialise a new chromosome with the exact same connections as a given instance of Chromosome.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>clone</code> - the chromosome to be copied.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-<!-- ============ METHOD DETAIL ========== -->
-<ul class="blockList">
-<li class="blockList"><a name="method.detail">
-<!--   -->
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-<h3>Method Detail</h3>
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-<!--   -->
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-<li class="blockList">
-<h4>reinitialiseConnections</h4>
-<pre>public&nbsp;void&nbsp;reinitialiseConnections()</pre>
-<div class="block">Sets random connections and functions across the entire
- chromosome. This method can be used more than once for
- each instance, if entirely random chromosomes are desired.</div>
-</li>
-</ul>
-<a name="copyGenes-jcgp.backend.population.Chromosome-">
-<!--   -->
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-<pre>public&nbsp;void&nbsp;copyGenes(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</pre>
-<div class="block">Creates a deep copy of the specified chromosome in the
- this instance. In practice, this iterates through the
- entire chromosome making equivalent connections and
- setting functions to the same values as those in the
- specified chromosome. It also sets the fitness of the
- copy to the same value as the original.
- <br>
- It is assumed that both chromosomes have the same 
- topology; while this method will still run if that is not
- the case, the effects might be undesirable and null pointer
- access might occur.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>clone</code> - the chromosome to clone.</dd>
-</dl>
-</li>
-</ul>
-<a name="getInput-int-">
-<!--   -->
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-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a>&nbsp;getInput(int&nbsp;index)</pre>
-<div class="block">Returns a reference to the indexed input.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the input index.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the input reference.</dd>
-</dl>
-</li>
-</ul>
-<a name="getNode-int-int-">
-<!--   -->
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-<h4>getNode</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&nbsp;getNode(int&nbsp;row,
-                    int&nbsp;column)</pre>
-<div class="block">Returns a reference to any node, addressed by row and column.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>row</code> - the row of the node.</dd>
-<dd><code>column</code> - the column of the node.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the addressed node.</dd>
-</dl>
-</li>
-</ul>
-<a name="getOutput-int-">
-<!--   -->
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-<h4>getOutput</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a>&nbsp;getOutput(int&nbsp;index)</pre>
-<div class="block">Returns a reference to the indexed output.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the output index.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the output reference.</dd>
-</dl>
-</li>
-</ul>
-<a name="getFitness--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getFitness</h4>
-<pre>public&nbsp;double&nbsp;getFitness()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the fitness of the chromosome.</dd>
-</dl>
-</li>
-</ul>
-<a name="setFitness-double-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>setFitness</h4>
-<pre>public&nbsp;void&nbsp;setFitness(double&nbsp;newFitness)</pre>
-<div class="block">Sets the fitness of the chromosome. This method
- should be used by the experiment problem when the
- population is evaluated in order to assign a fitness
- to each individual.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>newFitness</code> - the fitness to assign.</dd>
-</dl>
-</li>
-</ul>
-<a name="setInputs-java.lang.Object...-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>setInputs</h4>
-<pre>public&nbsp;void&nbsp;setInputs(java.lang.Object...&nbsp;values)</pre>
-<div class="block">Loops through the inputs and sets the specified values,
- so that evaluations can be performed. If the number of
- elements in the array of values does not match the
- number of inputs exactly, an exception is thrown.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>values</code> - the values the input should take.</dd>
-</dl>
-</li>
-</ul>
-<a name="getRandomMutable--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getRandomMutable</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;getRandomMutable()</pre>
-<div class="block">This method is useful for mutating chromosomes. It returns any
- random <code>Mutable</code> out of the chromosome with equal
- probability.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a random element that can be mutated - node or output.</dd>
-</dl>
-</li>
-</ul>
-<a name="getRandomConnection-int-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getRandomConnection</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;getRandomConnection(int&nbsp;column)</pre>
-<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>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>column</code> - the column to use as reference.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a random connection.</dd>
-</dl>
-</li>
-</ul>
-<a name="getRandomConnection--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getRandomConnection</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;getRandomConnection()</pre>
-<div class="block">This method will pick a completely random connection, independently
- of levels back, including inputs. It is useful for setting outputs.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a random connection regardless of levels back.</dd>
-</dl>
-</li>
-</ul>
-<a name="recomputeActiveNodes--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>recomputeActiveNodes</h4>
-<pre>public&nbsp;void&nbsp;recomputeActiveNodes()</pre>
-<div class="block">This causes the list of active nodes to be recomputed lazily (once it is actually requested).</div>
-</li>
-</ul>
-<a name="getActiveNodes--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getActiveNodes</h4>
-<pre>public&nbsp;java.util.ArrayList&lt;<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&gt;&nbsp;getActiveNodes()</pre>
-<div class="block">This method computes a list of active nodes (if necessary) and returns it.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the list of active nodes.</dd>
-</dl>
-</li>
-</ul>
-<a name="compareGenesTo-jcgp.backend.population.Chromosome-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>compareGenesTo</h4>
-<pre>public&nbsp;boolean&nbsp;compareGenesTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</pre>
-<div class="block">Performs a deep comparison between this chromosome and the provided one.
- This is done on a gene-by-gene basis.
- 
- This method returns true if and only if:
- <ul>
- <li>the chromosomes being compared are not the same instance;</li>
- <li>the connections of the compared chromosomes are not the same instance;</li>
- <li>the grid position of the chromosome's elements are the same;</li>
- </ul>
- <br><br>
- The relationship computed by this method is:
- <ul>
- <li>symmetric: a.copyOf(b) == b.copyOf(a);</li>
- <li>not reflexive: a.copyOf(a) returns false;</li>
- <li>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.</li>
- </ul></div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>chromosome</code> - the chromosome to compare to.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if it is a copy of this chromosome, but not the same chromosome.</dd>
-</dl>
-</li>
-</ul>
-<a name="compareActiveGenesTo-jcgp.backend.population.Chromosome-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>compareActiveGenesTo</h4>
-<pre>public&nbsp;boolean&nbsp;compareActiveGenesTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</pre>
-<div class="block">Does the same as <code>compareGenesto()</code> but only looks
- at the active portion of the chromosome.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>chromosome</code> - the chromosome to compare to.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if the two active portions are identical.</dd>
-</dl>
-</li>
-</ul>
-<a name="printNodes--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>printNodes</h4>
-<pre>public&nbsp;void&nbsp;printNodes()</pre>
-<div class="block">Iterates through the nodes and prints all connections and functions.
- This is intended for debugging purposes only and does not print to the
- GUI console.</div>
-</li>
-</ul>
-<a name="getResources--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getResources</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;getResources()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a reference to the resources based on which the chromosome was built.</dd>
-</dl>
-</li>
-</ul>
-<a name="compareTo-jcgp.backend.population.Chromosome-">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>compareTo</h4>
-<pre>public&nbsp;int&nbsp;compareTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;o)</pre>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code>compareTo</code>&nbsp;in interface&nbsp;<code>java.lang.Comparable&lt;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&gt;</code></dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
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-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
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-</div>
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diff --git a/doc/jcgp/backend/population/Connection.html b/doc/jcgp/backend/population/Connection.html
deleted file mode 100644
index 1e51eda..0000000
--- a/doc/jcgp/backend/population/Connection.html
+++ /dev/null
@@ -1,249 +0,0 @@
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-<!-- NewPage -->
-<html lang="en">
-<head>
-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:32 BST 2014 -->
-<title>Connection</title>
-<meta name="date" content="2014-05-22">
-<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="Connection";
-        }
-    }
-    catch(err) {
-    }
-//-->
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-<li><a href="package-summary.html">Package</a></li>
-<li class="navBarCell1Rev">Class</li>
-<li><a href="class-use/Connection.html">Use</a></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>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
-<li><a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
-</ul>
-<ul class="navList">
-<li><a href="../../../index.html?jcgp/backend/population/Connection.html" target="_top">Frames</a></li>
-<li><a href="Connection.html" target="_top">No&nbsp;Frames</a></li>
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-</ul>
-<ul class="subNavList">
-<li>Detail:&nbsp;</li>
-<li>Field&nbsp;|&nbsp;</li>
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-<!--   -->
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.population</div>
-<h2 title="Interface Connection" class="title">Interface Connection</h2>
-</div>
-<div class="contentContainer">
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>All Known Implementing Classes:</dt>
-<dd><a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a>, <a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public interface <span class="typeNameLabel">Connection</span></pre>
-<div class="block"><code>Connection</code> declares the expected behaviour of any
- part of a chromosome that can be connected to, specifically
- nodes or inputs. Outputs are not connections since they 
- mark the end of chromosome paths.
- <br><br>
- This interface provides a way to deal with connections
- generically without having to specify whether they are nodes
- or inputs. In this way a random connection can be picked and
- dealt with more easily, facilitating mutations.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
-</div>
-<div class="summary">
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-<!-- ========== METHOD SUMMARY =========== -->
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t3" class="tableTab"><span><a href="javascript:show(4);">Abstract Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>java.lang.Object</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Connection.html#getValue--">getValue</a></span>()</code>
-<div class="block">Compute and return the value of this connection.</div>
-</td>
-</tr>
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-</li>
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-<h4>getValue</h4>
-<pre>java.lang.Object&nbsp;getValue()</pre>
-<div class="block">Compute and return the value of this connection. In
- the case of inputs no computation is necessary, this
- simply returns the value the input is set to. In the
- case of nodes, the value is computed based on the
- node's function and the value of its own connections.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the connection's value.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<li class="navBarCell1Rev">Class</li>
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-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
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-<li><a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
-</ul>
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-<li><a href="../../../index.html?jcgp/backend/population/Connection.html" target="_top">Frames</a></li>
-<li><a href="Connection.html" target="_top">No&nbsp;Frames</a></li>
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diff --git a/doc/jcgp/backend/population/Input.html b/doc/jcgp/backend/population/Input.html
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- They do not have connections and instead provide a
- starting point for the chromosome's active paths.</div>
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-<dt><span class="simpleTagLabel">Author:</span></dt>
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-<div class="block">Compute and return the value of this connection. In
- the case of inputs no computation is necessary, this
- simply returns the value the input is set to. In the
- case of nodes, the value is computed based on the
- node's function and the value of its own connections.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
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-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
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diff --git a/doc/jcgp/backend/population/Mutable.html b/doc/jcgp/backend/population/Mutable.html
deleted file mode 100644
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+++ /dev/null
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-//-->
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-<div class="subTitle">jcgp.backend.population</div>
-<h2 title="Interface Mutable" class="title">Interface Mutable</h2>
-</div>
-<div class="contentContainer">
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>All Known Implementing Classes:</dt>
-<dd><a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>, <a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public interface <span class="typeNameLabel">Mutable</span></pre>
-<div class="block"><code>Mutable</code> declares the expected behaviour of any
- part of a chromosome that is mutable, more specifically
- nodes or outputs. Inputs are not mutable since they don't have
- connections or functions.
- <br><br>
- This interface provides a way to deal with mutable elements
- generically without having to specify whether they are nodes
- or outputs. When mutating a mutable, <code>mutate()</code> is guaranteed
- to perform a fair mutation.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
-</div>
-<div class="summary">
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-<!-- ========== METHOD SUMMARY =========== -->
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-</a>
-<h3>Method Summary</h3>
-<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t3" class="tableTab"><span><a href="javascript:show(4);">Abstract Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></span>(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</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>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Mutable.html#mutate--">mutate</a></span>()</code>
-<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.</div>
-</td>
-</tr>
-</table>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<div class="details">
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-<!-- ============ METHOD DETAIL ========== -->
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-<ul class="blockList">
-<li class="blockList">
-<h4>mutate</h4>
-<pre>void&nbsp;mutate()</pre>
-<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.
- <br><br>
- In the case of nodes, this chooses to mutate a function or connection
- fairly, and carries out the required mutation by using the node's own
- reference to chromosome.
- <br><br>
- In the case of outputs, this simply picks a random connection to serve
- as the source - any connection is allowed.</div>
-</li>
-</ul>
-<a name="copyOf-jcgp.backend.population.Mutable-">
-<!--   -->
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-<h4>copyOf</h4>
-<pre>boolean&nbsp;copyOf(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;element)</pre>
-<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:
- <ul>
- <li>the elements being compared are not the same instance;</li>
- <li>the connections of the compared elements are not the same instance;</li>
- <li>the elements have the same function (in the case of Node);</li>
- <li>the grid position of the elements themselves are the same;</li>
- <li>the grid position of all equivalent connections are the same;</li>
- </ul>
- <br><br>
- The relationship computed by this method is:
- <ul>
- <li>symmetric: a.copyOf(b) == b.copyOf(a);</li>
- <li>not reflexive: a.copyOf(a) returns false;</li>
- <li>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.</li>
- </ul></div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>element</code> - the mutable element to compare to.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if <code>element</code> is a copy of this element.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
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-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
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diff --git a/doc/jcgp/backend/population/MutableElement.html b/doc/jcgp/backend/population/MutableElement.html
deleted file mode 100644
index d3a6b6d..0000000
--- a/doc/jcgp/backend/population/MutableElement.html
+++ /dev/null
@@ -1,306 +0,0 @@
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-<!-- NewPage -->
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-<head>
-<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:06 BST 2014 -->
-<title>Mutable</title>
-<meta name="date" content="2014-05-06">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
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-</head>
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-<script type="text/javascript"><!--
-    try {
-        if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Mutable";
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-    }
-    catch(err) {
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-//-->
-var methods = {"i0":6,"i1":6};
-var tabs = {65535:["t0","All Methods"],2:["t2","Instance Methods"],4:["t3","Abstract Methods"]};
-var altColor = "altColor";
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-<li><a href="../../../deprecated-list.html">Deprecated</a></li>
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-</ul>
-</div>
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-<div class="subTitle">jcgp.backend.population</div>
-<h2 title="Interface Mutable" class="title">Interface Mutable</h2>
-</div>
-<div class="contentContainer">
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>All Known Implementing Classes:</dt>
-<dd><a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>, <a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public interface <span class="typeNameLabel">Mutable</span></pre>
-<div class="block"><code>Mutable</code> declares the expected behaviour of any
- part of a chromosome that is mutable, more specifically
- nodes or outputs. Inputs are not mutable since they don't have
- connections or functions.
- <br><br>
- This interface provides a way to deal with mutable elements
- generically without having to specify whether they are nodes
- or outputs. In this way a random mutable element can be picked and
- dealt with more easily, facilitating mutations.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
-</div>
-<div class="summary">
-<ul class="blockList">
-<li class="blockList">
-<!-- ========== METHOD SUMMARY =========== -->
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-<!--   -->
-</a>
-<h3>Method Summary</h3>
-<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t3" class="tableTab"><span><a href="javascript:show(4);">Abstract Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></span>(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</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>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Mutable.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>
-</table>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<div class="details">
-<ul class="blockList">
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-<a name="setConnection-int-jcgp.backend.population.Connection-">
-<!--   -->
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-<ul class="blockList">
-<li class="blockList">
-<h4>setConnection</h4>
-<pre>void&nbsp;setConnection(int&nbsp;index,
-                   <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</pre>
-<div class="block">This method sets the indexed connection to the specified new connection.
- Implementing classes may choose to ignore the given index (such as in the
- case of outputs, which only have one connection).</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the connection index to set.</dd>
-<dd><code>newConnection</code> - the chromosome element to connect to.</dd>
-</dl>
-</li>
-</ul>
-<a name="copyOf-jcgp.backend.population.Mutable-">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>copyOf</h4>
-<pre>boolean&nbsp;copyOf(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;element)</pre>
-<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:
- <ul>
- <li>the elements being compared are not the same instance;</li>
- <li>the connections of the compared elements are not the same instance;</li>
- <li>the elements have the same function (in the case of Node);</li>
- <li>the grid position of the elements themselves are the same;</li>
- <li>the grid position of all equivalent connections are the same;</li>
- </ul>
- <br><br>
- The relationship computed by this method is:
- <ul>
- <li>symmetric: a.copyOf(b) == b.copyOf(a);</li>
- <li>not reflexive: a.copyOf(a) returns false;</li>
- <li>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.</li>
- </ul></div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>element</code> - the mutable element to compare to.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if <code>element</code> is a copy of this element.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<!--   -->
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diff --git a/doc/jcgp/backend/population/Node.html b/doc/jcgp/backend/population/Node.html
deleted file mode 100644
index 12e3eea..0000000
--- a/doc/jcgp/backend/population/Node.html
+++ /dev/null
@@ -1,570 +0,0 @@
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-<!-- NewPage -->
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-<head>
-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:32 BST 2014 -->
-<title>Node</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../script.js"></script>
-</head>
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-<script type="text/javascript"><!--
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-<li><a href="package-summary.html">Package</a></li>
-<li class="navBarCell1Rev">Class</li>
-<li><a href="class-use/Node.html">Use</a></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>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
-<li><a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
-</ul>
-<ul class="navList">
-<li><a href="../../../index.html?jcgp/backend/population/Node.html" target="_top">Frames</a></li>
-<li><a href="Node.html" target="_top">No&nbsp;Frames</a></li>
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-<!--   -->
-</a></div>
-<!-- ========= END OF TOP NAVBAR ========= -->
-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.population</div>
-<h2 title="Class Node" class="title">Class Node</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.population.Node</li>
-</ul>
-</li>
-</ul>
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>All Implemented Interfaces:</dt>
-<dd><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>, <a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">Node</span>
-extends java.lang.Object
-implements <a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>, <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></pre>
-<div class="block">Nodes make up the main part of the chromosome, 
- where the actual functions are evolved. Each node
- contains a function and a number of connections.
- The node outputs the result of performing its function
- on the values of its connections. Nodes therefore
- implement both <code>Mutable</code> and <code>Connection</code>
- since they can be mutated but also connected to. 
- Nodes are constructed with a fixed number of connections
- (determined by the maximum arity of the function set)
- and must be reinstantiated if the experiment arity
- changes.
- <br><br>
- When mutating a node, it is easiest to use <code>mutate()</code>.
- Alternatively, you may also perform a specific mutation using
- <code>setConnection(...)</code> and <code>setFunction(...)</code>.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#Node-jcgp.backend.population.Chromosome-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)</code>
-<div class="block">Constructs a new instance of <code>Node</code> with the
- specified parameters.</div>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></span>(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</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>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#getColumn--">getColumn</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i2" 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"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#getConnection-int-">getConnection</a></span>(int&nbsp;index)</code>&nbsp;</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#getFunction--">getFunction</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#getRow--">getRow</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>java.lang.Object</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#getValue--">getValue</a></span>()</code>
-<div class="block">Compute and return the value of this connection.</div>
-</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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 id="i7" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#mutate--">mutate</a></span>()</code>
-<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.</div>
-</td>
-</tr>
-<tr id="i8" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
-<div class="block">This method sets the indexed connection to the specified new connection.</div>
-</td>
-</tr>
-<tr id="i9" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#setFunction-jcgp.backend.function.Function-">setFunction</a></span>(<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;newFunction)</code>
-<div class="block">Sets the node function.</div>
-</td>
-</tr>
-<tr id="i10" class="altColor">
-<td class="colFirst"><code>java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#toString--">toString</a></span>()</code>&nbsp;</td>
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-<code>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</code></li>
-</ul>
-</li>
-</ul>
-</li>
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-<h4>Node</h4>
-<pre>public&nbsp;Node(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
-            int&nbsp;row,
-            int&nbsp;column)</pre>
-<div class="block">Constructs a new instance of <code>Node</code> with the
- specified parameters. Nodes must contain their
- own row and column for ease of copying.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>chromosome</code> - the chromosome this node belongs to.</dd>
-<dd><code>row</code> - the node's row.</dd>
-<dd><code>column</code> - the node's column.</dd>
-</dl>
-</li>
-</ul>
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-<h4>initialise</h4>
-<pre>public&nbsp;void&nbsp;initialise(<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)</pre>
-<div class="block">Initialises the node with the specified values.
- The number of connections passed as argument must
- be exactly the same as the experiment arity, or 
- an <code>IllegalArgumentException</code> will be thrown.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>newFunction</code> - the node function to set.</dd>
-<dd><code>newConnections</code> - the node connections to set.</dd>
-</dl>
-</li>
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-<!--   -->
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-<h4>getColumn</h4>
-<pre>public&nbsp;int&nbsp;getColumn()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>this node's column.</dd>
-</dl>
-</li>
-</ul>
-<a name="getRow--">
-<!--   -->
-</a>
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-<h4>getRow</h4>
-<pre>public&nbsp;int&nbsp;getRow()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>this node's row.</dd>
-</dl>
-</li>
-</ul>
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-<!--   -->
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-<ul class="blockList">
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-<h4>getFunction</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;getFunction()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>this node's function.</dd>
-</dl>
-</li>
-</ul>
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-<!--   -->
-</a>
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-<h4>setFunction</h4>
-<pre>public&nbsp;void&nbsp;setFunction(<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;newFunction)</pre>
-<div class="block">Sets the node function.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>newFunction</code> - the new function to set.</dd>
-</dl>
-</li>
-</ul>
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-<!--   -->
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-<h4>getConnection</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;getConnection(int&nbsp;index)</pre>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the connection to return.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the indexed connection.</dd>
-</dl>
-</li>
-</ul>
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-<!--   -->
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-<pre>public&nbsp;void&nbsp;setConnection(int&nbsp;index,
-                          <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</pre>
-<div class="block">This method sets the indexed connection to the specified new connection.
- If the given connection is null or disrespects levels back, it is discarded
- and no connections are changed.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the connection index to set.</dd>
-<dd><code>newConnection</code> - the <code>Connection</code> to connect to.</dd>
-</dl>
-</li>
-</ul>
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-<pre>public&nbsp;boolean&nbsp;copyOf(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;element)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">Mutable</a></code></span></div>
-<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:
- <ul>
- <li>the elements being compared are not the same instance;</li>
- <li>the connections of the compared elements are not the same instance;</li>
- <li>the elements have the same function (in the case of Node);</li>
- <li>the grid position of the elements themselves are the same;</li>
- <li>the grid position of all equivalent connections are the same;</li>
- </ul>
- <br><br>
- The relationship computed by this method is:
- <ul>
- <li>symmetric: a.copyOf(b) == b.copyOf(a);</li>
- <li>not reflexive: a.copyOf(a) returns false;</li>
- <li>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.</li>
- </ul></div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>element</code> - the mutable element to compare to.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if <code>element</code> is a copy of this element.</dd>
-</dl>
-</li>
-</ul>
-<a name="getValue--">
-<!--   -->
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-<pre>public&nbsp;java.lang.Object&nbsp;getValue()</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../jcgp/backend/population/Connection.html#getValue--">Connection</a></code></span></div>
-<div class="block">Compute and return the value of this connection. In
- the case of inputs no computation is necessary, this
- simply returns the value the input is set to. In the
- case of nodes, the value is computed based on the
- node's function and the value of its own connections.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../jcgp/backend/population/Connection.html#getValue--">getValue</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the connection's value.</dd>
-</dl>
-</li>
-</ul>
-<a name="mutate--">
-<!--   -->
-</a>
-<ul class="blockList">
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-<h4>mutate</h4>
-<pre>public&nbsp;void&nbsp;mutate()</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html#mutate--">Mutable</a></code></span></div>
-<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.
- <br><br>
- In the case of nodes, this chooses to mutate a function or connection
- fairly, and carries out the required mutation by using the node's own
- reference to chromosome.
- <br><br>
- In the case of outputs, this simply picks a random connection to serve
- as the source - any connection is allowed.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../jcgp/backend/population/Mutable.html#mutate--">mutate</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></dd>
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-<pre>public&nbsp;java.lang.String&nbsp;toString()</pre>
-<dl>
-<dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
-<dd><code>toString</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
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diff --git a/doc/jcgp/backend/population/Output.html b/doc/jcgp/backend/population/Output.html
deleted file mode 100644
index 98897d4..0000000
--- a/doc/jcgp/backend/population/Output.html
+++ /dev/null
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:32 BST 2014 -->
-<title>Output</title>
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-<li><a href="package-summary.html">Package</a></li>
-<li class="navBarCell1Rev">Class</li>
-<li><a href="class-use/Output.html">Use</a></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>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
-<li><a href="../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
-</ul>
-<ul class="navList">
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-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.population</div>
-<h2 title="Class Output" class="title">Class Output</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
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-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">Output</span>
-extends java.lang.Object
-implements <a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></pre>
-<div class="block">This is a chromosome output. Outputs are a special
- type of mutable element with a single connection. It
- returns the value of its single connection, but it 
- may not be connected to - it terminates a chromosome
- active connection path. 
- <br><br>
- When mutating an output, it is easiest to use <code>mutate()</code>.
- Alternatively, you may also perform a specific mutation using
- <code>setSource(...)</code>.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><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 
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>java.lang.Object</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Output.html#calculate--">calculate</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Output.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></span>(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;m)</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>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
-<div class="block">Calls <code>getActive(...)</code> on this output's
- source.</div>
-</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Output.html#getIndex--">getIndex</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" 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"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Output.html#getSource--">getSource</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Output.html#mutate--">mutate</a></span>()</code>
-<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.</div>
-</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Output.html#setSource-jcgp.backend.population.Connection-">setSource</a></span>(<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 output source to the specified connection.</div>
-</td>
-</tr>
-<tr id="i7" class="rowColor">
-<td class="colFirst"><code>java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Output.html#toString--">toString</a></span>()</code>&nbsp;</td>
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-<!--   -->
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-<h3>Methods inherited from class&nbsp;java.lang.Object</h3>
-<code>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</code></li>
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-<pre>public&nbsp;Output(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
-              int&nbsp;index)</pre>
-<div class="block">Makes a new instance of <code>Output</code> with the 
- specified arguments.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>chromosome</code> - the chromosome this output belongs to.</dd>
-<dd><code>index</code> - the output index.</dd>
-</dl>
-</li>
-</ul>
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-</ul>
-<!-- ============ METHOD DETAIL ========== -->
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-<!--   -->
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-<li class="blockList">
-<h4>calculate</h4>
-<pre>public&nbsp;java.lang.Object&nbsp;calculate()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the value of the output's source.</dd>
-</dl>
-</li>
-</ul>
-<a name="getIndex--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getIndex</h4>
-<pre>public&nbsp;int&nbsp;getIndex()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>this output's index.</dd>
-</dl>
-</li>
-</ul>
-<a name="setSource-jcgp.backend.population.Connection-">
-<!--   -->
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-<pre>public&nbsp;void&nbsp;setSource(<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</pre>
-<div class="block">This method sets the output source to the specified connection.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>newConnection</code> - the <code>Connection</code> to connect to.</dd>
-</dl>
-</li>
-</ul>
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-<!--   -->
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-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;getSource()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the source of this output's value.</dd>
-</dl>
-</li>
-</ul>
-<a name="getActiveNodes-java.util.ArrayList-">
-<!--   -->
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-<pre>public&nbsp;void&nbsp;getActiveNodes(java.util.ArrayList&lt;<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&gt;&nbsp;activeNodes)</pre>
-<div class="block">Calls <code>getActive(...)</code> on this output's
- source. This kicks off a recursive process whereby
- all nodes connected to this output are added to the
- specified list of nodes. This is used to create a
- list of all active nodes.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>activeNodes</code> - the list to add all active nodes to.</dd>
-</dl>
-</li>
-</ul>
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-<!--   -->
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-<pre>public&nbsp;boolean&nbsp;copyOf(<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;m)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">Mutable</a></code></span></div>
-<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:
- <ul>
- <li>the elements being compared are not the same instance;</li>
- <li>the connections of the compared elements are not the same instance;</li>
- <li>the elements have the same function (in the case of Node);</li>
- <li>the grid position of the elements themselves are the same;</li>
- <li>the grid position of all equivalent connections are the same;</li>
- </ul>
- <br><br>
- The relationship computed by this method is:
- <ul>
- <li>symmetric: a.copyOf(b) == b.copyOf(a);</li>
- <li>not reflexive: a.copyOf(a) returns false;</li>
- <li>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.</li>
- </ul></div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>m</code> - the mutable element to compare to.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if <code>element</code> is a copy of this element.</dd>
-</dl>
-</li>
-</ul>
-<a name="mutate--">
-<!--   -->
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-<pre>public&nbsp;void&nbsp;mutate()</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html#mutate--">Mutable</a></code></span></div>
-<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.
- <br><br>
- In the case of nodes, this chooses to mutate a function or connection
- fairly, and carries out the required mutation by using the node's own
- reference to chromosome.
- <br><br>
- In the case of outputs, this simply picks a random connection to serve
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-<dl>
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diff --git a/doc/jcgp/backend/population/Population.html b/doc/jcgp/backend/population/Population.html
deleted file mode 100644
index 36e0af4..0000000
--- a/doc/jcgp/backend/population/Population.html
+++ /dev/null
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-<!-- NewPage -->
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:32 BST 2014 -->
-<title>Population</title>
-<meta name="date" content="2014-05-22">
-<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"><!--
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-<div class="header">
-<div class="subTitle">jcgp.backend.population</div>
-<h2 title="Class Population" class="title">Class Population</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.population.Population</li>
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-</li>
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-<pre>public class <span class="typeNameLabel">Population</span>
-extends java.lang.Object</pre>
-<div class="block">This class primarily holds a collection of chromosomes. In addition, 
- it provides a few utility methods for manipulating and copying 
- chromosomes, useful for evolutionary strategies.
- <br><br>
- <code>copyChromosome()</code> is used to create copies of chromosomes, 
- though it is also possible to create a new instance of population
- directly from a seed chromosome using the right constructor. 
- <br><br>
- For convenience, a random chromosome can be retrieved using
- <code>getRandomChromosome()</code>, which is guaranteed to use the
- experiment's specified seed. If an entirely random population
- is needed, <code>reinitialise()</code> should be used to randomise
- all chromosomes without creating a new instance of <code>Population</code>.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
-</div>
-<div class="summary">
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><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>
-<tr class="rowColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Population.html#Population-jcgp.backend.resources.Resources-">Population</a></span>(<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Initialise a random population according to the parameters specified
- in the resources.</div>
-</td>
-</tr>
-</table>
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-</ul>
-<!-- ========== METHOD SUMMARY =========== -->
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Population.html#copyChromosome-int-int-">copyChromosome</a></span>(int&nbsp;source,
-              int&nbsp;target)</code>
-<div class="block">Copy a chromosome into a different position.</div>
-</td>
-</tr>
-<tr id="i1" 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"><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 id="i2" 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"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Population.html#getRandomChromosome--">getRandomChromosome</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Population.html#reinitialise--">reinitialise</a></span>()</code>
-<div class="block">Loop through all chromosomes and randomise all connections
- and functions.</div>
-</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Population.html#sort--">sort</a></span>()</code>
-<div class="block">Sorts the population in ascending order of fitness quality.</div>
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-<!--   -->
-</a>
-<h3>Methods inherited from class&nbsp;java.lang.Object</h3>
-<code>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
-</ul>
-</li>
-</ul>
-</li>
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-<!-- ========= CONSTRUCTOR DETAIL ======== -->
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-<!--   -->
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-<!--   -->
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-<ul class="blockList">
-<li class="blockList">
-<h4>Population</h4>
-<pre>public&nbsp;Population(<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
-<div class="block">Initialise a random population according to the parameters specified
- in the resources.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>resources</code> - the experiment's resources.</dd>
-</dl>
-</li>
-</ul>
-<a name="Population-jcgp.backend.population.Chromosome-jcgp.backend.resources.Resources-">
-<!--   -->
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-<ul class="blockListLast">
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-<h4>Population</h4>
-<pre>public&nbsp;Population(<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)</pre>
-<div class="block">Initialise a population of copies of the given chromosome.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>parent</code> - the chromosome to use as a model.</dd>
-<dd><code>resources</code> - a reference to the experiment's resources.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-<!-- ============ METHOD DETAIL ========== -->
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-<li class="blockList"><a name="method.detail">
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-<li class="blockList">
-<h4>get</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;get(int&nbsp;index)</pre>
-<div class="block">Returns the indexed chromosome.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the chromosome to return.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the indexed chromosome.</dd>
-</dl>
-</li>
-</ul>
-<a name="getRandomChromosome--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>getRandomChromosome</h4>
-<pre>public&nbsp;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;getRandomChromosome()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a random chromosome from this population.</dd>
-</dl>
-</li>
-</ul>
-<a name="copyChromosome-int-int-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>copyChromosome</h4>
-<pre>public&nbsp;void&nbsp;copyChromosome(int&nbsp;source,
-                           int&nbsp;target)</pre>
-<div class="block">Copy a chromosome into a different position.
- After this returns, the target chromosome has
- identical connections and functions to the source
- one, though they are separate instances.
- 
- This method does nothing if source == target.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>source</code> - the chromosome to copy from.</dd>
-<dd><code>target</code> - the chromosome to copy to.</dd>
-</dl>
-</li>
-</ul>
-<a name="reinitialise--">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>reinitialise</h4>
-<pre>public&nbsp;void&nbsp;reinitialise()</pre>
-<div class="block">Loop through all chromosomes and randomise all connections
- and functions.</div>
-</li>
-</ul>
-<a name="sort--">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>sort</h4>
-<pre>public&nbsp;void&nbsp;sort()</pre>
-<div class="block">Sorts the population in ascending order of fitness quality.
- What this means is that the best fitness chromosome will be
- in the last position, even though it might have the lowest
- fitness value. Fitness orientation as specified in the resources
- is respected.</div>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<!-- ========= END OF CLASS DATA ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<!--   -->
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diff --git a/doc/jcgp/backend/population/class-use/Chromosome.html b/doc/jcgp/backend/population/class-use/Chromosome.html
deleted file mode 100644
index ec43d21..0000000
--- a/doc/jcgp/backend/population/class-use/Chromosome.html
+++ /dev/null
@@ -1,346 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Class jcgp.backend.population.Chromosome</title>
-<meta name="date" content="2014-05-22">
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-<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#print-jcgp.backend.population.Chromosome-jcgp.backend.resources.Resources-">print</a></span>(<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 to the console in .chr format.</div>
-</td>
-</tr>
-<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#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-">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)</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>
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-</ul>
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diff --git a/doc/jcgp/backend/population/class-use/Connection.html b/doc/jcgp/backend/population/class-use/Connection.html
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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/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">
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-</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>
-<div class="block">This method sets the indexed connection to the specified new connection.</div>
-</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#setSource-jcgp.backend.population.Connection-">setSource</a></span>(<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 output source to the specified 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>
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diff --git a/doc/jcgp/backend/population/class-use/Gene.html b/doc/jcgp/backend/population/class-use/Gene.html
deleted file mode 100644
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+++ /dev/null
@@ -1,194 +0,0 @@
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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>
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-<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">
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-<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>
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diff --git a/doc/jcgp/backend/population/class-use/Input.html b/doc/jcgp/backend/population/class-use/Input.html
deleted file mode 100644
index 31af741..0000000
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-<td class="colLast">&nbsp;</td>
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-<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
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-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
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-<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>
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-<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/Mutable.html b/doc/jcgp/backend/population/class-use/Mutable.html
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-<tr>
-<th class="colFirst" scope="col">Package</th>
-<th class="colLast" scope="col">Description</th>
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-<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
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-<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/Mutable.html" title="interface in jcgp.backend.population">Mutable</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/Mutable.html" title="interface in jcgp.backend.population">Mutable</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/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getRandomMutable--">getRandomMutable</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/Mutable.html" title="interface in jcgp.backend.population">Mutable</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.Mutable-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;element)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><span class="typeNameLabel">Mutable.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</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>
-<tr class="altColor">
-<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.Mutable-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;m)</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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-<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/Mutable.html" title="interface in jcgp.backend.population">Mutable</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/Mutable.html" title="interface in jcgp.backend.population">Mutable</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/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getRandomMutable--">getRandomMutable</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/Mutable.html" title="interface in jcgp.backend.population">Mutable</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.Mutable-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</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.Mutable-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;m)</code>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><span class="typeNameLabel">Mutable.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Mutable.html#copyOf-jcgp.backend.population.Mutable-">copyOf</a></span>(<a href="../../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</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>
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-</ul>
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diff --git a/doc/jcgp/backend/population/class-use/Node.html b/doc/jcgp/backend/population/class-use/Node.html
deleted file mode 100644
index 78bc572..0000000
--- a/doc/jcgp/backend/population/class-use/Node.html
+++ /dev/null
@@ -1,247 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
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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>
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-</li>
-<li class="blockList">
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-<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>
-<div class="block">Calls <code>getActive(...)</code> on this output's
- source.</div>
-</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>
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diff --git a/doc/jcgp/backend/population/class-use/Output.html b/doc/jcgp/backend/population/class-use/Output.html
deleted file mode 100644
index 11933ea..0000000
--- a/doc/jcgp/backend/population/class-use/Output.html
+++ /dev/null
@@ -1,202 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<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>
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-<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
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-<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>
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-<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
deleted file mode 100644
index 3dc813a..0000000
--- a/doc/jcgp/backend/population/class-use/Population.html
+++ /dev/null
@@ -1,258 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Class jcgp.backend.population.Population</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../../script.js"></script>
-</head>
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-<script type="text/javascript"><!--
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-            parent.document.title="Uses of Class jcgp.backend.population.Population";
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-//-->
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-<li class="navBarCell1Rev">Use</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>
-</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/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-">evaluate</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 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-">evaluate</a></span>(<a href="../../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a>&nbsp;population)</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-">evaluate</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>int</code></td>
-<td class="colLast"><span class="typeNameLabel">TestCaseProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.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">SymbolicRegressionProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</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#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</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="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#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution</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>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
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-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
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-<li><a href="../../../../overview-summary.html">Overview</a></li>
-<li><a href="../package-summary.html">Package</a></li>
-<li><a href="../../../../jcgp/backend/population/Population.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>
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-<li><a href="Population.html" target="_top">No&nbsp;Frames</a></li>
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diff --git a/doc/jcgp/backend/population/package-frame.html b/doc/jcgp/backend/population/package-frame.html
deleted file mode 100644
index 54d8974..0000000
--- a/doc/jcgp/backend/population/package-frame.html
+++ /dev/null
@@ -1,29 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>jcgp.backend.population</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../script.js"></script>
-</head>
-<body>
-<h1 class="bar"><a href="../../../jcgp/backend/population/package-summary.html" target="classFrame">jcgp.backend.population</a></h1>
-<div class="indexContainer">
-<h2 title="Interfaces">Interfaces</h2>
-<ul title="Interfaces">
-<li><a href="Connection.html" title="interface in jcgp.backend.population" target="classFrame"><span class="interfaceName">Connection</span></a></li>
-<li><a href="Mutable.html" title="interface in jcgp.backend.population" target="classFrame"><span class="interfaceName">Mutable</span></a></li>
-</ul>
-<h2 title="Classes">Classes</h2>
-<ul title="Classes">
-<li><a href="Chromosome.html" title="class in jcgp.backend.population" target="classFrame">Chromosome</a></li>
-<li><a href="Input.html" title="class in jcgp.backend.population" target="classFrame">Input</a></li>
-<li><a href="Node.html" title="class in jcgp.backend.population" target="classFrame">Node</a></li>
-<li><a href="Output.html" title="class in jcgp.backend.population" target="classFrame">Output</a></li>
-<li><a href="Population.html" title="class in jcgp.backend.population" target="classFrame">Population</a></li>
-</ul>
-</div>
-</body>
-</html>
diff --git a/doc/jcgp/backend/population/package-summary.html b/doc/jcgp/backend/population/package-summary.html
deleted file mode 100644
index 93123d4..0000000
--- a/doc/jcgp/backend/population/package-summary.html
+++ /dev/null
@@ -1,196 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
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-<title>jcgp.backend.population</title>
-<meta name="date" content="2014-05-22">
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-</head>
-<body>
-<script type="text/javascript"><!--
-    try {
-        if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="jcgp.backend.population";
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-//-->
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-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li class="navBarCell1Rev">Package</li>
-<li>Class</li>
-<li><a href="package-use.html">Use</a></li>
-<li><a href="package-tree.html">Tree</a></li>
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-<li><a href="../../../help-doc.html">Help</a></li>
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-<div class="subNav">
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-</script>
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<div class="header">
-<h1 title="Package" class="title">Package&nbsp;jcgp.backend.population</h1>
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-<div class="contentContainer">
-<ul class="blockList">
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-<tr>
-<th class="colFirst" scope="col">Interface</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></td>
-<td class="colLast">
-<div class="block"><code>Connection</code> declares the expected behaviour of any
- part of a chromosome that can be connected to, specifically
- nodes or inputs.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></td>
-<td class="colLast">
-<div class="block"><code>Mutable</code> declares the expected behaviour of any
- part of a chromosome that is mutable, more specifically
- nodes or outputs.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList">
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-<caption><span>Class Summary</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Class</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></td>
-<td class="colLast">
-<div class="block">This class encapsulates a CGP chromosome.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></td>
-<td class="colLast">
-<div class="block">This is a chromosome input.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></td>
-<td class="colLast">
-<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"><a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></td>
-<td class="colLast">
-<div class="block">This is a chromosome output.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a></td>
-<td class="colLast">
-<div class="block">This class primarily holds a collection of chromosomes.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
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-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
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-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li class="navBarCell1Rev">Package</li>
-<li>Class</li>
-<li><a href="package-use.html">Use</a></li>
-<li><a href="package-tree.html">Tree</a></li>
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-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
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-<div class="subNav">
-<ul class="navList">
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-<li><a href="../../../jcgp/backend/resources/package-summary.html">Next&nbsp;Package</a></li>
-</ul>
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diff --git a/doc/jcgp/backend/population/package-tree.html b/doc/jcgp/backend/population/package-tree.html
deleted file mode 100644
index 7abf92d..0000000
--- a/doc/jcgp/backend/population/package-tree.html
+++ /dev/null
@@ -1,146 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>jcgp.backend.population Class Hierarchy</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
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-<script type="text/javascript"><!--
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-            parent.document.title="jcgp.backend.population Class Hierarchy";
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-<li><a href="../../../jcgp/backend/resources/package-tree.html">Next</a></li>
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-<li><a href="package-tree.html" target="_top">No&nbsp;Frames</a></li>
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-<div class="header">
-<h1 class="title">Hierarchy For Package jcgp.backend.population</h1>
-<span class="packageHierarchyLabel">Package Hierarchies:</span>
-<ul class="horizontal">
-<li><a href="../../../overview-tree.html">All Packages</a></li>
-</ul>
-</div>
-<div class="contentContainer">
-<h2 title="Class Hierarchy">Class Hierarchy</h2>
-<ul>
-<li type="circle">java.lang.Object
-<ul>
-<li type="circle">jcgp.backend.population.<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population"><span class="typeNameLink">Chromosome</span></a> (implements java.lang.Comparable&lt;T&gt;)</li>
-<li type="circle">jcgp.backend.population.<a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population"><span class="typeNameLink">Input</span></a> (implements jcgp.backend.population.<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>)</li>
-<li type="circle">jcgp.backend.population.<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population"><span class="typeNameLink">Node</span></a> (implements jcgp.backend.population.<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>, jcgp.backend.population.<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>)</li>
-<li type="circle">jcgp.backend.population.<a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population"><span class="typeNameLink">Output</span></a> (implements jcgp.backend.population.<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>)</li>
-<li type="circle">jcgp.backend.population.<a href="../../../jcgp/backend/population/Population.html" title="class in jcgp.backend.population"><span class="typeNameLink">Population</span></a></li>
-</ul>
-</li>
-</ul>
-<h2 title="Interface Hierarchy">Interface Hierarchy</h2>
-<ul>
-<li type="circle">jcgp.backend.population.<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population"><span class="typeNameLink">Connection</span></a></li>
-<li type="circle">jcgp.backend.population.<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population"><span class="typeNameLink">Mutable</span></a></li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
-<!--   -->
-</a>
-<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
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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>Class</li>
-<li>Use</li>
-<li class="navBarCell1Rev">Tree</li>
-<li><a href="../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
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-<li><a href="../../../jcgp/backend/resources/package-tree.html">Next</a></li>
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diff --git a/doc/jcgp/backend/population/package-use.html b/doc/jcgp/backend/population/package-use.html
deleted file mode 100644
index 86fb03a..0000000
--- a/doc/jcgp/backend/population/package-use.html
+++ /dev/null
@@ -1,338 +0,0 @@
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-<!-- NewPage -->
-<html lang="en">
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Package jcgp.backend.population</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
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-</head>
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-<script type="text/javascript"><!--
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-<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
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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>Class</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>
-<li><a href="../../../help-doc.html">Help</a></li>
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-</div>
-<div class="subNav">
-<ul class="navList">
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-<h1 title="Uses of Package jcgp.backend.population" class="title">Uses of Package<br>jcgp.backend.population</h1>
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-<div class="contentContainer">
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-<caption><span>Packages that use <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">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.mutator">jcgp.backend.modules.mutator</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.backend.modules.problem">jcgp.backend.modules.problem</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.backend.parsers">jcgp.backend.parsers</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.backend.population">jcgp.backend.population</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.gui.population">jcgp.gui.population</a></td>
-<td class="colLast">&nbsp;</td>
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-<li class="blockList"><a name="jcgp">
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-</a>
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-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Population.html#jcgp">Population</a>
-<div class="block">This class primarily holds a collection of chromosomes.</div>
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-</tr>
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-<li class="blockList"><a name="jcgp.backend.modules.es">
-<!--   -->
-</a>
-<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> used by <a href="../../../jcgp/backend/modules/es/package-summary.html">jcgp.backend.modules.es</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Population.html#jcgp.backend.modules.es">Population</a>
-<div class="block">This class primarily holds a collection of chromosomes.</div>
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-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Chromosome.html#jcgp.backend.modules.mutator">Chromosome</a>
-<div class="block">This class encapsulates a CGP chromosome.</div>
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-</tr>
-</tbody>
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-<!--   -->
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-<table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
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-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Population.html#jcgp.backend.modules.problem">Population</a>
-<div class="block">This class primarily holds a collection of chromosomes.</div>
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-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Chromosome.html#jcgp.backend.parsers">Chromosome</a>
-<div class="block">This class encapsulates a CGP chromosome.</div>
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-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Chromosome.html#jcgp.backend.population">Chromosome</a>
-<div class="block">This class encapsulates a CGP chromosome.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Connection.html#jcgp.backend.population">Connection</a>
-<div class="block"><code>Connection</code> declares the expected behaviour of any
- part of a chromosome that can be connected to, specifically
- nodes or inputs.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Input.html#jcgp.backend.population">Input</a>
-<div class="block">This is a chromosome input.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colOne"><a href="../../../jcgp/backend/population/class-use/Mutable.html#jcgp.backend.population">Mutable</a>
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diff --git a/doc/jcgp/backend/resources/Console.html b/doc/jcgp/backend/resources/Console.html
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-<div class="block">Defines the basic model for a console.
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- and GUI packages such as JavaFX are usually single-threaded.
- If the CGP experiment is running on a side thread (which would
- be the case so as not to block the entire GUI), updating a GUI
- element such as the console from a different thread would lead
- to concurrency problems. For this reason, this console is 
- intended to buffer printed messages and only output them to the
- actual GUI control when <code>flush()</code> is called (which is
- guaranteed to be done in a thread-safe way by the library).</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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diff --git a/doc/jcgp/backend/resources/ModifiableResources.html b/doc/jcgp/backend/resources/ModifiableResources.html
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-<div class="subTitle">jcgp.backend.resources</div>
-<h2 title="Class ModifiableResources" class="title">Class ModifiableResources</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">jcgp.backend.resources.Resources</a></li>
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-<div class="block">This subclass of Resources allows modifications to be made.
- A read-only cast of this class is passed to modules for safety, 
- and only classes with access to a JCGP instance may modify
- the resources.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getArityParameter--">getArityParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getColumnsParameter--">getColumnsParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getCurrentGenerationParameter--">getCurrentGenerationParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getCurrentRunParameter--">getCurrentRunParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getGenerationsParameter--">getGenerationsParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getInputsParameter--">getInputsParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getLevelsBackParameter--">getLevelsBackParameter</a></span>()</code>&nbsp;</td>
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-<tr id="i7" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getOutputsParameter--">getOutputsParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i8" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getPopulationSizeParameter--">getPopulationSizeParameter</a></span>()</code>&nbsp;</td>
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-<tr id="i9" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getReportIntervalParameter--">getReportIntervalParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i10" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getRowsParameter--">getRowsParameter</a></span>()</code>&nbsp;</td>
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-<tr id="i11" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getRunsParameter--">getRunsParameter</a></span>()</code>&nbsp;</td>
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-<tr id="i12" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#getSeedParameter--">getSeedParameter</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i13" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#incrementGeneration--">incrementGeneration</a></span>()</code>
-<div class="block">Adds 1 to the current generation.</div>
-</td>
-</tr>
-<tr id="i14" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#incrementRun--">incrementRun</a></span>()</code>
-<div class="block">Adds 1 to the current generation.</div>
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-</tr>
-<tr id="i15" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setArity-int-">setArity</a></span>(int&nbsp;arity)</code>
-<div class="block">This is called automatically by the experiment when the arity changes.</div>
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-</tr>
-<tr id="i16" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setColumns-int-">setColumns</a></span>(int&nbsp;columns)</code>&nbsp;</td>
-</tr>
-<tr id="i17" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setConsole-jcgp.backend.resources.Console-">setConsole</a></span>(<a href="../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a>&nbsp;console)</code>
-<div class="block">This can be set to null if no extra console is desired.</div>
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-<tr id="i18" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setCurrentGeneration-int-">setCurrentGeneration</a></span>(int&nbsp;currentGeneration)</code>&nbsp;</td>
-</tr>
-<tr id="i19" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setCurrentRun-int-">setCurrentRun</a></span>(int&nbsp;currentRun)</code>&nbsp;</td>
-</tr>
-<tr id="i20" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setFitnessOrientation-jcgp.backend.modules.problem.BestFitness-">setFitnessOrientation</a></span>(<a href="../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a>&nbsp;newOrientation)</code>&nbsp;</td>
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-<tr id="i21" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setFunctionSet-jcgp.backend.function.FunctionSet-">setFunctionSet</a></span>(<a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a>&nbsp;functionSet)</code>
-<div class="block">Update the current function set.</div>
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-<tr id="i22" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setGenerations-int-">setGenerations</a></span>(int&nbsp;generations)</code>&nbsp;</td>
-</tr>
-<tr id="i23" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setInputs-int-">setInputs</a></span>(int&nbsp;inputs)</code>&nbsp;</td>
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-<tr id="i24" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setLevelsBack-int-">setLevelsBack</a></span>(int&nbsp;levelsBack)</code>&nbsp;</td>
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-<tr id="i25" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setOutputs-int-">setOutputs</a></span>(int&nbsp;outputs)</code>&nbsp;</td>
-</tr>
-<tr id="i26" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setPopulationSize-int-">setPopulationSize</a></span>(int&nbsp;populationSize)</code>&nbsp;</td>
-</tr>
-<tr id="i27" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setReportInterval-int-">setReportInterval</a></span>(int&nbsp;report)</code>&nbsp;</td>
-</tr>
-<tr id="i28" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setRows-int-">setRows</a></span>(int&nbsp;rows)</code>&nbsp;</td>
-</tr>
-<tr id="i29" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setRuns-int-">setRuns</a></span>(int&nbsp;runs)</code>&nbsp;</td>
-</tr>
-<tr id="i30" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/ModifiableResources.html#setSeed-long-">setSeed</a></span>(long&nbsp;seed)</code>&nbsp;</td>
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-<dd><code>columns</code> - the number of columns to set.</dd>
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-<dd><code>inputs</code> - the number of inputs to set.</dd>
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-<dd><code>outputs</code> - the number of outputs to set.</dd>
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-<dd><code>populationSize</code> - the population size to set.</dd>
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-<h4>setLevelsBack</h4>
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-<dd><code>currentGeneration</code> - the current generation to set.</dd>
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-<pre>public&nbsp;void&nbsp;incrementGeneration()</pre>
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-<h4>setGenerations</h4>
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-<dd><code>generations</code> - the total generations to set.</dd>
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-<h4>setCurrentRun</h4>
-<pre>public&nbsp;void&nbsp;setCurrentRun(int&nbsp;currentRun)</pre>
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-<dd><code>currentRun</code> - the current run to set.</dd>
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-<pre>public&nbsp;void&nbsp;incrementRun()</pre>
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-<h4>setRuns</h4>
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-<dd><code>runs</code> - the total runs to set.</dd>
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-<h4>setArity</h4>
-<pre>public&nbsp;void&nbsp;setArity(int&nbsp;arity)</pre>
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-<dl>
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-<h4>setSeed</h4>
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-<h4>setReportInterval</h4>
-<pre>public&nbsp;void&nbsp;setReportInterval(int&nbsp;report)</pre>
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-<h4>getRowsParameter</h4>
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-<pre>public&nbsp;<a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a>&nbsp;getOutputsParameter()</pre>
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-<pre>public&nbsp;<a href="../../../jcgp/backend/parameters/IntegerParameter.html" title="class in jcgp.backend.parameters">IntegerParameter</a>&nbsp;getPopulationSizeParameter()</pre>
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-<dl>
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-<dl>
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-<div class="block">Update the current function set.</div>
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-<div class="block">This can be set to null if no extra console is desired.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>console</code> - the extra console for the experiment to use.</dd>
-</dl>
-</li>
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diff --git a/doc/jcgp/backend/resources/Resources.html b/doc/jcgp/backend/resources/Resources.html
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-<li><a href="class-use/Resources.html">Use</a></li>
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-<li><a href="../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
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-<!-- ======== START OF CLASS DATA ======== -->
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-<div class="subTitle">jcgp.backend.resources</div>
-<h2 title="Class Resources" class="title">Class Resources</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.backend.resources.Resources</li>
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-</li>
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-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">Resources</span>
-extends java.lang.Object</pre>
-<div class="block">Encapsulates all of the resources based on which the program operates.
- Each instance of JCGP contains a single instance of <code>Resources</code>.
- <br><br>
- The experiment's <code>Resources</code> object is passed to modules as the program operates, and
- the actual parameter values can be obtained using getter methods. Note that, for code brevity,
- this class's getters do not start with the word "get". For instance, to get the number of rows, 
- one would use <code>rows()</code> instead of <code>getRows()</code> which doesn't exist.
- The fitness orientation of the problem being solved can also be retrieved using <code>fitnessOrientation()</code>.
- Evolutionary strategies will typically use this to perform selection.
- <br><br>
- In addition to parameters, this class also offers utility methods. Any necessary random numbers
- should be obtained using <code>getRandomInt()</code> and <code>getRandomDouble()</code> as these methods
- use a particular <code>Random</code> object guaranteed to generate random numbers based on the seed 
- parameter. Functions from the selected function set can be obtained through this class as well.
- Finally, printing to the console should be done via the resources using the report and print
- methods, so that these prints also get sent to the GUI console (if one is present).</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters"><code>Parameter</code></a></dd>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#Resources--">Resources</a></span>()</code>&nbsp;</td>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
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-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#arity--">arity</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#columns--">columns</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#currentGeneration--">currentGeneration</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#currentRun--">currentRun</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#fitnessOrientation--">fitnessOrientation</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#generations--">generations</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#getFunction-int-">getFunction</a></span>(int&nbsp;index)</code>
-<div class="block">Gets the indexed function out of the
- complete set of functions.</div>
-</td>
-</tr>
-<tr id="i7" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#getFunctionIndex-jcgp.backend.function.Function-">getFunctionIndex</a></span>(<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;function)</code>
-<div class="block">Returns the index of a specified function.</div>
-</td>
-</tr>
-<tr id="i8" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#getFunctionSet--">getFunctionSet</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i9" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#getRandomDouble--">getRandomDouble</a></span>()</code>
-<div class="block">Gets the next random integer using the experiment's random
- number generator.</div>
-</td>
-</tr>
-<tr id="i10" class="altColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#getRandomDouble-int-">getRandomDouble</a></span>(int&nbsp;limit)</code>
-<div class="block">Gets the next random double using the experiment's random
- number generator.</div>
-</td>
-</tr>
-<tr id="i11" class="rowColor">
-<td class="colFirst"><code><a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#getRandomFunction--">getRandomFunction</a></span>()</code>
-<div class="block">Gets a random allowed function from the problem function set.</div>
-</td>
-</tr>
-<tr id="i12" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#getRandomInt-int-">getRandomInt</a></span>(int&nbsp;limit)</code>
-<div class="block">Gets the next random integer using the experiment's random
- number generator.</div>
-</td>
-</tr>
-<tr id="i13" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#inputs--">inputs</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i14" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#levelsBack--">levelsBack</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i15" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#nodes--">nodes</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i16" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#outputs--">outputs</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i17" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#populationSize--">populationSize</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i18" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#print-java.lang.String-">print</a></span>(java.lang.String&nbsp;message)</code>
-<div class="block">Prints a message to the consoles ignoring
- report interval.</div>
-</td>
-</tr>
-<tr id="i19" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#println-java.lang.String-">println</a></span>(java.lang.String&nbsp;message)</code>
-<div class="block">Prints a message to the consoles ignoring
- report interval.</div>
-</td>
-</tr>
-<tr id="i20" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#report-java.lang.String-">report</a></span>(java.lang.String&nbsp;message)</code>
-<div class="block">Prints a message to the consoles taking into account the
- report interval parameter.</div>
-</td>
-</tr>
-<tr id="i21" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#reportInterval--">reportInterval</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i22" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#reportln-java.lang.String-">reportln</a></span>(java.lang.String&nbsp;message)</code>
-<div class="block">Prints a message to the consoles taking into account the
- report interval parameter.</div>
-</td>
-</tr>
-<tr id="i23" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/resources/Resources.html#rows--">rows</a></span>()</code>&nbsp;</td>
-</tr>
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diff --git a/doc/jcgp/backend/resources/class-use/Console.html b/doc/jcgp/backend/resources/class-use/Console.html
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-<tr>
-<th class="colFirst" scope="col">Package</th>
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-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp">jcgp</a></td>
-<td class="colLast">&nbsp;</td>
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-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.gui.console">jcgp.gui.console</a></td>
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-<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> with parameters of type <a href="../../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Modifier and Type</th>
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-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">JCGP.</span><code><span class="memberNameLink"><a href="../../../../jcgp/JCGP.html#setConsole-jcgp.backend.resources.Console-">setConsole</a></span>(<a href="../../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a>&nbsp;console)</code>
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-<tr class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">ModifiableResources.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html#setConsole-jcgp.backend.resources.Console-">setConsole</a></span>(<a href="../../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a>&nbsp;console)</code>
-<div class="block">This can be set to null if no extra console is desired.</div>
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-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.gui.console">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a> in <a href="../../../../jcgp/gui/console/package-summary.html">jcgp.gui.console</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/gui/console/package-summary.html">jcgp.gui.console</a> that implement <a href="../../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</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/gui/console/ConsolePane.html" title="class in jcgp.gui.console">ConsolePane</a></span></code>
-<div class="block">Console pane used by the GUI to display CGP output messages.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<li><a href="../../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
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diff --git a/doc/jcgp/backend/resources/class-use/ModifiableResources.html b/doc/jcgp/backend/resources/class-use/ModifiableResources.html
deleted file mode 100644
index d10eb29..0000000
--- a/doc/jcgp/backend/resources/class-use/ModifiableResources.html
+++ /dev/null
@@ -1,234 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Class jcgp.backend.resources.ModifiableResources</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
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-</head>
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-            parent.document.title="Uses of Class jcgp.backend.resources.ModifiableResources";
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-//-->
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-<li><a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
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-<h2 title="Uses of Class jcgp.backend.resources.ModifiableResources" class="title">Uses of Class<br>jcgp.backend.resources.ModifiableResources</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/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</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.problem">jcgp.backend.modules.problem</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.backend.parsers">jcgp.backend.parsers</a></td>
-<td class="colLast">&nbsp;</td>
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-<ul class="blockList">
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-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</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/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</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/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></code></td>
-<td class="colLast"><span class="typeNameLabel">JCGP.</span><code><span class="memberNameLink"><a href="../../../../jcgp/JCGP.html#getResources--">getResources</a></span>()</code>
-<div class="block">Returns a reference to the <code>ModifiableResources</code> used by the
- experiment.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.modules.problem">
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-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</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/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</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">TestCaseProblem.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></span>(java.io.File&nbsp;file,
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-</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#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></span>(java.io.File&nbsp;file,
-                <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</code>
-<div class="block">Parses the specified file and uses the parsed data to
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-<h3>Uses of <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</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/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</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">ParameterParser.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parsers/ParameterParser.html#parse-java.io.File-jcgp.backend.resources.ModifiableResources-">parse</a></span>(java.io.File&nbsp;file,
-     <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</code>
-<div class="block">Parses the parameters from a specified CGP parameter file and
- modifies the experiment resources appropriately.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><span class="typeNameLabel">TestCaseParser.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parsers/TestCaseParser.html#parse-java.io.File-jcgp.backend.modules.problem.TestCaseProblem-jcgp.backend.resources.ModifiableResources-">parse</a></span>(java.io.File&nbsp;file,
-     <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;?&gt;&nbsp;problem,
-     <a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a>&nbsp;resources)</code>
-<div class="block">Sets the number of inputs and outputs in the resources
- to match the given file, and parses each test case
- from the file into the specified problem.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<li><a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
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diff --git a/doc/jcgp/backend/resources/class-use/Resources.html b/doc/jcgp/backend/resources/class-use/Resources.html
deleted file mode 100644
index 7e05842..0000000
--- a/doc/jcgp/backend/resources/class-use/Resources.html
+++ /dev/null
@@ -1,350 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Class jcgp.backend.resources.Resources</title>
-<meta name="date" content="2014-05-22">
-<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.resources.Resources";
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-<noscript>
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-<li><a href="../package-summary.html">Package</a></li>
-<li><a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">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>
-<li><a href="../../../../help-doc.html">Help</a></li>
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-<li><a href="Resources.html" target="_top">No&nbsp;Frames</a></li>
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-<ul class="navList" id="allclasses_navbar_top">
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-<script type="text/javascript"><!--
-  allClassesLink = document.getElementById("allclasses_navbar_top");
-  if(window==top) {
-    allClassesLink.style.display = "block";
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-    allClassesLink.style.display = "none";
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-<h2 title="Uses of Class jcgp.backend.resources.Resources" class="title">Uses of Class<br>jcgp.backend.resources.Resources</h2>
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-<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/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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.es">jcgp.backend.modules.es</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.backend.modules.mutator">jcgp.backend.modules.mutator</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>
-<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.backend.resources">jcgp.backend.resources</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.es">
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-<h3>Uses of <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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 constructors, and an explanation">
-<caption><span>Constructors in <a href="../../../../jcgp/backend/modules/es/package-summary.html">jcgp.backend.modules.es</a> with parameters of type <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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/modules/es/MuPlusLambda.html#MuPlusLambda-jcgp.backend.resources.Resources-">MuPlusLambda</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Creates a new instance of MuPlusLambda.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/es/TournamentSelection.html#TournamentSelection-jcgp.backend.resources.Resources-">TournamentSelection</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Creates a new instance of TournamentSelection.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList"><a name="jcgp.backend.modules.mutator">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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 constructors, and an explanation">
-<caption><span>Constructors in <a href="../../../../jcgp/backend/modules/mutator/package-summary.html">jcgp.backend.modules.mutator</a> with parameters of type <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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/modules/mutator/FixedPointMutator.html#FixedPointMutator-jcgp.backend.resources.Resources-">FixedPointMutator</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Creates a new instance of FixedPointMutator.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/PercentPointMutator.html#PercentPointMutator-jcgp.backend.resources.Resources-">PercentPointMutator</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
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-</td>
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-<tr class="altColor">
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/mutator/ProbabilisticMutator.html#ProbabilisticMutator-jcgp.backend.resources.Resources-">ProbabilisticMutator</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
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-<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/modules/problem/package-summary.html">jcgp.backend.modules.problem</a> with parameters of type <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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/modules/problem/DigitalCircuitProblem.html#DigitalCircuitProblem-jcgp.backend.resources.Resources-">DigitalCircuitProblem</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Construct a new instance of DigitalCircuitProblem.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#SymbolicRegressionProblem-jcgp.backend.resources.Resources-">SymbolicRegressionProblem</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
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-</a>
-<h3>Uses of <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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>
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-<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">FunctionParser.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/parsers/FunctionParser.html#parse-java.io.File-jcgp.backend.function.FunctionSet-jcgp.backend.resources.Resources-">parse</a></span>(java.io.File&nbsp;file,
-     <a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a>&nbsp;functionSet,
-     <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Reads the specified file and attempts to enable 
- and disable the functions in the FunctionSet 
- accordingly.</div>
-</td>
-</tr>
-<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#print-jcgp.backend.population.Chromosome-jcgp.backend.resources.Resources-">print</a></span>(<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 to the console in .chr format.</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/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Chromosome.</span><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Chromosome.html#getResources--">getResources</a></span>()</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/backend/population/package-summary.html">jcgp.backend.population</a> with parameters of type <a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</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.resources.Resources-">Chromosome</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Initialise a chromosome with the specified parameters.</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>
-<tr class="altColor">
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/population/Population.html#Population-jcgp.backend.resources.Resources-">Population</a></span>(<a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
-<div class="block">Initialise a random population according to the parameters specified
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-<li class="blockList"><a name="jcgp.backend.resources">
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-<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/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a> in <a href="../../../../jcgp/backend/resources/package-summary.html">jcgp.backend.resources</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>
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-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></span></code>
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-<li><a href="../package-summary.html">Package</a></li>
-<li><a href="../../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">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 class="navList">
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diff --git a/doc/jcgp/backend/resources/package-frame.html b/doc/jcgp/backend/resources/package-frame.html
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index 594965c..0000000
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+++ /dev/null
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-<!-- NewPage -->
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-<title>jcgp.backend.resources</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../script.js"></script>
-</head>
-<body>
-<h1 class="bar"><a href="../../../jcgp/backend/resources/package-summary.html" target="classFrame">jcgp.backend.resources</a></h1>
-<div class="indexContainer">
-<h2 title="Interfaces">Interfaces</h2>
-<ul title="Interfaces">
-<li><a href="Console.html" title="interface in jcgp.backend.resources" target="classFrame"><span class="interfaceName">Console</span></a></li>
-</ul>
-<h2 title="Classes">Classes</h2>
-<ul title="Classes">
-<li><a href="ModifiableResources.html" title="class in jcgp.backend.resources" target="classFrame">ModifiableResources</a></li>
-<li><a href="Resources.html" title="class in jcgp.backend.resources" target="classFrame">Resources</a></li>
-</ul>
-</div>
-</body>
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diff --git a/doc/jcgp/backend/resources/package-summary.html b/doc/jcgp/backend/resources/package-summary.html
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-<script type="text/javascript"><!--
-    try {
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-<noscript>
-<div>JavaScript is disabled on your browser.</div>
-</noscript>
-<!-- ========= START OF TOP NAVBAR ======= -->
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-<!--   -->
-</a>
-<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
-<a name="navbar.top.firstrow">
-<!--   -->
-</a>
-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li class="navBarCell1Rev">Package</li>
-<li>Class</li>
-<li><a href="package-use.html">Use</a></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>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
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-<li><a href="../../../jcgp/backend/statistics/package-summary.html">Next&nbsp;Package</a></li>
-</ul>
-<ul class="navList">
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-<ul class="navList" id="allclasses_navbar_top">
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-<div>
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-  allClassesLink = document.getElementById("allclasses_navbar_top");
-  if(window==top) {
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-<!-- ========= END OF TOP NAVBAR ========= -->
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-<h1 title="Package" class="title">Package&nbsp;jcgp.backend.resources</h1>
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-<ul class="blockList">
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-<table class="typeSummary" border="0" cellpadding="3" cellspacing="0" summary="Interface Summary table, listing interfaces, and an explanation">
-<caption><span>Interface Summary</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Interface</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a></td>
-<td class="colLast">
-<div class="block">Defines the basic model for a console.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-<li class="blockList">
-<table class="typeSummary" border="0" cellpadding="3" cellspacing="0" summary="Class Summary table, listing classes, and an explanation">
-<caption><span>Class Summary</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Class</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></td>
-<td class="colLast">
-<div class="block">This subclass of Resources allows modifications to be made.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a></td>
-<td class="colLast">
-<div class="block">Encapsulates all of the resources based on which the program operates.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</div>
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
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-<!--   -->
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-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li class="navBarCell1Rev">Package</li>
-<li>Class</li>
-<li><a href="package-use.html">Use</a></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>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
-<li><a href="../../../jcgp/backend/population/package-summary.html">Prev&nbsp;Package</a></li>
-<li><a href="../../../jcgp/backend/statistics/package-summary.html">Next&nbsp;Package</a></li>
-</ul>
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-<li><a href="package-summary.html" target="_top">No&nbsp;Frames</a></li>
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-<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"><!--
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-<div>JavaScript is disabled on your browser.</div>
-</noscript>
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-<!--   -->
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-<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
-<a name="navbar.top.firstrow">
-<!--   -->
-</a>
-<ul class="navList" title="Navigation">
-<li><a href="../../../overview-summary.html">Overview</a></li>
-<li><a href="package-summary.html">Package</a></li>
-<li>Class</li>
-<li>Use</li>
-<li class="navBarCell1Rev">Tree</li>
-<li><a href="../../../deprecated-list.html">Deprecated</a></li>
-<li><a href="../../../index-files/index-1.html">Index</a></li>
-<li><a href="../../../help-doc.html">Help</a></li>
-</ul>
-</div>
-<div class="subNav">
-<ul class="navList">
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-<li><a href="../../../jcgp/backend/statistics/package-tree.html">Next</a></li>
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diff --git a/doc/jcgp/backend/statistics/RunEntry.html b/doc/jcgp/backend/statistics/RunEntry.html
deleted file mode 100644
index b455463..0000000
--- a/doc/jcgp/backend/statistics/RunEntry.html
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-<li><a href="package-summary.html">Package</a></li>
-<li class="navBarCell1Rev">Class</li>
-<li><a href="class-use/RunEntry.html">Use</a></li>
-<li><a href="package-tree.html">Tree</a></li>
-<li><a href="../../../deprecated-list.html">Deprecated</a></li>
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-</div>
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-<ul class="navList">
-<li>Prev&nbsp;Class</li>
-<li><a href="../../../jcgp/backend/statistics/StatisticsLogger.html" title="class in jcgp.backend.statistics"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
-</ul>
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-<li><a href="../../../index.html?jcgp/backend/statistics/RunEntry.html" target="_top">Frames</a></li>
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-<!-- ======== START OF CLASS DATA ======== -->
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-<div class="subTitle">jcgp.backend.statistics</div>
-<h2 title="Class RunEntry" class="title">Class RunEntry</h2>
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-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
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-<pre>public class <span class="typeNameLabel">RunEntry</span>
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- Once constructed, data can only be retrieved. Note that
- the generation argument in the constructor (and consequently
- the value returned by <code>getGeneration()</code> refer to the 
- last generation when improvement occurred.</div>
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-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../jcgp/backend/statistics/StatisticsLogger.html" title="class in jcgp.backend.statistics"><code>StatisticsLogger</code></a></dd>
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-        double&nbsp;fitness,
-        int&nbsp;active,
-        boolean&nbsp;successful)</code>
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-<th class="colLast" scope="col">Method and Description</th>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/RunEntry.html#getActiveNodes--">getActiveNodes</a></span>()</code>&nbsp;</td>
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-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/RunEntry.html#getFitness--">getFitness</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code>int</code></td>
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-                double&nbsp;fitness,
-                int&nbsp;active,
-                boolean&nbsp;successful)</pre>
-<div class="block">Creates a new run entry for a logger.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>generation</code> - the generation when fitness improvement last occurred.</dd>
-<dd><code>fitness</code> - the best fitness achieved.</dd>
-<dd><code>active</code> - the number of active nodes in the best solution found.</dd>
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-<div class="header">
-<div class="subTitle">jcgp.backend.statistics</div>
-<h2 title="Class StatisticsLogger" class="title">Class StatisticsLogger</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
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-<pre>public class <span class="typeNameLabel">StatisticsLogger</span>
-extends java.lang.Object</pre>
-<div class="block">This is a utility class for logging experiment statistics when doing multiple runs.
- <br><br>
- Information about each run is added via the <code>logRun()</code> method. The many getters
- can be used to obtain statistics about the logged runs, such as success rate and average
- fitness.
- <br><br>
- <code>JCGP</code> uses this class to perform its logging and print out experiment data at the end.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#StatisticsLogger--">StatisticsLogger</a></span>()</code>
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-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageActiveNodes--">getAverageActiveNodes</a></span>()</code>
-<div class="block">Averages the number of active nodes in the 
- best chromosomes obtained across all runs.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageActiveNodesStdDev--">getAverageActiveNodesStdDev</a></span>()</code>
-<div class="block">Calculates the standard deviation of
- the number of active nodes in the best solution
- in each run.</div>
-</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageFitness--">getAverageFitness</a></span>()</code>
-<div class="block">Averages the best fitness obtained in each run.</div>
-</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageFitnessStdDev--">getAverageFitnessStdDev</a></span>()</code>
-<div class="block">Calculates the standard deviation of
- the best fitness obtained in each run.</div>
-</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageGenerations--">getAverageGenerations</a></span>()</code>
-<div class="block">Calculates the average generation out of all runs.</div>
-</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageGenerationsStdDev--">getAverageGenerationsStdDev</a></span>()</code>
-<div class="block">Calculates the standard deviation of
- the average number of generations in
- each run.</div>
-</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageSuccessfulGenerations--">getAverageSuccessfulGenerations</a></span>()</code>
-<div class="block">Calculates the average generation out of successful runs only.</div>
-</td>
-</tr>
-<tr id="i7" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getAverageSuccessfulGenerationsStdDev--">getAverageSuccessfulGenerationsStdDev</a></span>()</code>
-<div class="block">Calculates the standard deviation of
- the average number of generations in
- each run where a perfect solution was found.</div>
-</td>
-</tr>
-<tr id="i8" class="altColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getHighestFitness--">getHighestFitness</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i9" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getLowestFitness--">getLowestFitness</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i10" class="altColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getSuccessfulRuns--">getSuccessfulRuns</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i11" class="rowColor">
-<td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#getSuccessRate--">getSuccessRate</a></span>()</code>
-<div class="block">Calculates the ratio of successful runs (runs where
- a perfect solution was found) to total number of runs.</div>
-</td>
-</tr>
-<tr id="i12" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html#logRun-int-double-int-boolean-">logRun</a></span>(int&nbsp;generation,
-      double&nbsp;fitness,
-      int&nbsp;active,
-      boolean&nbsp;successful)</code>
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-</ul>
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-<pre>public&nbsp;StatisticsLogger()</pre>
-<div class="block">Create a new statistics logger, use this when resetting is necessary.</div>
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-                   double&nbsp;fitness,
-                   int&nbsp;active,
-                   boolean&nbsp;successful)</pre>
-<div class="block">Log a new run. Calling any of the statistics getters will
- now take this logged run into account as well as all previously
- logged runs.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>generation</code> - the last generation when improvement occurred.</dd>
-<dd><code>fitness</code> - the best fitness achieved in the run.</dd>
-<dd><code>active</code> - the number of active nodes in the best chromosome found.</dd>
-<dd><code>successful</code> - true if a perfect solution was found, false if otherwise.</dd>
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-<div class="block">Averages the best fitness obtained in each run.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the average fitness.</dd>
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-<div class="block">Calculates the standard deviation of
- the best fitness obtained in each run.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the standard deviation of average fitnesses.</dd>
-</dl>
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- best chromosomes obtained across all runs.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the average number of active nodes.</dd>
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-<div class="block">Calculates the standard deviation of
- the number of active nodes in the best solution
- in each run.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the standard deviation of active node counts.</dd>
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- The generation value in each run corresponds to the
- last generation in which improvement happened. 
- <br><br>
- Note that this method includes runs where no perfect
- solution was found. For the average number of generations
- for perfect solutions only, use <code>getAverageSuccessfulGenerations</code>.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the average number of generations.</dd>
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- the average number of generations in
- each run.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the standard deviation of the number of generations.</dd>
-</dl>
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-<dd>the highest fitness across all runs.</dd>
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-<dd>the lowest fitness across all runs.</dd>
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-<dd>the number of runs in which a perfect solution was found.</dd>
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-<pre>public&nbsp;double&nbsp;getSuccessRate()</pre>
-<div class="block">Calculates the ratio of successful runs (runs where
- a perfect solution was found) to total number of runs.
- A double-precision value between 0 and 1 is returned, 
- where 0 means 0% success rate and 1 means 100% success rate.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the success rate across all runs.</dd>
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-<div class="block">Calculates the average generation out of successful runs only. 
- The generation value in each successful run corresponds to the
- generation in which the perfect solution was found.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the average number of generations for perfect solutions.</dd>
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-<pre>public&nbsp;double&nbsp;getAverageSuccessfulGenerationsStdDev()</pre>
-<div class="block">Calculates the standard deviation of
- the average number of generations in
- each run where a perfect solution was found.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the standard deviation of the number of generations in successful runs.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
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--- a/doc/jcgp/backend/statistics/class-use/RunEntry.html
+++ /dev/null
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deleted file mode 100644
index 8541c24..0000000
--- a/doc/jcgp/backend/statistics/class-use/StatisticsLogger.html
+++ /dev/null
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deleted file mode 100644
index 4c9ff7d..0000000
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+++ /dev/null
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-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/backend/statistics/RunEntry.html" title="class in jcgp.backend.statistics">RunEntry</a></td>
-<td class="colLast">
-<div class="block">This class encapsulates the data contained in a log entry.</div>
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-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/backend/statistics/StatisticsLogger.html" title="class in jcgp.backend.statistics">StatisticsLogger</a></td>
-<td class="colLast">
-<div class="block">This is a utility class for logging experiment statistics when doing multiple runs.</div>
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deleted file mode 100644
index 19101e7..0000000
--- a/doc/jcgp/backend/statistics/package-tree.html
+++ /dev/null
@@ -1,138 +0,0 @@
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-<li type="circle">jcgp.backend.statistics.<a href="../../../jcgp/backend/statistics/RunEntry.html" title="class in jcgp.backend.statistics"><span class="typeNameLink">RunEntry</span></a></li>
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diff --git a/doc/jcgp/class-use/JCGP.html b/doc/jcgp/class-use/JCGP.html
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-<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/package-summary.html">jcgp.gui</a> that return <a href="../../jcgp/JCGP.html" title="class in jcgp">JCGP</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<tr class="altColor">
-<td class="colFirst"><code><a href="../../jcgp/JCGP.html" title="class in jcgp">JCGP</a></code></td>
-<td class="colLast"><span class="typeNameLabel">GUI.</span><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#getExperiment--">getExperiment</a></span>()</code>&nbsp;</td>
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diff --git a/doc/jcgp/gui/GUI.html b/doc/jcgp/gui/GUI.html
deleted file mode 100644
index c8274c9..0000000
--- a/doc/jcgp/gui/GUI.html
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-<ul class="subNavList">
-<li>Summary:&nbsp;</li>
-<li><a href="#nested.classes.inherited.from.class.javafx.application.Application">Nested</a>&nbsp;|&nbsp;</li>
-<li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
-<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
-<li><a href="#method.summary">Method</a></li>
-</ul>
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-<li>Detail:&nbsp;</li>
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-<!--   -->
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.gui</div>
-<h2 title="Class GUI" class="title">Class GUI</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.application.Application</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.gui.GUI</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">GUI</span>
-extends javafx.application.Application</pre>
-<div class="block">Main class for the graphical user interface (GUI).
- <br><br>
- This class declares the main method used when running the GUI.
- In addition, all main GUI panes are declared and instantiated here.
- <br><br>
- The user interface is divided into 3 main components: the node grid
- (<a href="../../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population"><code>PopulationPane</code></a>), the control pane (<a href="../../jcgp/gui/settings/SettingsPane.html" title="class in jcgp.gui.settings"><code>SettingsPane</code></a>) and
- the console (<a href="../../jcgp/gui/console/ConsolePane.html" title="class in jcgp.gui.console"><code>ConsolePane</code></a>). Click on any of the links in
- brackets to see more information about each interface component.
- <br><br>
- This class also contains the instance of JCGP responsible for
- running the experiments in GUI mode. JCGP's execution must be delegated
- to a separate thread so that the GUI remains unblocked. This is done using
- a JavaFX <code>Service</code> which calls <code>nextGeneration()</code> in a loop
- until it is interrupted by the main JavaFX thread.
- <br>
- This service also handles flushing the console in a thread safe way. This
- is done by synchronizing the <code>nextGeneration()</code> and <code>flush()</code>
- method calls on a lock object.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-</dl>
-</li>
-</ul>
-</div>
-<div class="summary">
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-<!-- ======== NESTED CLASS SUMMARY ======== -->
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-<h3>Nested classes/interfaces inherited from class&nbsp;javafx.application.Application</h3>
-<code>javafx.application.Application.Parameters</code></li>
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-<h3>Field Summary</h3>
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-<caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Field and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#BAD_SELECTION_COLOUR">BAD_SELECTION_COLOUR</a></span></code>
-<div class="block">A string containing the hexadecimal colour used for representing a bad selection.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#CONSOLE_MIN_HEIGHT">CONSOLE_MIN_HEIGHT</a></span></code>
-<div class="block">The minimum width of the console pane, to prevent it
- from being resized beyond visibility.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#GOOD_SELECTION_COLOUR">GOOD_SELECTION_COLOUR</a></span></code>
-<div class="block">A string containing the hexadecimal colour used for representing a good selection.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#HARD_HIGHLIGHT_COLOUR">HARD_HIGHLIGHT_COLOUR</a></span></code>
-<div class="block">A string containing the hexadecimal colour used for representing a hard highlight.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#MEDIUM_HIGHLIGHT_COLOUR">MEDIUM_HIGHLIGHT_COLOUR</a></span></code>
-<div class="block">A string containing the hexadecimal colour used for a medium highlight.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#NEUTRAL_COLOUR">NEUTRAL_COLOUR</a></span></code>
-<div class="block">A string containing the hexadecimal colour used for representing neutrality.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#NEUTRAL_SELECTION_COLOUR">NEUTRAL_SELECTION_COLOUR</a></span></code>
-<div class="block">A string containing the hexadecimal colour used for representing a neutral selection.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#RESIZE_MARGIN">RESIZE_MARGIN</a></span></code>
-<div class="block">The width or height of the area that can be clicked on
- to drag-resize a pane.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static double</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#SETTINGS_MIN_WIDTH">SETTINGS_MIN_WIDTH</a></span></code>
-<div class="block">The minimum width of the settings pane, to prevent it
- from being resized beyond visibility.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static java.lang.String</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#SOFT_HIGHLIGHT_COLOUR">SOFT_HIGHLIGHT_COLOUR</a></span></code>
-<div class="block">A string containing the hexadecimal colour used for a soft highlight.</div>
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-<code>STYLESHEET_CASPIAN, STYLESHEET_MODENA</code></li>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#GUI--">GUI</a></span>()</code>
-<div class="block">Makes a new instance of GUI.</div>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#bringFunctionSelector-javafx.scene.input.MouseEvent-jcgp.gui.population.GUINode-">bringFunctionSelector</a></span>(javafx.scene.input.MouseEvent&nbsp;event,
-                     <a href="../../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</a>&nbsp;node)</code>
-<div class="block">Relocate the function selector to the right position
- relative to the specified node and set it visible.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#evaluateTestCase-jcgp.backend.modules.problem.TestCaseProblem.TestCase-">evaluateTestCase</a></span>(<a href="../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;java.lang.Object&gt;&nbsp;testCase)</code>
-<div class="block">Starts the evaluation process with the given test case.</div>
-</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#flushConsole--">flushConsole</a></span>()</code>
-<div class="block">Writes all buffered content out to the GUI console.</div>
-</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#getChromosomeIndex--">getChromosomeIndex</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code><a href="../../jcgp/JCGP.html" title="class in jcgp">JCGP</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#getExperiment--">getExperiment</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>javafx.stage.Stage</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#getStage--">getStage</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#hideGeneValues--">hideGeneValues</a></span>()</code>
-<div class="block">Hide all evaluated values.</div>
-</td>
-</tr>
-<tr id="i7" class="rowColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#isWorking--">isWorking</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i8" class="altColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#main-java.lang.String:A-">main</a></span>(java.lang.String[]&nbsp;args)</code>
-<div class="block">Start JCGP with the user interface.</div>
-</td>
-</tr>
-<tr id="i9" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#reDraw--">reDraw</a></span>()</code>
-<div class="block">Does a complete GUI refresh.</div>
-</td>
-</tr>
-<tr id="i10" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#reset--">reset</a></span>()</code>
-<div class="block">Reset button callback.</div>
-</td>
-</tr>
-<tr id="i11" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#runPause--">runPause</a></span>()</code>
-<div class="block">Run/pause method.</div>
-</td>
-</tr>
-<tr id="i12" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#setEvaluating-boolean-">setEvaluating</a></span>(boolean&nbsp;value)</code>
-<div class="block">Set the system into evaluation mode.</div>
-</td>
-</tr>
-<tr id="i13" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#start-javafx.stage.Stage-">start</a></span>(javafx.stage.Stage&nbsp;primaryStage)</code>&nbsp;</td>
-</tr>
-<tr id="i14" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#step--">step</a></span>()</code>
-<div class="block">Perform a single generation using <code>nextGeneration()</code>.</div>
-</td>
-</tr>
-<tr id="i15" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../jcgp/gui/GUI.html#updateFunctionSelector--">updateFunctionSelector</a></span>()</code>
-<div class="block">Refresh the function selector, used when functions are enabled or disabled.</div>
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- A "hard" select, for instance, happens when an output path is locked on the chromosome
- pane.</div>
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-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../constant-values.html#jcgp.gui.GUI.HARD_HIGHLIGHT_COLOUR">Constant Field Values</a></dd>
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- One example of such a selection is the colour applied to a node
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-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../constant-values.html#jcgp.gui.GUI.MEDIUM_HIGHLIGHT_COLOUR">Constant Field Values</a></dd>
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- Ideally a shade of green, used for instance when a manual connection is valid.</div>
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-<dd><a href="../../constant-values.html#jcgp.gui.GUI.GOOD_SELECTION_COLOUR">Constant Field Values</a></dd>
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-<dd><a href="../../constant-values.html#jcgp.gui.GUI.BAD_SELECTION_COLOUR">Constant Field Values</a></dd>
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-<dl>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../constant-values.html#jcgp.gui.GUI.RESIZE_MARGIN">Constant Field Values</a></dd>
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-<dl>
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-<dd><a href="../../constant-values.html#jcgp.gui.GUI.CONSOLE_MIN_HEIGHT">Constant Field Values</a></dd>
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-<div class="block">Makes a new instance of GUI. This initialises the JCGP experiment and 
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-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a reference to the <code>JCGP</code> experiment.</dd>
-</dl>
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-<div class="block">Starts the evaluation process with the given test case.
- It does so by calling <code>evaluateTestCase()</code> on
- the population pane.</div>
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-<dd><code>testCase</code> - the test case to evaluate.</dd>
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-<pre>public&nbsp;void&nbsp;setEvaluating(boolean&nbsp;value)</pre>
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-<dd>the index of the chromosome currently being looked at.</dd>
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-</ul>
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-</div>
-<!-- ========= END OF CLASS DATA ========= -->
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-<li><a href="package-summary.html">Package</a></li>
-<li class="navBarCell1Rev">Class</li>
-<li><a href="class-use/GUI.html">Use</a></li>
-<li><a href="package-tree.html">Tree</a></li>
-<li><a href="../../deprecated-list.html">Deprecated</a></li>
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diff --git a/doc/jcgp/gui/class-use/GUI.html b/doc/jcgp/gui/class-use/GUI.html
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-<caption><span>Packages that use <a href="../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</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.gui.population">jcgp.gui.population</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="#jcgp.gui.settings">jcgp.gui.settings</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="#jcgp.gui.settings.testcase">jcgp.gui.settings.testcase</a></td>
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-<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/gui/GUI.html" title="class in jcgp.gui">GUI</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>
-<tr class="rowColor">
-<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>
-<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>
-<tr class="rowColor">
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/PopulationPane.html#PopulationPane-jcgp.gui.GUI-">PopulationPane</a></span>(<a href="../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui)</code>&nbsp;</td>
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-<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/settings/package-summary.html">jcgp.gui.settings</a> with parameters of type <a href="../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#SettingsPane-jcgp.gui.GUI-">SettingsPane</a></span>(<a href="../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui)</code>
-<div class="block">Create a new instance of <code>SettingsPane</code> associated
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-<tbody>
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/testcase/TestCaseTable.html#TestCaseTable-jcgp.backend.modules.problem.TestCaseProblem-jcgp.gui.GUI-">TestCaseTable</a></span>(<a href="../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;java.lang.Object&gt;&nbsp;testCaseProblem,
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-<h2 title="Class ConsolePane" class="title">Class ConsolePane</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Node</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Parent</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.Region</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.Pane</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.AnchorPane</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.gui.console.ConsolePane</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
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-<dt>All Implemented Interfaces:</dt>
-<dd>javafx.css.Styleable, javafx.event.EventTarget, <a href="../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">ConsolePane</span>
-extends javafx.scene.layout.AnchorPane
-implements <a href="../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a></pre>
-<div class="block">Console pane used by the GUI to display CGP output messages.
- This class realises <code>Console</code>. It consists of a JavaFX
- <code>TextArea</code> and a <code>StringBuffer</code>. The buffer is filled
- as print messages are queued. Calling <code>flush()</code> writes the
- contents of the buffer to the <code>TextArea</code> and empties the buffer.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources"><code>Console</code></a></dd>
-</dl>
-</li>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/gui/console/ConsolePane.html#ConsolePane--">ConsolePane</a></span>()</code>
-<div class="block">Creates a new instance of this class.</div>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
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-<th class="colFirst" scope="col">Modifier and Type</th>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/console/ConsolePane.html#flush--">flush</a></span>()</code>
-<div class="block">Outputs all buffered messages to the console.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/console/ConsolePane.html#print-java.lang.String-">print</a></span>(java.lang.String&nbsp;s)</code>
-<div class="block">Prints a string without line break at the end (unless the string 
- itself specifies one).</div>
-</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/console/ConsolePane.html#println-java.lang.String-">println</a></span>(java.lang.String&nbsp;s)</code>
-<div class="block">Prints a string and automatically adds a line break at the end.</div>
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getOnMouseDragEntered, getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, hasProperties, hoverProperty, idProperty, impl_getAccessible, impl_getLeafTransform, impl_getMatchingStyles, impl_getPeer, impl_getPivotX, impl_getPivotY, impl_getPivotZ, impl_getStyleMap, impl_hasTransforms, impl_isShowMnemonics, impl_isTreeVisible, impl_pickNode, impl_processCSS, impl_reapplyCSS, impl_setShowMnemonics, impl_setStyleMap, impl_showMnemonicsProperty, impl_syncPeer, impl_transformsChanged, impl_traverse, inputMethodRequestsProperty, intersects, intersects, isCache, isDisable, isDisabled, isFocused, isFocusTraversable, isHover, isManaged, isMouseTransparent, isPickOnBounds, isPressed, isVisible, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParent, localToParent, localToParent, localToParent, localToParent, localToParentTransformProperty, localToScene, localToScene, localToScene, localToScene, localToScene, localToSceneTransformProperty, localToScreen, localToScreen, localToScreen, localToScreen, localToScreen, lookupAll, managedProperty, mouseTransparentProperty, nodeOrientationProperty, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, onDragEnteredProperty, onDragExitedProperty, onDragOverProperty, onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, parentToLocal, parentToLocal, parentToLocal, parentToLocal, parentToLocal, pickOnBoundsProperty, pressedProperty, pseudoClassStateChanged, relocate, removeEventFilter, removeEventHandler, requestFocus, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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-<pre>public&nbsp;ConsolePane()</pre>
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-<div class="block">Prints a string and automatically adds a line break at the end.</div>
-<dl>
-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../jcgp/backend/resources/Console.html#println-java.lang.String-">println</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a></code></dd>
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-<div class="block">Prints a string without line break at the end (unless the string 
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-<dd><code><a href="../../../jcgp/backend/resources/Console.html#print-java.lang.String-">print</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/resources/Console.html" title="interface in jcgp.backend.resources">Console</a></code></dd>
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-<div class="block">Outputs all buffered messages to the console. Only necessary
- if concurrent accesses must be avoided.</div>
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-<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
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-</dl>
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-<h2 title="Class GUIConsole" class="title">Class GUIConsole</h2>
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-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Node</li>
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-<li>javafx.scene.layout.Pane</li>
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deleted file mode 100644
index 3ecf53e..0000000
--- a/doc/jcgp/gui/console/class-use/ConsolePane.html
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deleted file mode 100644
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diff --git a/doc/jcgp/gui/dragresize/HorizontalDragResize.html b/doc/jcgp/gui/dragresize/HorizontalDragResize.html
deleted file mode 100644
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--- a/doc/jcgp/gui/dragresize/HorizontalDragResize.html
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-<div class="subTitle">jcgp.gui.dragresize</div>
-<h2 title="Class HorizontalDragResize" class="title">Class HorizontalDragResize</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.gui.dragresize.HorizontalDragResize</li>
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-<br>
-<pre>public class <span class="typeNameLabel">HorizontalDragResize</span>
-extends java.lang.Object</pre>
-<div class="block">This class adds horizontal drag resize functionality to any 
- arbitrary region provided. This is done by using the static
- method <code>makeDragResizable()</code>.
- <br><br>
- This is based on a class by Andrew Till found on:
- http://andrewtill.blogspot.co.uk/2012/12/dragging-to-resize-javafx-region.html</div>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/dragresize/HorizontalDragResize.html#makeDragResizable-javafx.scene.layout.Region-">makeDragResizable</a></span>(javafx.scene.layout.Region&nbsp;region)</code>
-<div class="block">Makes the specified region drag resizable.</div>
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-<h4>makeDragResizable</h4>
-<pre>public static&nbsp;void&nbsp;makeDragResizable(javafx.scene.layout.Region&nbsp;region)</pre>
-<div class="block">Makes the specified region drag resizable.
- This particular implementation only creates a resize 
- click-and-drag area on the left side of the region. 
- The resize area is defined by <code>GUI.RESIZE_MARGIN</code>.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>region</code> - the region to make resizable.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
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-<!-- ========= END OF CLASS DATA ========= -->
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diff --git a/doc/jcgp/gui/dragresize/VerticalDragResize.html b/doc/jcgp/gui/dragresize/VerticalDragResize.html
deleted file mode 100644
index 4897b4e..0000000
--- a/doc/jcgp/gui/dragresize/VerticalDragResize.html
+++ /dev/null
@@ -1,253 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
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-<meta name="date" content="2014-05-22">
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-    try {
-        if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="VerticalDragResize";
-        }
-    }
-    catch(err) {
-    }
-//-->
-var methods = {"i0":9};
-var tabs = {65535:["t0","All Methods"],1:["t1","Static Methods"],8:["t4","Concrete Methods"]};
-var altColor = "altColor";
-var rowColor = "rowColor";
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-</script>
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-<div class="subTitle">jcgp.gui.dragresize</div>
-<h2 title="Class VerticalDragResize" class="title">Class VerticalDragResize</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.gui.dragresize.VerticalDragResize</li>
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-<br>
-<pre>public class <span class="typeNameLabel">VerticalDragResize</span>
-extends java.lang.Object</pre>
-<div class="block">This class adds vertical drag resize functionality to any 
- arbitrary region provided. This is done by using the static
- method <code>makeDragResizable()</code>.
- <br><br>
- This is based on a class by Andrew Till found on:
- http://andrewtill.blogspot.co.uk/2012/12/dragging-to-resize-javafx-region.html</div>
-</li>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/dragresize/VerticalDragResize.html#makeDragResizable-javafx.scene.layout.Region-">makeDragResizable</a></span>(javafx.scene.layout.Region&nbsp;region)</code>
-<div class="block">Makes the specified region drag resizable.</div>
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-<h4>makeDragResizable</h4>
-<pre>public static&nbsp;void&nbsp;makeDragResizable(javafx.scene.layout.Region&nbsp;region)</pre>
-<div class="block">Makes the specified region drag resizable.
- This particular implementation only creates a resize 
- click-and-drag area on the top side of the region. 
- The resize area is defined by <code>GUI.RESIZE_MARGIN</code>.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>region</code> - the region to make resizable.</dd>
-</dl>
-</li>
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-<td class="colFirst"><a href="../../../jcgp/gui/dragresize/HorizontalDragResize.html" title="class in jcgp.gui.dragresize">HorizontalDragResize</a></td>
-<td class="colLast">
-<div class="block">This class adds horizontal drag resize functionality to any 
- arbitrary region provided.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/gui/dragresize/VerticalDragResize.html" title="class in jcgp.gui.dragresize">VerticalDragResize</a></td>
-<td class="colLast">
-<div class="block">This class adds vertical drag resize functionality to any 
- arbitrary region provided.</div>
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-<td class="colOne"><a href="../../jcgp/gui/class-use/GUI.html#jcgp.gui.population">GUI</a>
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diff --git a/doc/jcgp/gui/population/ChromosomePane.html b/doc/jcgp/gui/population/ChromosomePane.html
deleted file mode 100644
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--- a/doc/jcgp/gui/population/ChromosomePane.html
+++ /dev/null
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-<div class="subTitle">jcgp.gui.population</div>
-<h2 title="Class ChromosomePane" class="title">Class ChromosomePane</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Node</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Parent</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.Region</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.control.Control</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.control.ScrollPane</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.gui.population.ChromosomePane</li>
-</ul>
-</li>
-</ul>
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-<dd>javafx.css.Styleable, javafx.event.EventTarget, javafx.scene.control.Skinnable</dd>
-</dl>
-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">ChromosomePane</span>
-extends javafx.scene.control.ScrollPane</pre>
-<div class="block">This extension of <code>ScrollPane</code> contains a series of
- nodes, inputs and outputs spread across a grid. It also contains
- all of the connection lines overlaid over the nodes, inputs and outputs.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
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-<tr class="altColor">
-<td class="colOne"><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>
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/ChromosomePane.html#isEvaluating--">isEvaluating</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/ChromosomePane.html#relockOutputs--">relockOutputs</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/ChromosomePane.html#setInputs-java.lang.Object:A-">setInputs</a></span>(java.lang.Object[]&nbsp;values)</code>&nbsp;</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/ChromosomePane.html#unlockOutputs--">unlockOutputs</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/ChromosomePane.html#updateValues--">updateValues</a></span>()</code>&nbsp;</td>
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-                      <a href="../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui,
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diff --git a/doc/jcgp/gui/population/FunctionSelector.html b/doc/jcgp/gui/population/FunctionSelector.html
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diff --git a/doc/jcgp/gui/population/GUIGene.GUIGeneState.html b/doc/jcgp/gui/population/GUIGene.GUIGeneState.html
deleted file mode 100644
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-<div class="subTitle">jcgp.gui.population</div>
-<h2 title="Enum GUIGene.GUIGeneState" class="title">Enum GUIGene.GUIGeneState</h2>
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-<li>java.lang.Object</li>
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-<ul class="inheritance">
-<li>jcgp.gui.population.GUIGene.GUIGeneState</li>
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-<pre>public static enum <span class="typeNameLabel">GUIGene.GUIGeneState</span>
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-<h2 title="Class GUIInput" class="title">Class GUIInput</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Node</li>
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-<ul class="inheritance">
-<li>javafx.scene.Parent</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Group</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">jcgp.gui.population.GUIGene</a></li>
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-<ul class="inheritance">
-<li>jcgp.gui.population.GUIInput</li>
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-<dt>All Implemented Interfaces:</dt>
-<dd>javafx.css.Styleable, javafx.event.EventTarget</dd>
-</dl>
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-<br>
-<pre>public class <span class="typeNameLabel">GUIInput</span>
-extends <a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></pre>
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-<h3>Properties inherited from class&nbsp;javafx.scene.Group</h3>
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-<h3>Properties inherited from class&nbsp;javafx.scene.Node</h3>
-<code>blendModeProperty, boundsInLocalProperty, boundsInParentProperty, cacheHintProperty, cacheProperty, clipProperty, cursorProperty, depthTestProperty, disabledProperty, disableProperty, effectiveNodeOrientationProperty, effectProperty, eventDispatcherProperty, focusedProperty, focusTraversableProperty, hoverProperty, idProperty, impl_showMnemonicsProperty, inputMethodRequestsProperty, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParentTransformProperty, localToSceneTransformProperty, managedProperty, mouseTransparentProperty, nodeOrientationProperty, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, onDragEnteredProperty, onDragExitedProperty, onDragOverProperty, onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, pickOnBoundsProperty, pressedProperty, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, styleProperty, translateXProperty, translateYProperty, translateZProperty, visibleProperty</code></li>
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-<code><a href="../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a></code></li>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colOne" scope="col">Constructor and Description</th>
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-<tr class="altColor">
-<td class="colOne"><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,
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
-<tr>
-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
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-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#addLocks-int-">addLocks</a></span>(int&nbsp;value)</code>&nbsp;</td>
-</tr>
-<tr id="i1" 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"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#getChangingConnection--">getChangingConnection</a></span>()</code>&nbsp;</td>
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-<tr id="i2" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#removeLocks-int-">removeLocks</a></span>(int&nbsp;value)</code>&nbsp;</td>
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-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#resetState--">resetState</a></span>()</code>&nbsp;</td>
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-<tr id="i4" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
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-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine</a></span>(<a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a>&nbsp;gene)</code>&nbsp;</td>
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-<tr id="i6" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates</a></span>(<a href="../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>
-<div class="block">Set all connections to a given state.</div>
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-<tr id="i7" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState</a></span>(<a href="../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>&nbsp;</td>
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-<tr id="i8" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#setValue-java.lang.Object-">setValue</a></span>(java.lang.Object&nbsp;newValue)</code>&nbsp;</td>
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-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#updateLines--">updateLines</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIInput.html#updateText--">updateText</a></span>()</code>&nbsp;</td>
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-<code><a href="../../../jcgp/gui/population/GUIGene.html#getLocks--">getLocks</a>, <a href="../../../jcgp/gui/population/GUIGene.html#getState--">getState</a>, <a href="../../../jcgp/gui/population/GUIGene.html#isLocked--">isLocked</a></code></li>
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getOnKeyTyped, getOnMouseClicked, getOnMouseDragEntered, getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, hasProperties, hoverProperty, idProperty, impl_getAccessible, impl_getLeafTransform, impl_getMatchingStyles, impl_getPeer, impl_getPivotX, impl_getPivotY, impl_getPivotZ, impl_getStyleMap, impl_hasTransforms, impl_isShowMnemonics, impl_isTreeVisible, impl_pickNode, impl_processCSS, impl_reapplyCSS, impl_setShowMnemonics, impl_setStyleMap, impl_showMnemonicsProperty, impl_syncPeer, impl_transformsChanged, impl_traverse, inputMethodRequestsProperty, intersects, intersects, isCache, isDisable, isDisabled, isFocused, isFocusTraversable, isHover, isManaged, isMouseTransparent, isPickOnBounds, isPressed, isResizable, isVisible, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParent, localToParent, localToParent, localToParent, localToParent, localToParentTransformProperty, localToScene, localToScene, localToScene, localToScene, localToScene, localToSceneTransformProperty, localToScreen, localToScreen, localToScreen, localToScreen, localToScreen, lookupAll, managedProperty, maxHeight, maxWidth, mouseTransparentProperty, nodeOrientationProperty, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, onDragEnteredProperty, onDragExitedProperty, onDragOverProperty, onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, parentToLocal, parentToLocal, parentToLocal, parentToLocal, parentToLocal, pickOnBoundsProperty, pressedProperty, pseudoClassStateChanged, relocate, removeEventFilter, removeEventHandler, requestFocus, resize, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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-<code>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</code></li>
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-<div class="block">Set all connections to a given state.</div>
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-<dd><code><a href="../../../jcgp/gui/population/GUIGene.html#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates</a></code>&nbsp;in class&nbsp;<code><a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>newState</code> - the state to set connections to.</dd>
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-<dd><code><a href="../../../jcgp/gui/population/GUIGene.html#setChangingConnection-jcgp.backend.population.Connection-">setChangingConnection</a></code>&nbsp;in class&nbsp;<code><a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></code></dd>
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diff --git a/doc/jcgp/gui/population/GUINode.html b/doc/jcgp/gui/population/GUINode.html
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-<div class="subTitle">jcgp.gui.population</div>
-<h2 title="Class GUINode" class="title">Class GUINode</h2>
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-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUINode.html#getChangingConnection--">getChangingConnection</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code>void</code></td>
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-<tr id="i7" class="rowColor">
-<td class="colFirst"><code>void</code></td>
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-<td class="colFirst"><code>void</code></td>
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relocate, removeEventFilter, removeEventHandler, requestFocus, resize, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, 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-<li>Summary:&nbsp;</li>
-<li><a href="#nested.classes.inherited.from.class.jcgp.gui.population.GUIGene">Nested</a>&nbsp;|&nbsp;</li>
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-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.gui.population</div>
-<h2 title="Class GUIOutput" class="title">Class GUIOutput</h2>
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-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Node</li>
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-<li>javafx.scene.Parent</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Group</li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">jcgp.gui.population.GUIGene</a></li>
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-<li>jcgp.gui.population.GUIOutput</li>
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-<br>
-<pre>public class <span class="typeNameLabel">GUIOutput</span>
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-<code><a href="../../../jcgp/gui/population/GUIGene.html#NODE_RADIUS">NODE_RADIUS</a>, <a href="../../../jcgp/gui/population/GUIGene.html#NODE_TEXT">NODE_TEXT</a>, <a href="../../../jcgp/gui/population/GUIGene.html#SOCKET_RADIUS">SOCKET_RADIUS</a>, <a href="../../../jcgp/gui/population/GUIGene.html#SPACING">SPACING</a>, <a href="../../../jcgp/gui/population/GUIGene.html#THETA">THETA</a></code></li>
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-<td class="colOne"><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,
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-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#addLocks-int-">addLocks</a></span>(int&nbsp;value)</code>&nbsp;</td>
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-<td class="colFirst"><code><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#getChangingConnection--">getChangingConnection</a></span>()</code>&nbsp;</td>
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-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#lock--">lock</a></span>()</code>&nbsp;</td>
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-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#removeLocks-int-">removeLocks</a></span>(int&nbsp;value)</code>&nbsp;</td>
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-<tr id="i4" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#resetState--">resetState</a></span>()</code>&nbsp;</td>
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-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
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-<tr id="i6" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine</a></span>(<a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a>&nbsp;gene)</code>&nbsp;</td>
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-<tr id="i7" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates</a></span>(<a href="../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>&nbsp;</td>
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-<tr id="i8" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><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>
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-<tr id="i9" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState</a></span>(<a href="../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>&nbsp;</td>
-</tr>
-<tr id="i10" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#unlock--">unlock</a></span>()</code>&nbsp;</td>
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-<tr id="i11" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#updateLines--">updateLines</a></span>()</code>&nbsp;</td>
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-<tr id="i12" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/population/GUIOutput.html#updateText--">updateText</a></span>()</code>&nbsp;</td>
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getOnKeyTyped, getOnMouseClicked, getOnMouseDragEntered, getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, hasProperties, hoverProperty, idProperty, impl_getAccessible, impl_getLeafTransform, impl_getMatchingStyles, impl_getPeer, impl_getPivotX, impl_getPivotY, impl_getPivotZ, impl_getStyleMap, impl_hasTransforms, impl_isShowMnemonics, impl_isTreeVisible, impl_pickNode, impl_processCSS, impl_reapplyCSS, impl_setShowMnemonics, impl_setStyleMap, impl_showMnemonicsProperty, impl_syncPeer, impl_transformsChanged, impl_traverse, inputMethodRequestsProperty, intersects, intersects, isCache, isDisable, isDisabled, isFocused, isFocusTraversable, isHover, isManaged, isMouseTransparent, isPickOnBounds, isPressed, isResizable, isVisible, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParent, localToParent, localToParent, localToParent, localToParent, localToParentTransformProperty, localToScene, localToScene, localToScene, localToScene, localToScene, localToSceneTransformProperty, localToScreen, localToScreen, localToScreen, localToScreen, localToScreen, lookupAll, managedProperty, maxHeight, maxWidth, mouseTransparentProperty, nodeOrientationProperty, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, 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relocate, removeEventFilter, removeEventHandler, requestFocus, resize, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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diff --git a/doc/jcgp/gui/population/PopulationPane.html b/doc/jcgp/gui/population/PopulationPane.html
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diff --git a/doc/jcgp/gui/population/class-use/ChromosomePane.html b/doc/jcgp/gui/population/class-use/ChromosomePane.html
deleted file mode 100644
index add9624..0000000
--- a/doc/jcgp/gui/population/class-use/ChromosomePane.html
+++ /dev/null
@@ -1,175 +0,0 @@
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-<!-- NewPage -->
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-<head>
-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Class jcgp.gui.population.ChromosomePane</title>
-<meta name="date" content="2014-05-22">
-<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"><!--
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-            parent.document.title="Uses of Class jcgp.gui.population.ChromosomePane";
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-//-->
-</script>
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-<li><a href="../package-summary.html">Package</a></li>
-<li><a href="../../../../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
-<li><a href="../package-tree.html">Tree</a></li>
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-<h2 title="Uses of Class jcgp.gui.population.ChromosomePane" class="title">Uses of Class<br>jcgp.gui.population.ChromosomePane</h2>
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-<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.gui.population">jcgp.gui.population</a></td>
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-<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/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">ChromosomePane</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,
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-<tr class="rowColor">
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-       <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>
-<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>
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-<li><a href="../package-summary.html">Package</a></li>
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-<li class="navBarCell1Rev">Use</li>
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diff --git a/doc/jcgp/gui/population/class-use/FunctionSelector.html b/doc/jcgp/gui/population/class-use/FunctionSelector.html
deleted file mode 100644
index 15a596e..0000000
--- a/doc/jcgp/gui/population/class-use/FunctionSelector.html
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-<!-- NewPage -->
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-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Class jcgp.gui.population.FunctionSelector</title>
-<meta name="date" content="2014-05-22">
-<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 {
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-//-->
-</script>
-<noscript>
-<div>JavaScript is disabled on your browser.</div>
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diff --git a/doc/jcgp/gui/population/class-use/GUIGene.GUIGeneState.html b/doc/jcgp/gui/population/class-use/GUIGene.GUIGeneState.html
deleted file mode 100644
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+++ /dev/null
@@ -1,220 +0,0 @@
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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/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</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.gui.population">jcgp.gui.population</a></td>
-<td class="colLast">&nbsp;</td>
-</tr>
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-<li class="blockList">
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-<h3>Uses of <a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</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/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</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/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a></code></td>
-<td class="colLast"><span class="typeNameLabel">GUIGene.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIGene.html#getState--">getState</a></span>()</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>static <a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a></code></td>
-<td class="colLast"><span class="typeNameLabel">GUIGene.GUIGeneState.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html#valueOf-java.lang.String-">valueOf</a></span>(java.lang.String&nbsp;name)</code>
-<div class="block">Returns the enum constant of this type with the specified name.</div>
-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><code>static <a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>[]</code></td>
-<td class="colLast"><span class="typeNameLabel">GUIGene.GUIGeneState.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html#values--">values</a></span>()</code>
-<div class="block">Returns an array containing the constants of this enum type, in
-the order they are declared.</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/gui/population/package-summary.html">jcgp.gui.population</a> with parameters of type <a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</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#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</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#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>
-<div class="block">Set all connections to a given state.</div>
-</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#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</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#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>&nbsp;</td>
-</tr>
-<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#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</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#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</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#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>&nbsp;</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">GUIGene.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/GUIGene.html#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;newState)</code>&nbsp;</td>
-</tr>
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diff --git a/doc/jcgp/gui/population/class-use/GUIGene.html b/doc/jcgp/gui/population/class-use/GUIGene.html
deleted file mode 100644
index 32874c8..0000000
--- a/doc/jcgp/gui/population/class-use/GUIGene.html
+++ /dev/null
@@ -1,197 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
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-<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
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-<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/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</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.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.gui.population">
-<!--   -->
-</a>
-<h3>Uses of <a href="../../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</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 subclasses, and an explanation">
-<caption><span>Subclasses of <a href="../../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a> in <a href="../../../../jcgp/gui/population/package-summary.html">jcgp.gui.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/gui/population/GUIInput.html" title="class in jcgp.gui.population">GUIInput</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/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</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/gui/population/GUIOutput.html" title="class in jcgp.gui.population">GUIOutput</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/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</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#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a>&nbsp;gene)</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#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a>&nbsp;gene)</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#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a>&nbsp;gene)</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#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine</a></span>(<a href="../../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a>&nbsp;gene)</code>&nbsp;</td>
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diff --git a/doc/jcgp/gui/population/class-use/GUIInput.html b/doc/jcgp/gui/population/class-use/GUIInput.html
deleted file mode 100644
index c9b77ef..0000000
--- a/doc/jcgp/gui/population/class-use/GUIInput.html
+++ /dev/null
@@ -1,124 +0,0 @@
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diff --git a/doc/jcgp/gui/population/class-use/GUINode.html b/doc/jcgp/gui/population/class-use/GUINode.html
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--- a/doc/jcgp/gui/population/class-use/GUINode.html
+++ /dev/null
@@ -1,191 +0,0 @@
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-<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.gui">jcgp.gui</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>
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-<h3>Uses of <a href="../../../../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</a> in <a href="../../../../jcgp/gui/package-summary.html">jcgp.gui</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/package-summary.html">jcgp.gui</a> with parameters of type <a href="../../../../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</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">GUI.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/GUI.html#bringFunctionSelector-javafx.scene.input.MouseEvent-jcgp.gui.population.GUINode-">bringFunctionSelector</a></span>(javafx.scene.input.MouseEvent&nbsp;event,
-                     <a href="../../../../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</a>&nbsp;node)</code>
-<div class="block">Relocate the function selector to the right position
- relative to the specified node and set it visible.</div>
-</td>
-</tr>
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-</table>
-</li>
-<li class="blockList"><a name="jcgp.gui.population">
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-<h3>Uses of <a href="../../../../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</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/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</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">FunctionSelector.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/population/FunctionSelector.html#relocateAndShow-javafx.scene.input.MouseEvent-jcgp.gui.population.GUINode-">relocateAndShow</a></span>(javafx.scene.input.MouseEvent&nbsp;event,
-               <a href="../../../../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</a>&nbsp;node)</code>&nbsp;</td>
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diff --git a/doc/jcgp/gui/population/class-use/GUIOutput.html b/doc/jcgp/gui/population/class-use/GUIOutput.html
deleted file mode 100644
index fefc469..0000000
--- a/doc/jcgp/gui/population/class-use/GUIOutput.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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diff --git a/doc/jcgp/gui/population/class-use/PopulationPane.html b/doc/jcgp/gui/population/class-use/PopulationPane.html
deleted file mode 100644
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--- a/doc/jcgp/gui/population/class-use/PopulationPane.html
+++ /dev/null
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-<caption><span>Packages that use <a href="../../../../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Package</th>
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-<h3>Uses of <a href="../../../../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</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/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</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>
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diff --git a/doc/jcgp/gui/population/package-frame.html b/doc/jcgp/gui/population/package-frame.html
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-<div class="indexContainer">
-<h2 title="Classes">Classes</h2>
-<ul title="Classes">
-<li><a href="ChromosomePane.html" title="class in jcgp.gui.population" target="classFrame">ChromosomePane</a></li>
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-<li><a href="GUIGene.html" title="class in jcgp.gui.population" target="classFrame">GUIGene</a></li>
-<li><a href="GUIInput.html" title="class in jcgp.gui.population" target="classFrame">GUIInput</a></li>
-<li><a href="GUINode.html" title="class in jcgp.gui.population" target="classFrame">GUINode</a></li>
-<li><a href="GUIOutput.html" title="class in jcgp.gui.population" target="classFrame">GUIOutput</a></li>
-<li><a href="PopulationPane.html" title="class in jcgp.gui.population" target="classFrame">PopulationPane</a></li>
-</ul>
-<h2 title="Enums">Enums</h2>
-<ul title="Enums">
-<li><a href="GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population" target="classFrame">GUIGene.GUIGeneState</a></li>
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diff --git a/doc/jcgp/gui/population/package-summary.html b/doc/jcgp/gui/population/package-summary.html
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-<tr>
-<th class="colFirst" scope="col">Class</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">ChromosomePane</a></td>
-<td class="colLast">
-<div class="block">This extension of <code>ScrollPane</code> contains a series of
- nodes, inputs and outputs spread across a grid.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/gui/population/FunctionSelector.html" title="class in jcgp.gui.population">FunctionSelector</a></td>
-<td class="colLast">
-<div class="block">A menu class, exposes all of the allowed functions
- when called by a node, so that the node function can be changed.</div>
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-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></td>
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-<tr class="rowColor">
-<td class="colFirst"><a href="../../../jcgp/gui/population/GUIOutput.html" title="class in jcgp.gui.population">GUIOutput</a></td>
-<td class="colLast">&nbsp;</td>
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-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</a></td>
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-<th class="colFirst" scope="col">Enum</th>
-<th class="colLast" scope="col">Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../jcgp/gui/population/GUIGene.GUIGeneState.html" title="enum in jcgp.gui.population">GUIGene.GUIGeneState</a></td>
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diff --git a/doc/jcgp/gui/population/package-tree.html b/doc/jcgp/gui/population/package-tree.html
deleted file mode 100644
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--- a/doc/jcgp/gui/population/package-tree.html
+++ /dev/null
@@ -1,194 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!-- NewPage -->
-<html lang="en">
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-<span class="packageHierarchyLabel">Package Hierarchies:</span>
-<ul class="horizontal">
-<li><a href="../../../overview-tree.html">All Packages</a></li>
-</ul>
-</div>
-<div class="contentContainer">
-<h2 title="Class Hierarchy">Class Hierarchy</h2>
-<ul>
-<li type="circle">java.lang.Object
-<ul>
-<li type="circle">javafx.scene.Node (implements javafx.event.EventTarget, javafx.css.Styleable)
-<ul>
-<li type="circle">javafx.scene.Parent
-<ul>
-<li type="circle">javafx.scene.Group
-<ul>
-<li type="circle">jcgp.gui.population.<a href="../../../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population"><span class="typeNameLink">GUIGene</span></a>
-<ul>
-<li type="circle">jcgp.gui.population.<a href="../../../jcgp/gui/population/GUIInput.html" title="class in jcgp.gui.population"><span class="typeNameLink">GUIInput</span></a></li>
-<li type="circle">jcgp.gui.population.<a href="../../../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population"><span class="typeNameLink">GUINode</span></a></li>
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-</ul>
-</li>
-<li type="circle">javafx.scene.layout.Region
-<ul>
-<li type="circle">javafx.scene.control.Control (implements javafx.scene.control.Skinnable)
-<ul>
-<li type="circle">javafx.scene.control.ScrollPane
-<ul>
-<li type="circle">jcgp.gui.population.<a href="../../../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population"><span class="typeNameLink">ChromosomePane</span></a></li>
-</ul>
-</li>
-<li type="circle">javafx.scene.control.TabPane
-<ul>
-<li type="circle">jcgp.gui.population.<a href="../../../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population"><span class="typeNameLink">PopulationPane</span></a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li type="circle">javafx.scene.layout.Pane
-<ul>
-<li type="circle">javafx.scene.layout.VBox
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-</ul>
-</li>
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-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-<h2 title="Enum Hierarchy">Enum Hierarchy</h2>
-<ul>
-<li type="circle">java.lang.Object
-<ul>
-<li type="circle">java.lang.Enum&lt;E&gt; (implements java.lang.Comparable&lt;T&gt;, java.io.Serializable)
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diff --git a/doc/jcgp/gui/population/package-use.html b/doc/jcgp/gui/population/package-use.html
deleted file mode 100644
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+++ /dev/null
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-<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.gui">jcgp.gui</a></td>
-<td class="colLast">&nbsp;</td>
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-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/gui/population/class-use/GUINode.html#jcgp.gui">GUINode</a>&nbsp;</td>
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-<tr>
-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/gui/population/class-use/ChromosomePane.html#jcgp.gui.population">ChromosomePane</a>
-<div class="block">This extension of <code>ScrollPane</code> contains a series of
- nodes, inputs and outputs spread across a grid.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colOne"><a href="../../../jcgp/gui/population/class-use/GUIGene.html#jcgp.gui.population">GUIGene</a>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/gui/population/class-use/GUIGene.GUIGeneState.html#jcgp.gui.population">GUIGene.GUIGeneState</a>&nbsp;</td>
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-<tr class="rowColor">
-<td class="colOne"><a href="../../../jcgp/gui/population/class-use/GUINode.html#jcgp.gui.population">GUINode</a>&nbsp;</td>
-</tr>
-<tr class="altColor">
-<td class="colOne"><a href="../../../jcgp/gui/population/class-use/PopulationPane.html#jcgp.gui.population">PopulationPane</a>&nbsp;</td>
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diff --git a/doc/jcgp/gui/settings/SettingsPane.html b/doc/jcgp/gui/settings/SettingsPane.html
deleted file mode 100644
index bb1e7b2..0000000
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-<meta name="date" content="2014-05-22">
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-<div class="subTitle">jcgp.gui.settings</div>
-<h2 title="Class SettingsPane" class="title">Class SettingsPane</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Node</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Parent</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.Region</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.Pane</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.AnchorPane</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.gui.settings.SettingsPane</li>
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-</li>
-</ul>
-</li>
-</ul>
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-<dd>javafx.css.Styleable, javafx.event.EventTarget</dd>
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-<pre>public class <span class="typeNameLabel">SettingsPane</span>
-extends javafx.scene.layout.AnchorPane</pre>
-<div class="block">This is a fairly hefty class which encapsulates the entire right-hand
- control pane. It contains base parameters, module selectors and their
- associated parameters, flow controls and file loading/saving buttons.
- <br><br>
- A single instance of this class is used in <code>GUI</code>.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
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-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#SettingsPane-jcgp.gui.GUI-">SettingsPane</a></span>(<a href="../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui)</code>
-<div class="block">Create a new instance of <code>SettingsPane</code> associated
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-<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
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-</tr>
-<tr id="i0" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#applyParameters--">applyParameters</a></span>()</code>
-<div class="block">Calls applyValue() on every parameter.</div>
-</td>
-</tr>
-<tr id="i1" class="rowColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#areParametersValid--">areParametersValid</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i2" class="altColor">
-<td class="colFirst"><code><a href="../../../jcgp/gui/settings/testcase/TestCaseTable.html" title="class in jcgp.gui.settings.testcase">TestCaseTable</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#getTestCaseTable--">getTestCaseTable</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i3" class="rowColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#isExperimentRunning--">isExperimentRunning</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i4" class="altColor">
-<td class="colFirst"><code>boolean</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#isResetRequired--">isResetRequired</a></span>()</code>&nbsp;</td>
-</tr>
-<tr id="i5" class="rowColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#revalidateParameters--">revalidateParameters</a></span>()</code>
-<div class="block">Calls validate() on every parameter.</div>
-</td>
-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/gui/settings/SettingsPane.html#updateControls-boolean-boolean-">updateControls</a></span>(boolean&nbsp;running,
-              boolean&nbsp;finished)</code>
-<div class="block">Updates all of the controls to their appropriate state based on the status of the
- experiment, in order to prevent inappropriate operations if the experiment is
- running or finished.</div>
-</td>
-</tr>
-</table>
-<ul class="blockList">
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onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, parentToLocal, parentToLocal, parentToLocal, parentToLocal, parentToLocal, pickOnBoundsProperty, pressedProperty, pseudoClassStateChanged, relocate, removeEventFilter, removeEventHandler, requestFocus, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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- <br><br>
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-<pre>public&nbsp;void&nbsp;updateControls(boolean&nbsp;running,
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- experiment, in order to prevent inappropriate operations if the experiment is
- running or finished.</div>
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-<dd><code>running</code> - true if the experiment is running.</dd>
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-</li>
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diff --git a/doc/jcgp/gui/settings/class-use/SettingsPane.html b/doc/jcgp/gui/settings/class-use/SettingsPane.html
deleted file mode 100644
index 3576f53..0000000
--- a/doc/jcgp/gui/settings/class-use/SettingsPane.html
+++ /dev/null
@@ -1,167 +0,0 @@
-<!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 Thu May 22 06:02:33 BST 2014 -->
-<title>Uses of Class jcgp.gui.settings.SettingsPane</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../../script.js"></script>
-</head>
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-<script type="text/javascript"><!--
-    try {
-        if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Uses of Class jcgp.gui.settings.SettingsPane";
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-//-->
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-<li><a href="../package-summary.html">Package</a></li>
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-<li class="navBarCell1Rev">Use</li>
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-<h2 title="Uses of Class jcgp.gui.settings.SettingsPane" class="title">Uses of Class<br>jcgp.gui.settings.SettingsPane</h2>
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-<div class="classUseContainer">
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-<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.gui.settings.parameters">jcgp.gui.settings.parameters</a></td>
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-<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/settings/parameters/package-summary.html">jcgp.gui.settings.parameters</a> with parameters of type <a href="../../../../jcgp/gui/settings/SettingsPane.html" title="class in jcgp.gui.settings">SettingsPane</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 <a href="../../../../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters">GUIParameter</a>&lt;?&gt;</code></td>
-<td class="colLast"><span class="typeNameLabel">GUIParameter.</span><code><span class="memberNameLink"><a href="../../../../jcgp/gui/settings/parameters/GUIParameter.html#create-jcgp.backend.parameters.Parameter-jcgp.gui.settings.SettingsPane-">create</a></span>(<a href="../../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters">Parameter</a>&lt;?&gt;&nbsp;parameter,
-      <a href="../../../../jcgp/gui/settings/SettingsPane.html" title="class in jcgp.gui.settings">SettingsPane</a>&nbsp;sp)</code>
-<div class="block">Factory method to create @code{GUIParameter}s from @code{Parameter}s.</div>
-</td>
-</tr>
-</tbody>
-</table>
-</li>
-</ul>
-</li>
-</ul>
-</div>
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-<li><a href="../package-summary.html">Package</a></li>
-<li><a href="../../../../jcgp/gui/settings/SettingsPane.html" title="class in jcgp.gui.settings">Class</a></li>
-<li class="navBarCell1Rev">Use</li>
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-  allClassesLink = document.getElementById("allclasses_navbar_bottom");
-  if(window==top) {
-    allClassesLink.style.display = "block";
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-  }
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diff --git a/doc/jcgp/gui/settings/package-frame.html b/doc/jcgp/gui/settings/package-frame.html
deleted file mode 100644
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+++ /dev/null
@@ -1,20 +0,0 @@
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-<!-- NewPage -->
-<html lang="en">
-<head>
-<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
-<title>jcgp.gui.settings</title>
-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../script.js"></script>
-</head>
-<body>
-<h1 class="bar"><a href="../../../jcgp/gui/settings/package-summary.html" target="classFrame">jcgp.gui.settings</a></h1>
-<div class="indexContainer">
-<h2 title="Classes">Classes</h2>
-<ul title="Classes">
-<li><a href="SettingsPane.html" title="class in jcgp.gui.settings" target="classFrame">SettingsPane</a></li>
-</ul>
-</div>
-</body>
-</html>
diff --git a/doc/jcgp/gui/settings/package-summary.html b/doc/jcgp/gui/settings/package-summary.html
deleted file mode 100644
index a2cae25..0000000
--- a/doc/jcgp/gui/settings/package-summary.html
+++ /dev/null
@@ -1,145 +0,0 @@
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getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, hasProperties, hoverProperty, idProperty, impl_getAccessible, impl_getLeafTransform, impl_getMatchingStyles, impl_getPeer, impl_getPivotX, impl_getPivotY, impl_getPivotZ, impl_getStyleMap, impl_hasTransforms, impl_isShowMnemonics, impl_isTreeVisible, 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rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, hasProperties, hoverProperty, idProperty, impl_getAccessible, impl_getLeafTransform, impl_getMatchingStyles, impl_getPeer, impl_getPivotX, impl_getPivotY, impl_getPivotZ, impl_getStyleMap, impl_hasTransforms, impl_isShowMnemonics, impl_isTreeVisible, impl_pickNode, impl_processCSS, impl_reapplyCSS, impl_setShowMnemonics, impl_setStyleMap, impl_showMnemonicsProperty, impl_syncPeer, impl_transformsChanged, impl_traverse, inputMethodRequestsProperty, intersects, intersects, isCache, isDisable, isDisabled, isFocused, isFocusTraversable, isHover, isManaged, isMouseTransparent, isPickOnBounds, isPressed, isVisible, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParent, localToParent, localToParent, localToParent, localToParent, localToParentTransformProperty, localToScene, localToScene, localToScene, localToScene, localToScene, localToSceneTransformProperty, localToScreen, localToScreen, localToScreen, localToScreen, localToScreen, lookupAll, managedProperty, mouseTransparentProperty, nodeOrientationProperty, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, onDragEnteredProperty, onDragExitedProperty, onDragOverProperty, onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, parentToLocal, parentToLocal, parentToLocal, parentToLocal, parentToLocal, pickOnBoundsProperty, pressedProperty, pseudoClassStateChanged, relocate, removeEventFilter, removeEventHandler, requestFocus, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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-<div class="block">Update the control so it shows the correct value of the parameter. This method
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-<h2 title="Class GUIIntegerParameter" class="title">Class GUIIntegerParameter</h2>
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-<li>java.lang.Object</li>
-<li>
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-<li>
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-<li>
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-<li>javafx.scene.layout.Pane</li>
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-<li>
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-<li><a href="../../../../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters">jcgp.gui.settings.parameters.GUIParameter</a>&lt;java.lang.Number&gt;</li>
-<li>
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-<li>jcgp.gui.settings.parameters.GUIIntegerParameter</li>
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-<br>
-<pre>public class <span class="typeNameLabel">GUIIntegerParameter</span>
-extends <a href="../../../../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters">GUIParameter</a>&lt;java.lang.Number&gt;</pre>
-<div class="block">This extension of @code{GUIParameter} uses a @code{TextField} to display
- the value of a @code{IntegerParameter}. It cannot be constructed
- directly - instead, use @code{GUIParameter.create()}.
- <br><br>
- See <a href="../../../../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters"><code>GUIParameter</code></a> for more information.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
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-<td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/gui/settings/parameters/GUIIntegerParameter.html#refreshValue--">refreshValue</a></span>()</code>
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getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, hasProperties, hoverProperty, idProperty, impl_getAccessible, impl_getLeafTransform, impl_getMatchingStyles, impl_getPeer, impl_getPivotX, impl_getPivotY, impl_getPivotZ, impl_getStyleMap, impl_hasTransforms, impl_isShowMnemonics, impl_isTreeVisible, impl_pickNode, impl_processCSS, impl_reapplyCSS, impl_setShowMnemonics, impl_setStyleMap, impl_showMnemonicsProperty, impl_syncPeer, impl_transformsChanged, impl_traverse, inputMethodRequestsProperty, intersects, intersects, isCache, isDisable, isDisabled, isFocused, isFocusTraversable, isHover, isManaged, isMouseTransparent, isPickOnBounds, isPressed, isVisible, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParent, localToParent, localToParent, localToParent, localToParent, localToParentTransformProperty, localToScene, localToScene, localToScene, localToScene, localToScene, localToSceneTransformProperty, localToScreen, localToScreen, localToScreen, localToScreen, localToScreen, lookupAll, managedProperty, mouseTransparentProperty, nodeOrientationProperty, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, onDragEnteredProperty, onDragExitedProperty, onDragOverProperty, onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, parentToLocal, parentToLocal, parentToLocal, parentToLocal, parentToLocal, pickOnBoundsProperty, pressedProperty, pseudoClassStateChanged, relocate, removeEventFilter, removeEventHandler, requestFocus, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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-<div class="block">Update the control so it shows the correct value of the parameter. This method
- is used exclusively by the thread-safe binding created if the module is a monitor.</div>
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diff --git a/doc/jcgp/gui/settings/parameters/GUIParameter.html b/doc/jcgp/gui/settings/parameters/GUIParameter.html
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-<div class="subTitle">jcgp.gui.settings.parameters</div>
-<h2 title="Class GUIParameter" class="title">Class GUIParameter&lt;T&gt;</h2>
-</div>
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-<ul class="inheritance">
-<li>java.lang.Object</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Node</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.Parent</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.Region</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.Pane</li>
-<li>
-<ul class="inheritance">
-<li>javafx.scene.layout.HBox</li>
-<li>
-<ul class="inheritance">
-<li>jcgp.gui.settings.parameters.GUIParameter&lt;T&gt;</li>
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-<dt><span class="paramLabel">Type Parameters:</span></dt>
-<dd><code>T</code> - the parameter data type</dd>
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-<dl>
-<dt>All Implemented Interfaces:</dt>
-<dd>javafx.css.Styleable, javafx.event.EventTarget</dd>
-</dl>
-<dl>
-<dt>Direct Known Subclasses:</dt>
-<dd><a href="../../../../jcgp/gui/settings/parameters/GUIBooleanParameter.html" title="class in jcgp.gui.settings.parameters">GUIBooleanParameter</a>, <a href="../../../../jcgp/gui/settings/parameters/GUIDoubleParameter.html" title="class in jcgp.gui.settings.parameters">GUIDoubleParameter</a>, <a href="../../../../jcgp/gui/settings/parameters/GUIIntegerParameter.html" title="class in jcgp.gui.settings.parameters">GUIIntegerParameter</a></dd>
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-<pre>public abstract class <span class="typeNameLabel">GUIParameter&lt;T&gt;</span>
-extends javafx.scene.layout.HBox</pre>
-<div class="block">This is the base class for all @code{GUIParameter}s. Using the factory method @code{GUIParameter.create()}
- generates an appropriate instance of this class for the specified parameter.
- <br><br>
- A @code{GUIParameter} is an @code{HBox} containing a @code{Text} for the parameter name 
- and a @code{Control} for interaction.
- It stores an instance of its associated @code{Parameter} object and also contains a @code{Tooltip} for 
- displaying status information.
- <br><br>
- Monitor parameters are updated automatically and have their @code{Control} disabled so
- that no changes can be made via the GUI.
- Non-monitor parameters are updated automatically as well, but may be changed by the user
- if the program is not evolving.</div>
-<dl>
-<dt><span class="simpleTagLabel">Author:</span></dt>
-<dd>Eduardo Pedroni</dd>
-<dt><span class="seeLabel">See Also:</span></dt>
-<dd><a href="../../../../jcgp/backend/parameters/Parameter.html" title="class in jcgp.backend.parameters"><code>Parameter</code></a></dd>
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-<td class="colFirst"><code>boolean</code></td>
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-<div class="block">Certain parameter changes might require the experiment to be reset, either
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-<td class="colFirst"><code>void</code></td>
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getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, hasProperties, hoverProperty, idProperty, impl_getAccessible, impl_getLeafTransform, impl_getMatchingStyles, impl_getPeer, impl_getPivotX, impl_getPivotY, impl_getPivotZ, impl_getStyleMap, impl_hasTransforms, impl_isShowMnemonics, impl_isTreeVisible, impl_pickNode, impl_processCSS, impl_reapplyCSS, impl_setShowMnemonics, impl_setStyleMap, impl_showMnemonicsProperty, impl_syncPeer, impl_transformsChanged, impl_traverse, inputMethodRequestsProperty, intersects, intersects, isCache, isDisable, isDisabled, isFocused, isFocusTraversable, isHover, isManaged, isMouseTransparent, isPickOnBounds, isPressed, isVisible, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParent, localToParent, localToParent, localToParent, localToParent, localToParentTransformProperty, localToScene, localToScene, localToScene, localToScene, localToScene, localToSceneTransformProperty, localToScreen, localToScreen, localToScreen, localToScreen, localToScreen, lookupAll, managedProperty, mouseTransparentProperty, nodeOrientationProperty, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, onDragEnteredProperty, onDragExitedProperty, onDragOverProperty, onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, parentToLocal, parentToLocal, parentToLocal, parentToLocal, parentToLocal, pickOnBoundsProperty, pressedProperty, pseudoClassStateChanged, relocate, removeEventFilter, removeEventHandler, requestFocus, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setEffect, setEventDispatcher, setFocusTraversable, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, visibleProperty</code></li>
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-<div class="block">Factory method to create @code{GUIParameter}s from @code{Parameter}s. 
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- rather than manually downcasting the @code{Parameter} object every time.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>parameter</code> - a parameter for which to generate a @code{GUIParameter}.</dd>
-<dd><code>sp</code> - a reference to the @code{SettingsPane}.</dd>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>an appropriate instance of @code{GUIParameter}.</dd>
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-<pre>public&nbsp;boolean&nbsp;requiresReset()</pre>
-<div class="block">Certain parameter changes might require the experiment to be reset, either
- because the parameter is critical or because its status requires a reset.</div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>true if an experiment reset is required due to this parameter changing.</dd>
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- The new reference value will be used to determine the validity of the parameter, 
- should its value change.</div>
-</li>
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-<caption><span>Subclasses of <a href="../../../../../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters">GUIParameter</a> in <a href="../../../../../jcgp/gui/settings/parameters/package-summary.html">jcgp.gui.settings.parameters</a></span><span class="tabEnd">&nbsp;</span></caption>
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-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Class and Description</th>
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-<tr class="altColor">
-<td class="colFirst"><code>class&nbsp;</code></td>
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-<td class="colFirst"><code>class&nbsp;</code></td>
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-      <a href="../../../../../jcgp/gui/settings/SettingsPane.html" title="class in jcgp.gui.settings">SettingsPane</a>&nbsp;sp)</code>
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-<td class="colLast">
-<div class="block">This extension of @code{GUIParameter} uses a @code{CheckBox} to display
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-<td class="colFirst"><a href="../../../../jcgp/gui/settings/parameters/GUIDoubleParameter.html" title="class in jcgp.gui.settings.parameters">GUIDoubleParameter</a></td>
-<td class="colLast">
-<div class="block">This extension of @code{GUIParameter} uses a @code{TextField} to display
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-</td>
-</tr>
-<tr class="altColor">
-<td class="colFirst"><a href="../../../../jcgp/gui/settings/parameters/GUIIntegerParameter.html" title="class in jcgp.gui.settings.parameters">GUIIntegerParameter</a></td>
-<td class="colLast">
-<div class="block">This extension of @code{GUIParameter} uses a @code{TextField} to display
- the value of a @code{IntegerParameter}.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colFirst"><a href="../../../../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters">GUIParameter</a>&lt;T&gt;</td>
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-<th class="colFirst" scope="col">Package</th>
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-<th class="colOne" scope="col">Class and Description</th>
-</tr>
-<tbody>
-<tr class="altColor">
-<td class="colOne"><a href="../../../../jcgp/gui/settings/parameters/class-use/GUIParameter.html#jcgp.gui.settings.parameters">GUIParameter</a>
-<div class="block">This is the base class for all @code{GUIParameter}s.</div>
-</td>
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diff --git a/doc/jcgp/gui/settings/testcase/TestCaseTable.html b/doc/jcgp/gui/settings/testcase/TestCaseTable.html
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-<h2 title="Class TestCaseTable" class="title">Class TestCaseTable</h2>
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-<pre>public&nbsp;TestCaseTable(<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;java.lang.Object&gt;&nbsp;testCaseProblem,
-                     <a href="../../../../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a>&nbsp;gui)</pre>
-<div class="block">Make a new instance of <code>TestCaseTable</code>.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>testCaseProblem</code> - the <code>TestCaseProblem</code> whose data must be displayed.</dd>
-<dd><code>gui</code> - a reference to the GUI.</dd>
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-<pre>public&nbsp;javafx.scene.control.TableView&lt;<a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a>&lt;java.lang.Object&gt;&gt;&nbsp;getTable()</pre>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>a reference to the actual table of test cases.</dd>
-</dl>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
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-<!-- ========= END OF CLASS DATA ========= -->
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-<li class="navBarCell1Rev">Class</li>
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-<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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-</div>
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diff --git a/doc/jcgp/gui/settings/testcase/class-use/TestCaseTable.html b/doc/jcgp/gui/settings/testcase/class-use/TestCaseTable.html
deleted file mode 100644
index e265c24..0000000
--- a/doc/jcgp/gui/settings/testcase/class-use/TestCaseTable.html
+++ /dev/null
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-<meta name="date" content="2014-05-22">
-<link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
-<script type="text/javascript" src="../../../../../script.js"></script>
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diff --git a/doc/jcgp/package-frame.html b/doc/jcgp/package-frame.html
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diff --git a/doc/jcgp/package-summary.html b/doc/jcgp/package-summary.html
deleted file mode 100644
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-- 
cgit v1.2.3