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diff --git a/doc/jcgp/backend/population/Chromosome.html b/doc/jcgp/backend/population/Chromosome.html new file mode 100644 index 0000000..ffcb6f8 --- /dev/null +++ b/doc/jcgp/backend/population/Chromosome.html @@ -0,0 +1,742 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<!-- NewPage --> +<html lang="en"> +<head> +<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:06 BST 2014 --> +<title>Chromosome</title> +<meta name="date" content="2014-05-06"> +<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style"> +<script type="text/javascript" src="../../../script.js"></script> +</head> +<body> +<script type="text/javascript"><!-- + try { + if (location.href.indexOf('is-external=true') == -1) { + parent.document.title="Chromosome"; + } + } + 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":10,"i13":10,"i14":10,"i15":10,"i16":10,"i17":10}; +var tabs = {65535:["t0","All Methods"],2:["t2","Instance Methods"],8:["t4","Concrete Methods"]}; +var altColor = "altColor"; +var rowColor = "rowColor"; +var tableTab = "tableTab"; +var activeTableTab = "activeTableTab"; +</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="navBarCell1Rev">Class</li> +<li><a href="class-use/Chromosome.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>Prev Class</li> +<li><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population"><span class="typeNameLink">Next Class</span></a></li> +</ul> +<ul class="navList"> +<li><a href="../../../index.html?jcgp/backend/population/Chromosome.html" target="_top">Frames</a></li> +<li><a href="Chromosome.html" target="_top">No Frames</a></li> +</ul> +<ul class="navList" id="allclasses_navbar_top"> +<li><a href="../../../allclasses-noframe.html">All 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> +<div> +<ul class="subNavList"> +<li>Summary: </li> +<li>Nested | </li> +<li>Field | </li> +<li><a href="#constructor.summary">Constr</a> | </li> +<li><a href="#method.summary">Method</a></li> +</ul> +<ul class="subNavList"> +<li>Detail: </li> +<li>Field | </li> +<li><a href="#constructor.detail">Constr</a> | </li> +<li><a href="#method.detail">Method</a></li> +</ul> +</div> +<a name="skip.navbar.top"> +<!-- --> +</a></div> +<!-- ========= END OF TOP NAVBAR ========= --> +<!-- ======== 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<<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>></dd> +</dl> +<hr> +<br> +<pre>public class <span class="typeNameLabel">Chromosome</span> +extends java.lang.Object +implements java.lang.Comparable<<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>></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 ======== --> +<ul class="blockList"> +<li class="blockList"><a name="constructor.summary"> +<!-- --> +</a> +<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"> </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> 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> resources)</code> +<div class="block">Initialise a chromosome with the specified parameters.</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"> </span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd"> </span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd"> </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> 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> 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> o)</code> </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> 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<<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#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> </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 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 row, + int 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 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 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/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a></code></td> +<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getRandomMutableElement--">getRandomMutableElement</a></span>()</code> +<div class="block">This method is useful for mutating chromosomes.</div> +</td> +</tr> +<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> </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 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... 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 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 Chromosome(<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a> 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-"> +<!-- --> +</a> +<ul class="blockListLast"> +<li class="blockList"> +<h4>Chromosome</h4> +<pre>public Chromosome(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> 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"> +<!-- --> +</a> +<h3>Method Detail</h3> +<a name="reinitialiseConnections--"> +<!-- --> +</a> +<ul class="blockList"> +<li class="blockList"> +<h4>reinitialiseConnections</h4> +<pre>public void 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-"> +<!-- --> +</a> +<ul class="blockList"> +<li class="blockList"> +<h4>copyGenes</h4> +<pre>public void copyGenes(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> 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="getNode-int-int-"> +<!-- --> +</a> +<ul class="blockList"> +<li class="blockList"> +<h4>getNode</h4> +<pre>public <a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a> getNode(int row, + int 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-"> +<!-- --> +</a> +<ul class="blockList"> +<li class="blockList"> +<h4>getOutput</h4> +<pre>public <a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a> getOutput(int 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="getInput-int-"> +<!-- --> +</a> +<ul class="blockList"> +<li class="blockList"> +<h4>getInput</h4> +<pre>public <a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a> getInput(int 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="getFitness--"> +<!-- --> +</a> +<ul class="blockList"> +<li class="blockList"> +<h4>getFitness</h4> +<pre>public double 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 void setFitness(double 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 void setInputs(java.lang.Object... 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="getRandomMutableElement--"> +<!-- --> +</a> +<ul class="blockList"> +<li class="blockList"> +<h4>getRandomMutableElement</h4> +<pre>public <a href="../../../jcgp/backend/population/MutableElement.html" title="interface in jcgp.backend.population">MutableElement</a> getRandomMutableElement()</pre> +<div class="block">This method is useful for mutating chromosomes. It returns any + random <code>MutableElement</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 <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a> getRandomConnection(int 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 <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a> 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 void 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 java.util.ArrayList<<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>> 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 boolean compareGenesTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> 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 boolean compareActiveGenesTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> 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 void 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 <a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a> 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 int compareTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a> o)</pre> +<dl> +<dt><span class="overrideSpecifyLabel">Specified by:</span></dt> +<dd><code>compareTo</code> in interface <code>java.lang.Comparable<<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>></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"> +<!-- --> +</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="navBarCell1Rev">Class</li> +<li><a href="class-use/Chromosome.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>Prev Class</li> +<li><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population"><span class="typeNameLink">Next Class</span></a></li> +</ul> +<ul class="navList"> +<li><a href="../../../index.html?jcgp/backend/population/Chromosome.html" target="_top">Frames</a></li> +<li><a href="Chromosome.html" target="_top">No Frames</a></li> +</ul> +<ul class="navList" id="allclasses_navbar_bottom"> +<li><a href="../../../allclasses-noframe.html">All 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> +<div> +<ul class="subNavList"> +<li>Summary: </li> +<li>Nested | </li> +<li>Field | </li> +<li><a href="#constructor.summary">Constr</a> | </li> +<li><a href="#method.summary">Method</a></li> +</ul> +<ul class="subNavList"> +<li>Detail: </li> +<li>Field | </li> +<li><a href="#constructor.detail">Constr</a> | </li> +<li><a href="#method.detail">Method</a></li> +</ul> +</div> +<a name="skip.navbar.bottom"> +<!-- --> +</a></div> +<!-- ======== END OF BOTTOM NAVBAR ======= --> +</body> +</html> |