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<h2 title="Class Chromosome" class="title">Class Chromosome</h2>
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<li>java.lang.Object</li>
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<li>jcgp.backend.population.Chromosome</li>
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<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>
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<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>
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<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>
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<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>
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<h3>Methods inherited from class java.lang.Object</h3>
<code>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
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<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>
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<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>
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<a name="reinitialiseConnections--">
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<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>
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<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>
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<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>
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<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>
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<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>
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<h4>getFitness</h4>
<pre>public double getFitness()</pre>
<dl>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>the fitness of the chromosome.</dd>
</dl>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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