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authorEduardo Pedroni <e.pedroni91@gmail.com>2014-10-18 15:21:45 +0200
committerEduardo Pedroni <e.pedroni91@gmail.com>2014-10-18 15:21:45 +0200
commit4f26361eb08aa09334d1eea0a124110c20d809ce (patch)
treeea2652193f376eee5c9c44776895378b123be7c8 /doc/jcgp/backend/modules/problem
parentfc0f9ce2aa46444ff69e89e9b9e09f3610eedd74 (diff)
Moved javadocs to a different repository for hosting, updated README
Diffstat (limited to 'doc/jcgp/backend/modules/problem')
-rw-r--r--doc/jcgp/backend/modules/problem/BestFitness.html352
-rw-r--r--doc/jcgp/backend/modules/problem/DigitalCircuitProblem.html423
-rw-r--r--doc/jcgp/backend/modules/problem/Problem.html464
-rw-r--r--doc/jcgp/backend/modules/problem/SymbolicRegressionProblem.html436
-rw-r--r--doc/jcgp/backend/modules/problem/TestCaseProblem.TestCase.html320
-rw-r--r--doc/jcgp/backend/modules/problem/TestCaseProblem.html415
-rw-r--r--doc/jcgp/backend/modules/problem/TravellingSalesmanProblem.html433
-rw-r--r--doc/jcgp/backend/modules/problem/class-use/BestFitness.html212
-rw-r--r--doc/jcgp/backend/modules/problem/class-use/DigitalCircuitProblem.html124
-rw-r--r--doc/jcgp/backend/modules/problem/class-use/Problem.html208
-rw-r--r--doc/jcgp/backend/modules/problem/class-use/SymbolicRegressionProblem.html124
-rw-r--r--doc/jcgp/backend/modules/problem/class-use/TestCaseProblem.TestCase.html251
-rw-r--r--doc/jcgp/backend/modules/problem/class-use/TestCaseProblem.html227
-rw-r--r--doc/jcgp/backend/modules/problem/class-use/TravellingSalesmanProblem.html124
-rw-r--r--doc/jcgp/backend/modules/problem/package-frame.html28
-rw-r--r--doc/jcgp/backend/modules/problem/package-summary.html191
-rw-r--r--doc/jcgp/backend/modules/problem/package-tree.html163
-rw-r--r--doc/jcgp/backend/modules/problem/package-use.html311
18 files changed, 0 insertions, 4806 deletions
diff --git a/doc/jcgp/backend/modules/problem/BestFitness.html b/doc/jcgp/backend/modules/problem/BestFitness.html
deleted file mode 100644
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-<h2 title="Enum BestFitness" class="title">Enum BestFitness</h2>
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-<pre>public enum <span class="typeNameLabel">BestFitness</span>
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-<div class="block">Enum type to allow problems to indicate their fitness
- orientation.
- <br><br>
- <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>
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-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/BestFitness.html#HIGH">HIGH</a></span></code>&nbsp;</td>
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-<div class="block">Returns the enum constant of this type with the specified name.</div>
-</td>
-</tr>
-<tr id="i1" 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"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/BestFitness.html#values--">values</a></span>()</code>
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-<div class="block">Returns an array containing the constants of this enum type, in
-the order they are declared. This method may be used to iterate
-over the constants as follows:
-<pre>
-for (BestFitness c : BestFitness.values())
-&nbsp; System.out.println(c);
-</pre></div>
-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>an array containing the constants of this enum type, in the order they are declared</dd>
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-<div class="block">Returns the enum constant of this type with the specified name.
-The string must match <i>exactly</i> an identifier used to declare an
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-not permitted.)</div>
-<dl>
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diff --git a/doc/jcgp/backend/modules/problem/DigitalCircuitProblem.html b/doc/jcgp/backend/modules/problem/DigitalCircuitProblem.html
deleted file mode 100644
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--- a/doc/jcgp/backend/modules/problem/DigitalCircuitProblem.html
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-<script type="text/javascript" src="../../../../script.js"></script>
-</head>
-<body>
-<script type="text/javascript"><!--
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-<!-- -->
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-<!-- ========= END OF TOP NAVBAR ========= -->
-<!-- ======== START OF CLASS DATA ======== -->
-<div class="header">
-<div class="subTitle">jcgp.backend.modules.problem</div>
-<h2 title="Class DigitalCircuitProblem" class="title">Class DigitalCircuitProblem</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">
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-<li>jcgp.backend.modules.problem.DigitalCircuitProblem</li>
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-<hr>
-<br>
-<pre>public class <span class="typeNameLabel">DigitalCircuitProblem</span>
-extends <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a>&lt;<a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a>&gt;</pre>
-<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>
-</dl>
-</li>
-</ul>
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-<tr class="altColor">
-<td class="colOne"><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>
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-<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/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>
-<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>
-</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;<a href="../../../../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a>&gt;</code></td>
-<td class="colLast"><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>
-<div class="block">This method is used internally by <code>addTestCase()</code> in order
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- test cases.</div>
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-<code><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#addTestCase-java.lang.String:A-java.lang.String:A-">addTestCase</a>, <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#clearTestCases--">clearTestCases</a>, <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#getTestCases--">getTestCases</a>, <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#hasImprovement-jcgp.backend.population.Population-">hasImprovement</a>, <a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">parseProblemData</a></code></li>
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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#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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-<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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-<code>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</code></li>
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-<h4>DigitalCircuitProblem</h4>
-<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>
-</dl>
-</li>
-</ul>
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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-">
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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;<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>
-<dt><span class="returnLabel">Returns:</span></dt>
-<dd>the parsed test case.</dd>
-</dl>
-</li>
-</ul>
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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>
-</ul>
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diff --git a/doc/jcgp/backend/modules/problem/Problem.html b/doc/jcgp/backend/modules/problem/Problem.html
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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>
-</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/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a></dd>
-</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>
-</dl>
-</li>
-</ul>
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-<!-- ========== METHOD SUMMARY =========== -->
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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><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>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>
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-<td class="colFirst"><code><a href="../../../../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a></code></td>
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-<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
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-</tr>
-<tr id="i6" class="altColor">
-<td class="colFirst"><code>abstract int</code></td>
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-<div class="block">Used to assert whether a given population contains a perfect solution
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-</td>
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-<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>
-</dl>
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-<pre>public abstract&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">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>
-</dl>
-</li>
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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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-<pre>public abstract&nbsp;void&nbsp;parseProblemData(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. 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>
-</dl>
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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>
-</dl>
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-<dl>
-<dt><span class="returnLabel">Returns:</span></dt>
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-<dl>
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-<dd>the current best fitness, in other words, the fitness
- value of the fittest chromosome in the current generation.</dd>
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-<pre>public&nbsp;void&nbsp;reset()</pre>
-<div class="block">Resets the bestFitness parameter.</div>
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-<div class="subTitle">jcgp.backend.modules.problem</div>
-<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>
-</li>
-</ul>
-</li>
-</ul>
-</li>
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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>
-</ul>
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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/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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-<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/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>
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-<tr id="i2" class="altColor">
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- java.lang.String[]&nbsp;outputs)</code>
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-<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>
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-</li>
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-<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>
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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;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>
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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>
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-<h2 title="Class TestCaseProblem.TestCase" class="title">Class TestCaseProblem.TestCase&lt;U&gt;</h2>
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-<dd><code>U</code> - the data type of the test case.</dd>
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-<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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-<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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- <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="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>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
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-<dt><span class="paramLabel">Type Parameters:</span></dt>
-<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>
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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/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
- contains arrays of inputs and outputs and associated getters.</div>
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-<!-- ========== METHOD SUMMARY =========== -->
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-<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>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,
- java.lang.String[]&nbsp;outputs)</code>
-<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>
-<tr id="i2" class="altColor">
-<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>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../jcgp/backend/modules/problem/TestCaseProblem.html#getTestCases--">getTestCases</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/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
- set up the problem type instance appropriately.</div>
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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#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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-<a name="getTestCases--">
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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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-<!-- -->
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-<h4>addTestCase</h4>
-<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>
-</ul>
-<a name="clearTestCases--">
-<!-- -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>clearTestCases</h4>
-<pre>public&nbsp;void&nbsp;clearTestCases()</pre>
-<div class="block">Remove all test cases.</div>
-</li>
-</ul>
-<a name="parseProblemData-java.io.File-jcgp.backend.resources.ModifiableResources-">
-<!-- -->
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-<ul class="blockList">
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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>
-</ul>
-<a name="hasImprovement-jcgp.backend.population.Population-">
-<!-- -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<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 ========= -->
-<!-- ======= START OF BOTTOM NAVBAR ====== -->
-<div class="bottomNav"><a name="navbar.bottom">
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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>
-</li>
-</ul>
-</li>
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-<br>
-<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>
-</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/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>
-</td>
-</tr>
-</table>
-</li>
-</ul>
-<!-- ========== 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="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
- set up the problem type instance appropriately.</div>
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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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-<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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-<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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-<li class="blockList"><a name="constructor.detail">
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-<h3>Constructor Detail</h3>
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-<h4>TravellingSalesmanProblem</h4>
-<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>
-</ul>
-<!-- ============ METHOD DETAIL ========== -->
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-</a>
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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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-<th class="colFirst" scope="col">Package</th>
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-<tr class="altColor">
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-<th class="colFirst" scope="col">Modifier and Type</th>
-<th class="colLast" scope="col">Method and Description</th>
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-<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>
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-<td class="colFirst"><code>static <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a></code></td>
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-<td class="colFirst"><code>static <a href="../../../../../jcgp/backend/modules/problem/BestFitness.html" title="enum in jcgp.backend.modules.problem">BestFitness</a>[]</code></td>
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-<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>
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-<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>
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-<tr class="altColor">
-<td class="colFirst"><code>void</code></td>
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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">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>
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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/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">Modifier and Type</th>
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-<td class="colFirst"><code><a href="../../../../../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></code></td>
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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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-<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/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a></span><span class="tabEnd">&nbsp;</span></caption>
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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;java.lang.Double&gt;</code></td>
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-<td class="colFirst"><a href="#jcgp.backend.parsers">jcgp.backend.parsers</a></td>
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diff --git a/doc/jcgp/backend/modules/problem/package-frame.html b/doc/jcgp/backend/modules/problem/package-frame.html
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