22 files changed, 156 insertions, 105 deletions
diff --git a/doc/index-files/index-1.html b/doc/index-files/index-1.html
index 930eb20..bc5e84e 100644
--- a/doc/index-files/index-1.html
+++ b/doc/index-files/index-1.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>A-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-10.html b/doc/index-files/index-10.html
index b6c43a6..521d288 100644
--- a/doc/index-files/index-10.html
+++ b/doc/index-files/index-10.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>J-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-11.html b/doc/index-files/index-11.html
index 7b3feeb..c35e4e4 100644
--- a/doc/index-files/index-11.html
+++ b/doc/index-files/index-11.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>L-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-12.html b/doc/index-files/index-12.html
index 999529d..f64a1e9 100644
--- a/doc/index-files/index-12.html
+++ b/doc/index-files/index-12.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>M-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -75,7 +75,9 @@
 <h2 class="title">M</h2>
 <dl>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Start JCGP with the user interface.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/JCGP.html#main-java.lang.String...-">main(String...)</a></span> - Static method in class jcgp.<a href="../jcgp/JCGP.html" title="class in jcgp">JCGP</a></dt>
 <dd>
 <div class="block">JCGP main method, this is used to execute JCGP from the command line.</div>
@@ -89,7 +91,9 @@
 <div class="block">Makes the specified region drag resizable.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#MEDIUM_HIGHLIGHT_COLOUR">MEDIUM_HIGHLIGHT_COLOUR</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A string containing the hexadecimal colour used for a medium highlight.</div>
+</dd>
 <dt><a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources"><span class="typeNameLink">ModifiableResources</span></a> - Class in <a href="../jcgp/backend/resources/package-summary.html">jcgp.backend.resources</a></dt>
 <dd>
 <div class="block">This subclass of Resources allows modifications to be made.</div>
@@ -132,6 +136,14 @@
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/modules/mutator/ProbabilisticMutator.html#mutate-jcgp.backend.population.Chromosome-">mutate(Chromosome)</a></span> - Method in class jcgp.backend.modules.mutator.<a href="../jcgp/backend/modules/mutator/ProbabilisticMutator.html" title="class in jcgp.backend.modules.mutator">ProbabilisticMutator</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Mutable.html#mutate--">mutate()</a></span> - Method in interface jcgp.backend.population.<a href="../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></dt>
+<dd>
+<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.</div>
+</dd>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Node.html#mutate--">mutate()</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></dt>
+<dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Output.html#mutate--">mutate()</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></dt>
+<dd>&nbsp;</dd>
 <dt><a href="../jcgp/backend/modules/mutator/Mutator.html" title="class in jcgp.backend.modules.mutator"><span class="typeNameLink">Mutator</span></a> - Class in <a href="../jcgp/backend/modules/mutator/package-summary.html">jcgp.backend.modules.mutator</a></dt>
 <dd>
 <div class="block">This class specifies the basic characteristics of a mutation operator.</div>
diff --git a/doc/index-files/index-13.html b/doc/index-files/index-13.html
index 90318c6..5555fa8 100644
--- a/doc/index-files/index-13.html
+++ b/doc/index-files/index-13.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>N-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -79,9 +79,13 @@
 <dt><span class="memberNameLink"><a href="../jcgp/backend/function/SymbolicRegressionFunctions.NaturalLog.html#NaturalLog--">NaturalLog()</a></span> - Constructor for class jcgp.backend.function.<a href="../jcgp/backend/function/SymbolicRegressionFunctions.NaturalLog.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.NaturalLog</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#NEUTRAL_COLOUR">NEUTRAL_COLOUR</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A string containing the hexadecimal colour used for representing neutrality.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#NEUTRAL_SELECTION_COLOUR">NEUTRAL_SELECTION_COLOUR</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A string containing the hexadecimal colour used for representing a neutral selection.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/JCGP.html#nextGeneration--">nextGeneration()</a></span> - Method in class jcgp.<a href="../jcgp/JCGP.html" title="class in jcgp">JCGP</a></dt>
 <dd>
 <div class="block">Performs one full generational cycle.</div>
@@ -91,7 +95,7 @@
 <div class="block">Nodes make up the main part of the chromosome, 
  where the actual functions are evolved.</div>
 </dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Node.html#Node-jcgp.backend.population.Chromosome-int-int-int-">Node(Chromosome, int, int, int)</a></span> - Constructor for class jcgp.backend.population.<a href="../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Node.html#Node-jcgp.backend.population.Chromosome-int-int-">Node(Chromosome, int, int)</a></span> - Constructor for class jcgp.backend.population.<a href="../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></dt>
 <dd>
 <div class="block">Constructs a new instance of <code>Node</code> with the
  specified parameters.</div>
diff --git a/doc/index-files/index-14.html b/doc/index-files/index-14.html
index 29f2538..2238ebb 100644
--- a/doc/index-files/index-14.html
+++ b/doc/index-files/index-14.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>O-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-15.html b/doc/index-files/index-15.html
index 704a021..280a433 100644
--- a/doc/index-files/index-15.html
+++ b/doc/index-files/index-15.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>P-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -207,10 +207,6 @@
 <dd>
 <div class="block">Defines the general behaviour of a CGP problem.</div>
 </dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/Problem.html#Problem-jcgp.backend.resources.Resources-">Problem(Resources)</a></span> - Constructor for class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></dt>
-<dd>
-<div class="block">Initialises the two problem-wide parameters, maxFitness and bestFitness.</div>
-</dd>
 </dl>
 <a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">L</a>&nbsp;<a href="index-12.html">M</a>&nbsp;<a href="index-13.html">N</a>&nbsp;<a href="index-14.html">O</a>&nbsp;<a href="index-15.html">P</a>&nbsp;<a href="index-16.html">R</a>&nbsp;<a href="index-17.html">S</a>&nbsp;<a href="index-18.html">T</a>&nbsp;<a href="index-19.html">U</a>&nbsp;<a href="index-20.html">V</a>&nbsp;<a href="index-21.html">W</a>&nbsp;<a href="index-22.html">X</a>&nbsp;</div>
 <!-- ======= START OF BOTTOM NAVBAR ====== -->
diff --git a/doc/index-files/index-16.html b/doc/index-files/index-16.html
index f7d6bbb..27f9063 100644
--- a/doc/index-files/index-16.html
+++ b/doc/index-files/index-16.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>R-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -81,7 +81,9 @@
 <div class="block">This causes the list of active nodes to be recomputed lazily (once it is actually requested).</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#reDraw--">reDraw()</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Does a complete GUI refresh.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/settings/parameters/GUIBooleanParameter.html#refreshValue--">refreshValue()</a></span> - Method in class jcgp.gui.settings.parameters.<a href="../jcgp/gui/settings/parameters/GUIBooleanParameter.html" title="class in jcgp.gui.settings.parameters">GUIBooleanParameter</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/settings/parameters/GUIDoubleParameter.html#refreshValue--">refreshValue()</a></span> - Method in class jcgp.gui.settings.parameters.<a href="../jcgp/gui/settings/parameters/GUIDoubleParameter.html" title="class in jcgp.gui.settings.parameters">GUIDoubleParameter</a></dt>
@@ -138,7 +140,9 @@
 <div class="block">Resets the bestFitness parameter.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#reset--">reset()</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Reset button callback.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/JCGP.html#reset--">reset()</a></span> - Method in class jcgp.<a href="../jcgp/JCGP.html" title="class in jcgp">JCGP</a></dt>
 <dd>
 <div class="block">Resets the experiment.</div>
@@ -152,7 +156,10 @@
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIOutput.html#resetState--">resetState()</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIOutput.html" title="class in jcgp.gui.population">GUIOutput</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#RESIZE_MARGIN">RESIZE_MARGIN</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">The width or height of the area that can be clicked on
+ to drag-resize a pane.</div>
+</dd>
 <dt><a href="../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources"><span class="typeNameLink">Resources</span></a> - Class in <a href="../jcgp/backend/resources/package-summary.html">jcgp.backend.resources</a></dt>
 <dd>
 <div class="block">Encapsulates all of the resources based on which the program operates.</div>
@@ -284,7 +291,9 @@
 <div class="block">Creates a new run entry for a logger.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#runPause--">runPause()</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Run/pause method.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/resources/Resources.html#runs--">runs()</a></span> - Method in class jcgp.backend.resources.<a href="../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a></dt>
 <dd>&nbsp;</dd>
 </dl>
diff --git a/doc/index-files/index-17.html b/doc/index-files/index-17.html
index b279eb1..97e57a3 100644
--- a/doc/index-files/index-17.html
+++ b/doc/index-files/index-17.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>S-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -110,17 +110,9 @@
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/resources/ModifiableResources.html#setColumns-int-">setColumns(int)</a></span> - Method in class jcgp.backend.resources.<a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Mutable.html#setConnection-int-jcgp.backend.population.Connection-">setConnection(int, Connection)</a></span> - Method in interface jcgp.backend.population.<a href="../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></dt>
-<dd>
-<div class="block">This method sets the indexed connection to the specified new connection.</div>
-</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Node.html#setConnection-int-jcgp.backend.population.Connection-">setConnection(int, Connection)</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Output.html#setConnection-int-jcgp.backend.population.Connection-">setConnection(int, Connection)</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></dt>
 <dd>
-<div class="block">When mutating an output, the index parameter
- is simply ignored and the output source is
- set.</div>
+<div class="block">This method sets the indexed connection to the specified new connection.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIGene.html#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine(GUIGene)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></dt>
 <dd>&nbsp;</dd>
@@ -130,15 +122,15 @@
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIOutput.html#setConnectionLine-jcgp.gui.population.GUIGene-">setConnectionLine(GUIGene)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIOutput.html" title="class in jcgp.gui.population">GUIOutput</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIGene.html#setConnections-jcgp.gui.population.GUIGene.GUIGeneState-">setConnections(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIGene.html#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIInput.html#setConnections-jcgp.gui.population.GUIGene.GUIGeneState-">setConnections(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIInput.html" title="class in jcgp.gui.population">GUIInput</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIInput.html#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIInput.html" title="class in jcgp.gui.population">GUIInput</a></dt>
 <dd>
 <div class="block">Set all connections to a given state.</div>
 </dd>
-<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUINode.html#setConnections-jcgp.gui.population.GUIGene.GUIGeneState-">setConnections(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUINode.html#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIOutput.html#setConnections-jcgp.gui.population.GUIGene.GUIGeneState-">setConnections(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIOutput.html" title="class in jcgp.gui.population">GUIOutput</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIOutput.html#setConnectionStates-jcgp.gui.population.GUIGene.GUIGeneState-">setConnectionStates(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIOutput.html" title="class in jcgp.gui.population">GUIOutput</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/resources/ModifiableResources.html#setConsole-jcgp.backend.resources.Console-">setConsole(Console)</a></span> - Method in class jcgp.backend.resources.<a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></dt>
 <dd>
@@ -157,7 +149,9 @@
 <div class="block">Sets a new string containing details about the current status.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#setEvaluating-boolean-">setEvaluating(boolean)</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Set the system into evaluation mode.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/PopulationPane.html#setEvaluating-boolean-">setEvaluating(boolean)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/JCGP.html#setEvolutionaryStrategy-int-">setEvolutionaryStrategy(int)</a></span> - Method in class jcgp.<a href="../jcgp/JCGP.html" title="class in jcgp">JCGP</a></dt>
@@ -209,8 +203,12 @@
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/resources/ModifiableResources.html#setRuns-int-">setRuns(int)</a></span> - Method in class jcgp.backend.resources.<a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/resources/ModifiableResources.html#setSeed-int-">setSeed(int)</a></span> - Method in class jcgp.backend.resources.<a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/resources/ModifiableResources.html#setSeed-long-">setSeed(long)</a></span> - Method in class jcgp.backend.resources.<a href="../jcgp/backend/resources/ModifiableResources.html" title="class in jcgp.backend.resources">ModifiableResources</a></dt>
 <dd>&nbsp;</dd>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/population/Output.html#setSource-jcgp.backend.population.Connection-">setSource(Connection)</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></dt>
+<dd>
+<div class="block">This method sets the output source to the specified connection.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIGene.html#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIInput.html#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIInput.html" title="class in jcgp.gui.population">GUIInput</a></dt>
@@ -220,11 +218,20 @@
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIOutput.html#setState-jcgp.gui.population.GUIGene.GUIGeneState-">setState(GUIGene.GUIGeneState)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIOutput.html" title="class in jcgp.gui.population">GUIOutput</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#SETTINGS_MIN_WIDTH">SETTINGS_MIN_WIDTH</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">The minimum width of the settings pane, to prevent it
+ from being resized beyond visibility.</div>
+</dd>
 <dt><a href="../jcgp/gui/settings/SettingsPane.html" title="class in jcgp.gui.settings"><span class="typeNameLink">SettingsPane</span></a> - Class in <a href="../jcgp/gui/settings/package-summary.html">jcgp.gui.settings</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">This is a fairly hefty class which encapsulates the entire right-hand
+ control pane.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/settings/SettingsPane.html#SettingsPane-jcgp.gui.GUI-">SettingsPane(GUI)</a></span> - Constructor for class jcgp.gui.settings.<a href="../jcgp/gui/settings/SettingsPane.html" title="class in jcgp.gui.settings">SettingsPane</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Create a new instance of <code>SettingsPane</code> associated
+ with the specified <code>GUI</code> object.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Input.html#setValue-java.lang.Object-">setValue(Object)</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></dt>
 <dd>
 <div class="block">Sets this input's value.</div>
@@ -238,7 +245,9 @@
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUIGene.html#SOCKET_RADIUS">SOCKET_RADIUS</a></span> - Static variable in class jcgp.gui.population.<a href="../jcgp/gui/population/GUIGene.html" title="class in jcgp.gui.population">GUIGene</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#SOFT_HIGHLIGHT_COLOUR">SOFT_HIGHLIGHT_COLOUR</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A string containing the hexadecimal colour used for a soft highlight.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Population.html#sort--">sort()</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Population.html" title="class in jcgp.backend.population">Population</a></dt>
 <dd>
 <div class="block">Sorts the population in ascending order of fitness quality.</div>
@@ -269,7 +278,9 @@
 <div class="block">Create a new statistics logger, use this when resetting is necessary.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#step--">step()</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Perform a single generation using <code>nextGeneration()</code>.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/function/SymbolicRegressionFunctions.Subtraction.html#Subtraction--">Subtraction()</a></span> - Constructor for class jcgp.backend.function.<a href="../jcgp/backend/function/SymbolicRegressionFunctions.Subtraction.html" title="class in jcgp.backend.function">SymbolicRegressionFunctions.Subtraction</a></dt>
 <dd>&nbsp;</dd>
 <dt><a href="../jcgp/backend/function/SymbolicRegressionFunctions.html" title="class in jcgp.backend.function"><span class="typeNameLink">SymbolicRegressionFunctions</span></a> - Class in <a href="../jcgp/backend/function/package-summary.html">jcgp.backend.function</a></dt>
diff --git a/doc/index-files/index-18.html b/doc/index-files/index-18.html
index ed24a92..5d9d7b7 100644
--- a/doc/index-files/index-18.html
+++ b/doc/index-files/index-18.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>T-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -92,10 +92,6 @@
 <dd>
 <div class="block">Abstract model for a problem that uses test cases.</div>
 </dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/TestCaseProblem.html#TestCaseProblem-jcgp.backend.resources.Resources-">TestCaseProblem(Resources)</a></span> - Constructor for class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/TestCaseProblem.html" title="class in jcgp.backend.modules.problem">TestCaseProblem</a></dt>
-<dd>
-<div class="block">Creates a new TestCaseProblem object.</div>
-</dd>
 <dt><a href="../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem"><span class="typeNameLink">TestCaseProblem.TestCase</span></a>&lt;<a href="../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="type parameter in TestCaseProblem.TestCase">U</a>&gt; - Class in <a href="../jcgp/backend/modules/problem/package-summary.html">jcgp.backend.modules.problem</a></dt>
 <dd>
 <div class="block">Basic data type for encapsulating test cases, it simply
diff --git a/doc/index-files/index-19.html b/doc/index-files/index-19.html
index 88a6413..22c6ffb 100644
--- a/doc/index-files/index-19.html
+++ b/doc/index-files/index-19.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>U-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -88,10 +88,6 @@
 <dd>
 <div class="block">Makes a new instance of UnsignedInteger with a specified value.</div>
 </dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/function/UnsignedInteger.html#UnsignedInteger-java.lang.Integer-">UnsignedInteger(Integer)</a></span> - Constructor for class jcgp.backend.function.<a href="../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></dt>
-<dd>
-<div class="block">Makes a new instance of UnsignedInteger with a specified value.</div>
-</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/function/UnsignedInteger.html#UnsignedInteger-java.lang.String-">UnsignedInteger(String)</a></span> - Constructor for class jcgp.backend.function.<a href="../jcgp/backend/function/UnsignedInteger.html" title="class in jcgp.backend.function">UnsignedInteger</a></dt>
 <dd>
 <div class="block">Makes a new instance of UnsignedInteger from the string representation
@@ -104,7 +100,9 @@
  running or finished.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#updateFunctionSelector--">updateFunctionSelector()</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Refresh the function selector, used when functions are enabled or disabled.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/ChromosomePane.html#updateGenes-jcgp.backend.population.Chromosome-">updateGenes(Chromosome)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">ChromosomePane</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/PopulationPane.html#updateGenes--">updateGenes()</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</a></dt>
diff --git a/doc/index-files/index-2.html b/doc/index-files/index-2.html
index 92997ff..e851a2d 100644
--- a/doc/index-files/index-2.html
+++ b/doc/index-files/index-2.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>B-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -75,7 +75,9 @@
 <h2 class="title">B</h2>
 <dl>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#BAD_SELECTION_COLOUR">BAD_SELECTION_COLOUR</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A string containing the hexadecimal colour used for representing a bad selection.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/settings/parameters/GUIParameter.html#BASE_CHECKBOX_STYLE">BASE_CHECKBOX_STYLE</a></span> - Static variable in class jcgp.gui.settings.parameters.<a href="../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters">GUIParameter</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/settings/parameters/GUIParameter.html#BASE_TEXT_STYLE">BASE_TEXT_STYLE</a></span> - Static variable in class jcgp.gui.settings.parameters.<a href="../jcgp/gui/settings/parameters/GUIParameter.html" title="class in jcgp.gui.settings.parameters">GUIParameter</a></dt>
@@ -115,7 +117,10 @@
 <dt><span class="memberNameLink"><a href="../jcgp/backend/function/TravellingSalesmanFunctions.BoundedDivision.html#BoundedDivision--">BoundedDivision()</a></span> - Constructor for class jcgp.backend.function.<a href="../jcgp/backend/function/TravellingSalesmanFunctions.BoundedDivision.html" title="class in jcgp.backend.function">TravellingSalesmanFunctions.BoundedDivision</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#bringFunctionSelector-javafx.scene.input.MouseEvent-jcgp.gui.population.GUINode-">bringFunctionSelector(MouseEvent, GUINode)</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Relocate the function selector to the right position
+ relative to the specified node and set it visible.</div>
+</dd>
 </dl>
 <a href="index-1.html">A</a>&nbsp;<a href="index-2.html">B</a>&nbsp;<a href="index-3.html">C</a>&nbsp;<a href="index-4.html">D</a>&nbsp;<a href="index-5.html">E</a>&nbsp;<a href="index-6.html">F</a>&nbsp;<a href="index-7.html">G</a>&nbsp;<a href="index-8.html">H</a>&nbsp;<a href="index-9.html">I</a>&nbsp;<a href="index-10.html">J</a>&nbsp;<a href="index-11.html">L</a>&nbsp;<a href="index-12.html">M</a>&nbsp;<a href="index-13.html">N</a>&nbsp;<a href="index-14.html">O</a>&nbsp;<a href="index-15.html">P</a>&nbsp;<a href="index-16.html">R</a>&nbsp;<a href="index-17.html">S</a>&nbsp;<a href="index-18.html">T</a>&nbsp;<a href="index-19.html">U</a>&nbsp;<a href="index-20.html">V</a>&nbsp;<a href="index-21.html">W</a>&nbsp;<a href="index-22.html">X</a>&nbsp;</div>
 <!-- ======= START OF BOTTOM NAVBAR ====== -->
diff --git a/doc/index-files/index-20.html b/doc/index-files/index-20.html
index 1a78e05..447d8c6 100644
--- a/doc/index-files/index-20.html
+++ b/doc/index-files/index-20.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>V-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-21.html b/doc/index-files/index-21.html
index 652ffa2..e2175bf 100644
--- a/doc/index-files/index-21.html
+++ b/doc/index-files/index-21.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>W-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-22.html b/doc/index-files/index-22.html
index 5039c54..8d86d01 100644
--- a/doc/index-files/index-22.html
+++ b/doc/index-files/index-22.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>X-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-3.html b/doc/index-files/index-3.html
index 9549185..4ec92a7 100644
--- a/doc/index-files/index-3.html
+++ b/doc/index-files/index-3.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>C-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -89,7 +89,10 @@
 <div class="block">Copy constructor.</div>
 </dd>
 <dt><a href="../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population"><span class="typeNameLink">ChromosomePane</span></a> - Class in <a href="../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">This extension of <code>ScrollPane</code> contains a series of
+ nodes, inputs and outputs spread across a grid.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/ChromosomePane.html#ChromosomePane-jcgp.backend.population.Chromosome-jcgp.gui.GUI-jcgp.gui.population.PopulationPane-">ChromosomePane(Chromosome, GUI, PopulationPane)</a></span> - Constructor for class jcgp.gui.population.<a href="../jcgp/gui/population/ChromosomePane.html" title="class in jcgp.gui.population">ChromosomePane</a></dt>
 <dd>&nbsp;</dd>
 <dt><a href="../jcgp/backend/parsers/ChromosomeParser.html" title="class in jcgp.backend.parsers"><span class="typeNameLink">ChromosomeParser</span></a> - Class in <a href="../jcgp/backend/parsers/package-summary.html">jcgp.backend.parsers</a></dt>
@@ -127,7 +130,10 @@
 <div class="block">Defines the basic model for a console.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#CONSOLE_MIN_HEIGHT">CONSOLE_MIN_HEIGHT</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">The minimum width of the console pane, to prevent it
+ from being resized beyond visibility.</div>
+</dd>
 <dt><a href="../jcgp/gui/console/ConsolePane.html" title="class in jcgp.gui.console"><span class="typeNameLink">ConsolePane</span></a> - Class in <a href="../jcgp/gui/console/package-summary.html">jcgp.gui.console</a></dt>
 <dd>
 <div class="block">Console pane used by the GUI to display CGP output messages.</div>
diff --git a/doc/index-files/index-4.html b/doc/index-files/index-4.html
index 38673b5..3f5c353 100644
--- a/doc/index-files/index-4.html
+++ b/doc/index-files/index-4.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>D-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
diff --git a/doc/index-files/index-5.html b/doc/index-files/index-5.html
index 70705a5..f1fd3eb 100644
--- a/doc/index-files/index-5.html
+++ b/doc/index-files/index-5.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>E-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -78,16 +78,18 @@
 <dd>
 <div class="block">Disables the indexed function.</div>
 </dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/DigitalCircuitProblem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">evaluate(Population, Resources)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/DigitalCircuitProblem.html" title="class in jcgp.backend.modules.problem">DigitalCircuitProblem</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/DigitalCircuitProblem.html#evaluate-jcgp.backend.population.Population-">evaluate(Population)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/DigitalCircuitProblem.html" title="class in jcgp.backend.modules.problem">DigitalCircuitProblem</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">evaluate(Population, Resources)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/Problem.html#evaluate-jcgp.backend.population.Population-">evaluate(Population)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></dt>
 <dd>
 <div class="block">The most important method of the problem type.</div>
 </dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#evaluate-jcgp.backend.population.Population-jcgp.backend.resources.Resources-">evaluate(Population, Resources)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem">SymbolicRegressionProblem</a></dt>
+<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#evaluate-jcgp.backend.population.Population-">evaluate(Population)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem">SymbolicRegressionProblem</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#evaluateTestCase-jcgp.backend.modules.problem.TestCaseProblem.TestCase-">evaluateTestCase(TestCaseProblem.TestCase&lt;Object&gt;)</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Starts the evaluation process with the given test case.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/PopulationPane.html#evaluateTestCase-jcgp.backend.modules.problem.TestCaseProblem.TestCase-">evaluateTestCase(TestCaseProblem.TestCase&lt;Object&gt;)</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</a></dt>
 <dd>&nbsp;</dd>
 <dt><a href="../jcgp/backend/modules/es/EvolutionaryStrategy.html" title="class in jcgp.backend.modules.es"><span class="typeNameLink">EvolutionaryStrategy</span></a> - Class in <a href="../jcgp/backend/modules/es/package-summary.html">jcgp.backend.modules.es</a></dt>
diff --git a/doc/index-files/index-6.html b/doc/index-files/index-6.html
index 8512e0b..cd9390d 100644
--- a/doc/index-files/index-6.html
+++ b/doc/index-files/index-6.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>F-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -95,7 +95,9 @@
 <dt><span class="memberNameLink"><a href="../jcgp/gui/console/ConsolePane.html#flush--">flush()</a></span> - Method in class jcgp.gui.console.<a href="../jcgp/gui/console/ConsolePane.html" title="class in jcgp.gui.console">ConsolePane</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#flushConsole--">flushConsole()</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Writes all buffered content out to the GUI console.</div>
+</dd>
 <dt><a href="../jcgp/backend/function/Function.html" title="class in jcgp.backend.function"><span class="typeNameLink">Function</span></a> - Class in <a href="../jcgp/backend/function/package-summary.html">jcgp.backend.function</a></dt>
 <dd>
 <div class="block">Function is a callback wrapper.</div>
@@ -110,7 +112,10 @@
 <dt><span class="memberNameLink"><a href="../jcgp/backend/parsers/FunctionParser.html#FunctionParser--">FunctionParser()</a></span> - Constructor for class jcgp.backend.parsers.<a href="../jcgp/backend/parsers/FunctionParser.html" title="class in jcgp.backend.parsers">FunctionParser</a></dt>
 <dd>&nbsp;</dd>
 <dt><a href="../jcgp/gui/population/FunctionSelector.html" title="class in jcgp.gui.population"><span class="typeNameLink">FunctionSelector</span></a> - Class in <a href="../jcgp/gui/population/package-summary.html">jcgp.gui.population</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A menu class, exposes all of the allowed functions
+ when called by a node, so that the node function can be changed.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/FunctionSelector.html#FunctionSelector-jcgp.backend.function.FunctionSet-">FunctionSelector(FunctionSet)</a></span> - Constructor for class jcgp.gui.population.<a href="../jcgp/gui/population/FunctionSelector.html" title="class in jcgp.gui.population">FunctionSelector</a></dt>
 <dd>&nbsp;</dd>
 <dt><a href="../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function"><span class="typeNameLink">FunctionSet</span></a> - Class in <a href="../jcgp/backend/function/package-summary.html">jcgp.backend.function</a></dt>
diff --git a/doc/index-files/index-7.html b/doc/index-files/index-7.html
index fe440f2..2ad33db 100644
--- a/doc/index-files/index-7.html
+++ b/doc/index-files/index-7.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>G-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -95,7 +95,10 @@
 <div class="block">This method computes a list of active nodes (if necessary) and returns it.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Output.html#getActiveNodes-java.util.ArrayList-">getActiveNodes(ArrayList&lt;Node&gt;)</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Calls <code>getActive(...)</code> on this output's
+ source.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/statistics/RunEntry.html#getActiveNodes--">getActiveNodes()</a></span> - Method in class jcgp.backend.statistics.<a href="../jcgp/backend/statistics/RunEntry.html" title="class in jcgp.backend.statistics">RunEntry</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/function/FunctionSet.html#getAllowedFunction-int-">getAllowedFunction(int)</a></span> - Method in class jcgp.backend.function.<a href="../jcgp/backend/function/FunctionSet.html" title="class in jcgp.backend.function">FunctionSet</a></dt>
@@ -322,8 +325,6 @@
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Output.html#getIndex--">getIndex()</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html#getInput-int-">getInput(int)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a></dt>
-<dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Chromosome.html#getInput-int-">getInput(int)</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></dt>
 <dd>
 <div class="block">Returns a reference to the indexed input.</div>
@@ -358,8 +359,6 @@
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/GUINode.html#getNode--">getNode()</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/GUINode.html" title="class in jcgp.gui.population">GUINode</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html#getOutput-int-">getOutput(int)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/TestCaseProblem.TestCase.html" title="class in jcgp.backend.modules.problem">TestCaseProblem.TestCase</a></dt>
-<dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Chromosome.html#getOutput-int-">getOutput(int)</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a></dt>
 <dd>
 <div class="block">Returns a reference to the indexed output.</div>
@@ -461,13 +460,17 @@
 <dt><span class="memberNameLink"><a href="../jcgp/backend/population/Node.html#getValue--">getValue()</a></span> - Method in class jcgp.backend.population.<a href="../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#GOOD_SELECTION_COLOUR">GOOD_SELECTION_COLOUR</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A string containing the hexadecimal colour used for representing a good selection.</div>
+</dd>
 <dt><a href="../jcgp/gui/GUI.html" title="class in jcgp.gui"><span class="typeNameLink">GUI</span></a> - Class in <a href="../jcgp/gui/package-summary.html">jcgp.gui</a></dt>
 <dd>
 <div class="block">Main class for the graphical user interface (GUI).</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#GUI--">GUI()</a></span> - Constructor for class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Makes a new instance of GUI.</div>
+</dd>
 <dt><a href="../jcgp/gui/settings/parameters/GUIBooleanParameter.html" title="class in jcgp.gui.settings.parameters"><span class="typeNameLink">GUIBooleanParameter</span></a> - Class in <a href="../jcgp/gui/settings/parameters/package-summary.html">jcgp.gui.settings.parameters</a></dt>
 <dd>
 <div class="block">This extension of @code{GUIParameter} uses a @code{CheckBox} to display
diff --git a/doc/index-files/index-8.html b/doc/index-files/index-8.html
index 0e628a8..b1079b9 100644
--- a/doc/index-files/index-8.html
+++ b/doc/index-files/index-8.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>H-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>
@@ -75,7 +75,9 @@
 <h2 class="title">H</h2>
 <dl>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#HARD_HIGHLIGHT_COLOUR">HARD_HIGHLIGHT_COLOUR</a></span> - Static variable in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">A string containing the hexadecimal colour used for representing a hard highlight.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/Problem.html#hasImprovement-jcgp.backend.population.Population-">hasImprovement(Population)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/Problem.html" title="class in jcgp.backend.modules.problem">Problem</a></dt>
 <dd>
 <div class="block">Used to assert whether a given population has a chromosome that is an improvement over 
@@ -93,7 +95,9 @@
 <dt><span class="memberNameLink"><a href="../jcgp/backend/modules/problem/SymbolicRegressionProblem.html#hasPerfectSolution-jcgp.backend.population.Population-">hasPerfectSolution(Population)</a></span> - Method in class jcgp.backend.modules.problem.<a href="../jcgp/backend/modules/problem/SymbolicRegressionProblem.html" title="class in jcgp.backend.modules.problem">SymbolicRegressionProblem</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/GUI.html#hideGeneValues--">hideGeneValues()</a></span> - Method in class jcgp.gui.<a href="../jcgp/gui/GUI.html" title="class in jcgp.gui">GUI</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Hide all evaluated values.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../jcgp/gui/population/PopulationPane.html#hideValues--">hideValues()</a></span> - Method in class jcgp.gui.population.<a href="../jcgp/gui/population/PopulationPane.html" title="class in jcgp.gui.population">PopulationPane</a></dt>
 <dd>&nbsp;</dd>
 <dt><a href="../jcgp/gui/dragresize/HorizontalDragResize.html" title="class in jcgp.gui.dragresize"><span class="typeNameLink">HorizontalDragResize</span></a> - Class in <a href="../jcgp/gui/dragresize/package-summary.html">jcgp.gui.dragresize</a></dt>
diff --git a/doc/index-files/index-9.html b/doc/index-files/index-9.html
index 3d6872d..3a7bcd7 100644
--- a/doc/index-files/index-9.html
+++ b/doc/index-files/index-9.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:45 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:33 BST 2014 -->
 <title>I-Index</title>
-<meta name="date" content="2014-05-12">
+<meta name="date" content="2014-05-22">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 <script type="text/javascript" src="../script.js"></script>
 </head>