From 2b571f08d091dc062cedbb9816c29dcf0cbd4f12 Mon Sep 17 00:00:00 2001
From: Eduardo Pedroni <ep625@york.ac.uk>
Date: Thu, 22 May 2014 07:44:52 +0100
Subject: Final commit, will release later today.

---
 doc/jcgp/backend/population/Node.html | 104 +++++++++++++++++++++-------------
 1 file changed, 65 insertions(+), 39 deletions(-)

(limited to 'doc/jcgp/backend/population/Node.html')
diff --git a/doc/jcgp/backend/population/Node.html b/doc/jcgp/backend/population/Node.html
index d79d08c..12e3eea 100644
--- a/doc/jcgp/backend/population/Node.html
+++ b/doc/jcgp/backend/population/Node.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Mon May 12 23:05:44 BST 2014 -->
+<!-- Generated by javadoc (1.8.0_05) on Thu May 22 06:02:32 BST 2014 -->
 <title>Node</title>
-<meta name="date" content="2014-05-12">
+<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>
@@ -18,7 +18,7 @@
     catch(err) {
     }
 //-->
-var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":10,"i7":10,"i8":10,"i9":10};
+var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":10,"i7":10,"i8":10,"i9":10,"i10":10};
 var tabs = {65535:["t0","All Methods"],2:["t2","Instance Methods"],8:["t4","Concrete Methods"]};
 var altColor = "altColor";
 var rowColor = "rowColor";
@@ -126,7 +126,11 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
  Nodes are constructed with a fixed number of connections
  (determined by the maximum arity of the function set)
  and must be reinstantiated if the experiment arity
- changes.</div>
+ changes.
+ <br><br>
+ When mutating a node, it is easiest to use <code>mutate()</code>.
+ Alternatively, you may also perform a specific mutation using
+ <code>setConnection(...)</code> and <code>setFunction(...)</code>.</div>
 <dl>
 <dt><span class="simpleTagLabel">Author:</span></dt>
 <dd>Eduardo Pedroni</dd>
@@ -149,10 +153,9 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 <th class="colOne" scope="col">Constructor and Description</th>
 </tr>
 <tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#Node-jcgp.backend.population.Chromosome-int-int-int-">Node</a></span>(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
+<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#Node-jcgp.backend.population.Chromosome-int-int-">Node</a></span>(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
     int&nbsp;row,
-    int&nbsp;column,
-    int&nbsp;arity)</code>
+    int&nbsp;column)</code>
 <div class="block">Constructs a new instance of <code>Node</code> with the
  specified parameters.</div>
 </td>
@@ -226,18 +229,24 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 </tr>
 <tr id="i7" class="rowColor">
 <td class="colFirst"><code>void</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#mutate--">mutate</a></span>()</code>
+<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.</div>
+</td>
+</tr>
+<tr id="i8" class="altColor">
+<td class="colFirst"><code>void</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#setConnection-int-jcgp.backend.population.Connection-">setConnection</a></span>(int&nbsp;index,
              <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</code>
 <div class="block">This method sets the indexed connection to the specified new connection.</div>
 </td>
 </tr>
-<tr id="i8" class="altColor">
+<tr id="i9" class="rowColor">
 <td class="colFirst"><code>void</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#setFunction-jcgp.backend.function.Function-">setFunction</a></span>(<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;newFunction)</code>
 <div class="block">Sets the node function.</div>
 </td>
 </tr>
-<tr id="i9" class="rowColor">
+<tr id="i10" class="altColor">
 <td class="colFirst"><code>java.lang.String</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Node.html#toString--">toString</a></span>()</code>&nbsp;</td>
 </tr>
@@ -263,7 +272,7 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 <!--   -->
 </a>
 <h3>Constructor Detail</h3>
-<a name="Node-jcgp.backend.population.Chromosome-int-int-int-">
+<a name="Node-jcgp.backend.population.Chromosome-int-int-">
 <!--   -->
 </a>
 <ul class="blockListLast">
@@ -271,8 +280,7 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 <h4>Node</h4>
 <pre>public&nbsp;Node(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome,
             int&nbsp;row,
-            int&nbsp;column,
-            int&nbsp;arity)</pre>
+            int&nbsp;column)</pre>
 <div class="block">Constructs a new instance of <code>Node</code> with the
  specified parameters. Nodes must contain their
  own row and column for ease of copying.</div>
@@ -281,7 +289,6 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 <dd><code>chromosome</code> - the chromosome this node belongs to.</dd>
 <dd><code>row</code> - the node's row.</dd>
 <dd><code>column</code> - the node's column.</dd>
-<dd><code>arity</code> - the maximum arity of the experiment.</dd>
 </dl>
 </li>
 </ul>
@@ -293,20 +300,6 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 <!--   -->
 </a>
 <h3>Method Detail</h3>
-<a name="setFunction-jcgp.backend.function.Function-">
-<!--   -->
-</a>
-<ul class="blockList">
-<li class="blockList">
-<h4>setFunction</h4>
-<pre>public&nbsp;void&nbsp;setFunction(<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;newFunction)</pre>
-<div class="block">Sets the node function.</div>
-<dl>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>newFunction</code> - the new function to set.</dd>
-</dl>
-</li>
-</ul>
 <a name="initialise-jcgp.backend.function.Function-jcgp.backend.population.Connection...-">
 <!--   -->
 </a>
@@ -365,6 +358,20 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 </dl>
 </li>
 </ul>
+<a name="setFunction-jcgp.backend.function.Function-">
+<!--   -->
+</a>
+<ul class="blockList">
+<li class="blockList">
+<h4>setFunction</h4>
+<pre>public&nbsp;void&nbsp;setFunction(<a href="../../../jcgp/backend/function/Function.html" title="class in jcgp.backend.function">Function</a>&nbsp;newFunction)</pre>
+<div class="block">Sets the node function.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>newFunction</code> - the new function to set.</dd>
+</dl>
+</li>
+</ul>
 <a name="getConnection-int-">
 <!--   -->
 </a>
@@ -380,6 +387,24 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 </dl>
 </li>
 </ul>
+<a name="setConnection-int-jcgp.backend.population.Connection-">
+<!--   -->
+</a>
+<ul class="blockList">
+<li class="blockList">
+<h4>setConnection</h4>
+<pre>public&nbsp;void&nbsp;setConnection(int&nbsp;index,
+                          <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</pre>
+<div class="block">This method sets the indexed connection to the specified new connection.
+ If the given connection is null or disrespects levels back, it is discarded
+ and no connections are changed.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>index</code> - the connection index to set.</dd>
+<dd><code>newConnection</code> - the <code>Connection</code> to connect to.</dd>
+</dl>
+</li>
+</ul>
 <a name="copyOf-jcgp.backend.population.Mutable-">
 <!--   -->
 </a>
@@ -437,24 +462,25 @@ implements <a href="../../../jcgp/backend/population/Mutable.html" title="interf
 </dl>
 </li>
 </ul>
-<a name="setConnection-int-jcgp.backend.population.Connection-">
+<a name="mutate--">
 <!--   -->
 </a>
 <ul class="blockList">
 <li class="blockList">
-<h4>setConnection</h4>
-<pre>public&nbsp;void&nbsp;setConnection(int&nbsp;index,
-                          <a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;newConnection)</pre>
-<div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html#setConnection-int-jcgp.backend.population.Connection-">Mutable</a></code></span></div>
-<div class="block">This method sets the indexed connection to the specified new connection.
- Implementing classes may choose to ignore the given index (such as in the
- case of outputs, which only have one connection).</div>
+<h4>mutate</h4>
+<pre>public&nbsp;void&nbsp;mutate()</pre>
+<div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html#mutate--">Mutable</a></code></span></div>
+<div class="block">This method performs an arbitrary mutation on the <code>Mutable</code>.
+ <br><br>
+ In the case of nodes, this chooses to mutate a function or connection
+ fairly, and carries out the required mutation by using the node's own
+ reference to chromosome.
+ <br><br>
+ In the case of outputs, this simply picks a random connection to serve
+ as the source - any connection is allowed.</div>
 <dl>
 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
-<dd><code><a href="../../../jcgp/backend/population/Mutable.html#setConnection-int-jcgp.backend.population.Connection-">setConnection</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></dd>
-<dt><span class="paramLabel">Parameters:</span></dt>
-<dd><code>index</code> - the connection index to set.</dd>
-<dd><code>newConnection</code> - the chromosome element to connect to.</dd>
+<dd><code><a href="../../../jcgp/backend/population/Mutable.html#mutate--">mutate</a></code>&nbsp;in interface&nbsp;<code><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></dd>
 </dl>
 </li>
 </ul>
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