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evosynth 0.1.0

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data/docs/rdoc/classes/EvoSynth/Mutations/OneGeneFlipping.html ADDED

@@ -0,0 +1,295 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Class: EvoSynth::Mutations::OneGeneFlipping [EvoSynth Documentation]</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
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+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">EvoSynth::Mutations::OneGeneFlipping</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../../files/lib/evosynth/operators/mutations/one_gene_flipping_rb.html">
+                lib/evosynth/operators/mutations/one_gene_flipping.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+This mutations flips (inverts) one gene in the genome of a given individual
+using the given flip function (a lambda) and returns a mutated individual.
+To use this mutation the flip_function has to return the negation/inverse
+of a given gene. This mutations is based on EIN-BIT-BINAERE-MUTATION
+(Weicker 2007, page 48).
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+        <a href="#M000079">mutate</a>&nbsp;&nbsp;
+        <a href="#M000078">new</a>&nbsp;&nbsp;
+        <a href="#M000080">to_s</a>&nbsp;&nbsp;
+      </div>
+    </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <div id="attribute-list">
+      <h3 class="section-bar">Attributes</h3>
+      <div class="name-list">
+        <table>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">flip_function</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+This function is used to flip each gene
+</td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+      <div id="method-M000078" class="method-detail">
+        <a name="M000078"></a>
+        <div class="method-heading">
+          <a href="#M000078" class="method-signature">
+          <span class="method-name">OneGeneFlipping.new(Lambda) &rarr; OneGeneFlipping<br />
+</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Returns a new <a href="OneGeneFlipping.html">OneGeneFlipping</a>.
+</p>
+<pre>
+    custom_flip_function = lambda { |gene| EvoSynth.rand(42 * gene) }
+    OneGeneFlipping.new(custom_flip_function)
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000078-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000078-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/one_gene_flipping.rb, line 47</span>
+47:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">flip_function</span>)
+48:                                 <span class="ruby-ivar">@flip_function</span> = <span class="ruby-identifier">flip_function</span>
+49:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <h3 class="section-bar">Public Instance methods</h3>
+      <div id="method-M000079" class="method-detail">
+        <a name="M000079"></a>
+        <div class="method-heading">
+          <a href="#M000079" class="method-signature">
+          <span class="method-name">mutate(Individual) &rarr; Individual<br />
+</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Returns the mutation (one gene will be flipped with the given flip
+function) of a given individual.
+</p>
+<pre>
+    m = OneGeneFlipping.new
+    m.mutate(a_individual)   #=&gt; a_new_individual
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000079-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000079-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/one_gene_flipping.rb, line 59</span>
+59:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mutate</span>(<span class="ruby-identifier">individual</span>)
+60:                                 <span class="ruby-identifier">mutated</span> = <span class="ruby-identifier">individual</span>.<span class="ruby-identifier">deep_clone</span>
+61:                                 <span class="ruby-identifier">genome</span> = <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>
+62:
+63:                                 <span class="ruby-identifier">rand_index</span> = <span class="ruby-constant">EvoSynth</span>.<span class="ruby-identifier">rand</span>(<span class="ruby-identifier">genome</span>.<span class="ruby-identifier">size</span>)
+64:                                 <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@flip_function</span>.<span class="ruby-identifier">arity</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
+65:                                         <span class="ruby-identifier">genome</span>[<span class="ruby-identifier">rand_index</span>] = <span class="ruby-ivar">@flip_function</span>.<span class="ruby-identifier">call</span>(<span class="ruby-identifier">genome</span>[<span class="ruby-identifier">rand_index</span>])
+66:                                 <span class="ruby-keyword kw">else</span>
+67:                                         <span class="ruby-identifier">genome</span>[<span class="ruby-identifier">rand_index</span>] = <span class="ruby-ivar">@flip_function</span>.<span class="ruby-identifier">call</span>
+68:                                 <span class="ruby-keyword kw">end</span>
+69:
+70:                                 <span class="ruby-identifier">mutated</span>
+71:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000080" class="method-detail">
+        <a name="M000080"></a>
+        <div class="method-heading">
+          <a href="#M000080" class="method-signature">
+          <span class="method-name">to_s &rarr; string<br />
+</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Returns description of this mutation
+</p>
+<pre>
+    m = OneGeneFlipping.new
+    m.to_s                   #=&gt; &quot;one-gene-flipping&quot;
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000080-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000080-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/one_gene_flipping.rb, line 81</span>
+81:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
+82:                                 <span class="ruby-value str">&quot;one-gene-flipping&quot;</span>
+83:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>

data/docs/rdoc/classes/EvoSynth/Mutations/SelfAdaptiveGaussMutation.html ADDED

@@ -0,0 +1,347 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Class: EvoSynth::Mutations::SelfAdaptiveGaussMutation [EvoSynth Documentation]</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">EvoSynth::Mutations::SelfAdaptiveGaussMutation</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../../files/lib/evosynth/operators/mutations/self_adaptive_gauss_mutation_rb.html">
+                lib/evosynth/operators/mutations/self_adaptive_gauss_mutation.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+SELBSTADAPTIVE-GAUSS-MUTATION (Weicker page 114)
+</p>
+<p>
+TODO: needs rdoc
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+        <a href="#M000075">add_sigma</a>&nbsp;&nbsp;
+        <a href="#M000073">mutate</a>&nbsp;&nbsp;
+        <a href="#M000072">new</a>&nbsp;&nbsp;
+        <a href="#M000074">to_s</a>&nbsp;&nbsp;
+      </div>
+    </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <div id="constants-list">
+      <h3 class="section-bar">Constants</h3>
+      <div class="name-list">
+        <table summary="Constants">
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">DEFAULT_INITIAL_SIGMA</td>
+          <td>=</td>
+          <td class="context-item-value">1.0</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">DEFAULT_LOWER_BOUND</td>
+          <td>=</td>
+          <td class="context-item-value">-1 * Float::MAX</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">DEFAULT_UPPER_BOUND</td>
+          <td>=</td>
+          <td class="context-item-value">Float::MAX</td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <div id="attribute-list">
+      <h3 class="section-bar">Attributes</h3>
+      <div class="name-list">
+        <table>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">initial_sigma</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">lower_bound</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">upper_bound</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+      <div id="method-M000072" class="method-detail">
+        <a name="M000072"></a>
+        <div class="method-heading">
+          <a href="#M000072" class="method-signature">
+          <span class="method-name">new</span><span class="method-args">(initial_sigma = DEFAULT_INITIAL_SIGMA, lower_bound = DEFAULT_LOWER_BOUND, upper_bound = DEFAULT_UPPER_BOUND)</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000072-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000072-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/self_adaptive_gauss_mutation.rb, line 39</span>
+39:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">initial_sigma</span> = <span class="ruby-constant">DEFAULT_INITIAL_SIGMA</span>, <span class="ruby-identifier">lower_bound</span> = <span class="ruby-constant">DEFAULT_LOWER_BOUND</span>, <span class="ruby-identifier">upper_bound</span> = <span class="ruby-constant">DEFAULT_UPPER_BOUND</span>)
+40:                                 <span class="ruby-ivar">@initial_sigma</span> = <span class="ruby-identifier">initial_sigma</span>
+41:                                 <span class="ruby-ivar">@lower_bound</span> = <span class="ruby-identifier">lower_bound</span>
+42:                                 <span class="ruby-ivar">@upper_bound</span> = <span class="ruby-identifier">upper_bound</span>
+43:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <h3 class="section-bar">Public Instance methods</h3>
+      <div id="method-M000075" class="method-detail">
+        <a name="M000075"></a>
+        <div class="method-heading">
+          <a href="#M000075" class="method-signature">
+          <span class="method-name">add_sigma</span><span class="method-args">(individual)</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000075-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000075-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/self_adaptive_gauss_mutation.rb, line 65</span>
+65:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_sigma</span>(<span class="ruby-identifier">individual</span>)
+66:                                 <span class="ruby-identifier">individual</span>.<span class="ruby-identifier">instance_eval</span>(<span class="ruby-value str">&quot;def sigma; @sigma end; def sigma=(value); @sigma = value end&quot;</span>)
+67:                                 <span class="ruby-identifier">individual</span>.<span class="ruby-identifier">sigma</span> = <span class="ruby-ivar">@initial_sigma</span>
+68:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000073" class="method-detail">
+        <a name="M000073"></a>
+        <div class="method-heading">
+          <a href="#M000073" class="method-signature">
+          <span class="method-name">mutate</span><span class="method-args">(individual)</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000073-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000073-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/self_adaptive_gauss_mutation.rb, line 45</span>
+45:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mutate</span>(<span class="ruby-identifier">individual</span>)
+46:                                 <span class="ruby-identifier">mutated</span> = <span class="ruby-identifier">individual</span>.<span class="ruby-identifier">deep_clone</span>
+47:                                 <span class="ruby-identifier">add_sigma</span>(<span class="ruby-identifier">mutated</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">defined?</span> <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">sigma</span>
+48:
+49:                                 <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">sigma</span> <span class="ruby-operator">*=</span> <span class="ruby-constant">Math</span>.<span class="ruby-identifier">exp</span>( (<span class="ruby-value">1</span> <span class="ruby-operator">/</span> <span class="ruby-constant">Math</span>.<span class="ruby-identifier">sqrt</span>(<span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>.<span class="ruby-identifier">size</span>)) <span class="ruby-operator">*</span> <span class="ruby-constant">EvoSynth</span>.<span class="ruby-identifier">nrand</span>)
+50:
+51:                                 <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>.<span class="ruby-identifier">map!</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gene</span><span class="ruby-operator">|</span>
+52:                                         <span class="ruby-identifier">gene</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">EvoSynth</span>.<span class="ruby-identifier">nrand</span>(<span class="ruby-value">0</span><span class="ruby-value">.0</span>, <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">sigma</span>)
+53:                                         <span class="ruby-identifier">gene</span> = <span class="ruby-ivar">@lower_bound</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">gene</span> <span class="ruby-operator">&lt;</span> <span class="ruby-ivar">@lower_bound</span>
+54:                                         <span class="ruby-identifier">gene</span> = <span class="ruby-ivar">@upper_bound</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">gene</span> <span class="ruby-operator">&gt;</span> <span class="ruby-ivar">@upper_bound</span>
+55:                                         <span class="ruby-identifier">gene</span>
+56:                                 <span class="ruby-keyword kw">end</span>
+57:
+58:                                 <span class="ruby-identifier">mutated</span>
+59:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000074" class="method-detail">
+        <a name="M000074"></a>
+        <div class="method-heading">
+          <a href="#M000074" class="method-signature">
+          <span class="method-name">to_s</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000074-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000074-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/self_adaptive_gauss_mutation.rb, line 61</span>
+61:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
+62:                                 <span class="ruby-node">&quot;self adaptive gauss mutation &lt;sigma: #{@sigma}, lower bound: #{@lower_bound}, upper_bound: #{@upper_bound}&gt;&quot;</span>
+63:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>