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evosynth 0.1.0

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

@@ -0,0 +1,336 @@
+<!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::BinaryMutation [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::BinaryMutation</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../../files/lib/evosynth/operators/mutations/binary_mutation_rb.html">
+                lib/evosynth/operators/mutations/binary_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>
+This mutations flips each gene in the genome of a given individual using
+the given flip function (a lambda) with a given probability 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
+BINAERE-MUTATION (Weicker 2007, page 59).
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+        <a href="#M000065">mutate</a>&nbsp;&nbsp;
+        <a href="#M000064">new</a>&nbsp;&nbsp;
+        <a href="#M000066">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_PROBABILITY</td>
+          <td>=</td>
+          <td class="context-item-value">0.1</td>
+          <td>&nbsp;</td>
+          <td class="context-item-desc">
+the default mutation probability
+</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">flip_function</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+This function (lambda) is used to flip each gene
+</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">probability</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+Each gene is flipped with this probability (should be between 0 and 1)
+</td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+      <div id="method-M000064" class="method-detail">
+        <a name="M000064"></a>
+        <div class="method-heading">
+          <a href="#M000064" class="method-signature">
+          <span class="method-name">BinaryMutation.new(Lambda) &rarr; BinaryMutation<br />
+BinaryMutation.new(Lambda, Float) &rarr; BinaryMutation (overrides default probability)<br />
+</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Returns a new <a href="BinaryMutation.html">BinaryMutation</a>. In the
+first form, the default mutation probability
+BinaryMutation::DEFAULT_PROBABILITY (0.1) is used. In the second it creates
+a <a href="BinaryMutation.html">BinaryMutation</a> with the given
+probability.
+</p>
+<pre>
+    custom_flip_function = lambda { |gene| EvoSynth.rand(42 * gene) }
+    BinaryMutation.new(custom_flip_function)
+    BinaryMutation.new(EvoSynth::Mutations::Functions::FLIP_BOOLEAN, 0.01)
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000064-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000064-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/binary_mutation.rb, line 57</span>
+57:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">flip_function</span>, <span class="ruby-identifier">probability</span> = <span class="ruby-constant">DEFAULT_PROBABILITY</span>)
+58:                                 <span class="ruby-ivar">@flip_function</span> = <span class="ruby-identifier">flip_function</span>
+59:                                 <span class="ruby-ivar">@probability</span> = <span class="ruby-identifier">probability</span>
+60:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <h3 class="section-bar">Public Instance methods</h3>
+      <div id="method-M000065" class="method-detail">
+        <a name="M000065"></a>
+        <div class="method-heading">
+          <a href="#M000065" class="method-signature">
+          <span class="method-name">mutate(Individual) &rarr; Individual<br />
+</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Returns the mutation (with the given flip function) of a given individual.
+</p>
+<pre>
+    m = BinaryMutation.new
+    m.mutate(a_individual)   #=&gt; a_new_individual
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000065-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000065-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/binary_mutation.rb, line 70</span>
+70:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mutate</span>(<span class="ruby-identifier">individual</span>)
+71:                                 <span class="ruby-identifier">mutated</span> = <span class="ruby-identifier">individual</span>.<span class="ruby-identifier">deep_clone</span>
+72:                                 <span class="ruby-identifier">genome</span> = <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>
+73:
+74:                                 <span class="ruby-identifier">genome</span>.<span class="ruby-identifier">size</span>.<span class="ruby-identifier">times</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">index</span><span class="ruby-operator">|</span>
+75:                                         <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>
+76:                                                 <span class="ruby-identifier">genome</span>[<span class="ruby-identifier">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">index</span>]) <span class="ruby-keyword kw">if</span> <span class="ruby-constant">EvoSynth</span>.<span class="ruby-identifier">rand</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-ivar">@probability</span>
+77:                                         <span class="ruby-keyword kw">else</span>
+78:                                                 <span class="ruby-identifier">genome</span>[<span class="ruby-identifier">index</span>] = <span class="ruby-ivar">@flip_function</span>.<span class="ruby-identifier">call</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">EvoSynth</span>.<span class="ruby-identifier">rand</span> <span class="ruby-operator">&lt;=</span> <span class="ruby-ivar">@probability</span>
+79:                                         <span class="ruby-keyword kw">end</span>
+80:                                 <span class="ruby-keyword kw">end</span>
+81:
+82:                                 <span class="ruby-identifier">mutated</span>
+83:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000066" class="method-detail">
+        <a name="M000066"></a>
+        <div class="method-heading">
+          <a href="#M000066" 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 = BinaryMutation.new(0.01)
+    m.to_s                   #=&gt; &quot;binary mutation &lt;probability: 0.01&gt;&quot;
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000066-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000066-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/binary_mutation.rb, line 93</span>
+93:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
+94:                                 <span class="ruby-node">&quot;binary mutation &lt;probability: #{@probability}&gt;&quot;</span>
+95:                         <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/EfficientBinaryMutation.html ADDED

@@ -0,0 +1,345 @@
+<!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::EfficientBinaryMutation [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::EfficientBinaryMutation</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../../files/lib/evosynth/operators/mutations/efficient_binary_mutation_rb.html">
+                lib/evosynth/operators/mutations/efficient_binary_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>
+This mutation is basically a optimized version of the <a
+href="BinaryMutation.html">BinaryMutation</a> and should have a better
+performance on long genomes.
+</p>
+<p>
+It flips each gene in the genome of a given individual using the given flip
+function (a lambda) with a given probability 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
+EFFIZIENTE-BINAERE-MUTATION (Weicker 2007, page 130).
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+        <a href="#M000087">mutate</a>&nbsp;&nbsp;
+        <a href="#M000086">new</a>&nbsp;&nbsp;
+        <a href="#M000088">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_PROBABILITY</td>
+          <td>=</td>
+          <td class="context-item-value">0.1</td>
+          <td>&nbsp;</td>
+          <td class="context-item-desc">
+the default mutation probability
+</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">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>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">probability</td>
+          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
+          <td class="context-item-desc">
+Each gene is flipped with this probability (should be between 0 and 1)
+</td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+      <div id="method-M000086" class="method-detail">
+        <a name="M000086"></a>
+        <div class="method-heading">
+          <a href="#M000086" class="method-signature">
+          <span class="method-name">EfficientBinaryMutation.new(Lambda) &rarr; EfficientBinaryMutation<br />
+EfficientBinaryMutation.new(Lambda, Float) &rarr; EfficientBinaryMutation (overrides default probability)<br />
+</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Returns a new <a
+href="EfficientBinaryMutation.html">EfficientBinaryMutation</a>. In the
+first form, the default mutation probability
+BinaryMutation::DEFAULT_PROBABILITY (0.1) is used. In the second it creates
+a <a href="BinaryMutation.html">BinaryMutation</a> with the given
+probability.
+</p>
+<pre>
+    custom_flip_function = lambda { |gene| EvoSynth.rand(42 * gene) }
+    EfficientBinaryMutation.new(custom_flip_function)
+    EfficientBinaryMutation.new(EvoSynth::Mutations::Functions::FLIP_BOOLEAN, 0.01)
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000086-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000086-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/efficient_binary_mutation.rb, line 59</span>
+59:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">flip_function</span>, <span class="ruby-identifier">probability</span> = <span class="ruby-constant">DEFAULT_PROBABILITY</span>)
+60:                                 <span class="ruby-ivar">@flip_function</span> = <span class="ruby-identifier">flip_function</span>
+61:                                 <span class="ruby-ivar">@probability</span> = <span class="ruby-identifier">probability</span>
+62:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <h3 class="section-bar">Public Instance methods</h3>
+      <div id="method-M000087" class="method-detail">
+        <a name="M000087"></a>
+        <div class="method-heading">
+          <a href="#M000087" class="method-signature">
+          <span class="method-name">mutate(Individual) &rarr; Individual<br />
+</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Returns the mutation (with the given flip function) of a given individual.
+</p>
+<pre>
+    m = EfficientBinaryMutation.new
+    m.mutate(a_individual)   #=&gt; a_new_individual
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000087-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000087-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/efficient_binary_mutation.rb, line 72</span>
+72:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mutate</span>(<span class="ruby-identifier">individual</span>)
+73:                                 <span class="ruby-identifier">mutated</span> = <span class="ruby-identifier">individual</span>.<span class="ruby-identifier">deep_clone</span>
+74:                                 <span class="ruby-ivar">@next_index</span> = <span class="ruby-constant">EvoSynth</span>.<span class="ruby-identifier">rand</span>(<span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>.<span class="ruby-identifier">size</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">defined?</span> <span class="ruby-ivar">@next_index</span>
+75:
+76:                                 <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@next_index</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>.<span class="ruby-identifier">size</span>
+77:                                         <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>
+78:                                                 <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>[<span class="ruby-ivar">@next_index</span>] = <span class="ruby-ivar">@flip_function</span>.<span class="ruby-identifier">call</span>(<span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>[<span class="ruby-ivar">@next_index</span>])
+79:                                         <span class="ruby-keyword kw">else</span>
+80:                                                 <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>[<span class="ruby-ivar">@next_index</span>] = <span class="ruby-ivar">@flip_function</span>.<span class="ruby-identifier">call</span>
+81:                                         <span class="ruby-keyword kw">end</span>
+82:
+83:                                         <span class="ruby-ivar">@next_index</span> <span class="ruby-operator">+=</span> (<span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-constant">EvoSynth</span>.<span class="ruby-identifier">rand</span>) <span class="ruby-operator">/</span> <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-value">1</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@probability</span>)).<span class="ruby-identifier">ceil</span>
+84:                                 <span class="ruby-keyword kw">end</span>
+85:
+86:                                 <span class="ruby-ivar">@next_index</span> <span class="ruby-operator">-=</span> <span class="ruby-identifier">mutated</span>.<span class="ruby-identifier">genome</span>.<span class="ruby-identifier">size</span>
+87:                                 <span class="ruby-identifier">mutated</span>
+88:                         <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000088" class="method-detail">
+        <a name="M000088"></a>
+        <div class="method-heading">
+          <a href="#M000088" 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 = EfficientBinaryMutation.new(0.91)
+    m.to_s                   #=&gt; &quot;efficient binary muation &lt;probability: 0.01&gt;&quot;
+</pre>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000088-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000088-source">
+<pre>
+     <span class="ruby-comment cmt"># File lib/evosynth/operators/mutations/efficient_binary_mutation.rb, line 98</span>
+ 98:                         <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
+ 99:                                 <span class="ruby-node">&quot;efficient binary muation &lt;probability: #{@probability}&gt;&quot;</span>
+100:                         <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>