evolvable 1.2.0 → 2.0.0

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Files changed (79) hide show
  1. checksums.yaml +4 -4
  2. data/.yardopts +2 -0
  3. data/CHANGELOG.md +24 -0
  4. data/Gemfile +2 -2
  5. data/Gemfile.lock +44 -25
  6. data/README.md +498 -190
  7. data/README_YARD.md +85 -166
  8. data/bin/console +10 -19
  9. data/docs/Evolvable/ClassMethods.html +1233 -0
  10. data/docs/Evolvable/Community/ClassMethods.html +708 -0
  11. data/docs/Evolvable/Community.html +1342 -0
  12. data/docs/Evolvable/CountGene.html +886 -0
  13. data/docs/Evolvable/EqualizeGoal.html +347 -0
  14. data/docs/Evolvable/Error.html +134 -0
  15. data/docs/Evolvable/Evaluation.html +773 -0
  16. data/docs/Evolvable/Evolution.html +616 -0
  17. data/docs/Evolvable/Gene/ClassMethods.html +413 -0
  18. data/docs/Evolvable/Gene.html +522 -0
  19. data/docs/Evolvable/GeneCluster/ClassMethods.html +431 -0
  20. data/docs/Evolvable/GeneCluster.html +280 -0
  21. data/docs/Evolvable/GeneCombination.html +515 -0
  22. data/docs/Evolvable/GeneSpace.html +619 -0
  23. data/docs/Evolvable/Genome.html +1070 -0
  24. data/docs/Evolvable/Goal.html +500 -0
  25. data/docs/Evolvable/MaximizeGoal.html +348 -0
  26. data/docs/Evolvable/MinimizeGoal.html +348 -0
  27. data/docs/Evolvable/Mutation.html +729 -0
  28. data/docs/Evolvable/PointCrossover.html +444 -0
  29. data/docs/Evolvable/Population.html +2826 -0
  30. data/docs/Evolvable/RigidCountGene.html +501 -0
  31. data/docs/Evolvable/Selection.html +594 -0
  32. data/docs/Evolvable/Serializer.html +293 -0
  33. data/docs/Evolvable/UniformCrossover.html +286 -0
  34. data/docs/Evolvable.html +1619 -0
  35. data/docs/_index.html +341 -0
  36. data/docs/class_list.html +54 -0
  37. data/docs/css/common.css +1 -0
  38. data/docs/css/full_list.css +58 -0
  39. data/docs/css/style.css +503 -0
  40. data/docs/file.README.html +750 -0
  41. data/docs/file_list.html +59 -0
  42. data/docs/frames.html +22 -0
  43. data/docs/index.html +750 -0
  44. data/docs/js/app.js +344 -0
  45. data/docs/js/full_list.js +242 -0
  46. data/docs/js/jquery.js +4 -0
  47. data/docs/method_list.html +1302 -0
  48. data/docs/top-level-namespace.html +110 -0
  49. data/evolvable.gemspec +6 -6
  50. data/examples/ascii_art.rb +5 -9
  51. data/examples/stickman.rb +25 -33
  52. data/{examples/hello_world.rb → exe/hello_evolvable_world} +46 -30
  53. data/lib/evolvable/community.rb +190 -0
  54. data/lib/evolvable/count_gene.rb +65 -0
  55. data/lib/evolvable/equalize_goal.rb +2 -9
  56. data/lib/evolvable/evaluation.rb +113 -14
  57. data/lib/evolvable/evolution.rb +38 -15
  58. data/lib/evolvable/gene.rb +124 -25
  59. data/lib/evolvable/gene_cluster.rb +106 -0
  60. data/lib/evolvable/gene_combination.rb +57 -16
  61. data/lib/evolvable/gene_space.rb +111 -0
  62. data/lib/evolvable/genome.rb +32 -4
  63. data/lib/evolvable/goal.rb +19 -24
  64. data/lib/evolvable/maximize_goal.rb +2 -9
  65. data/lib/evolvable/minimize_goal.rb +3 -9
  66. data/lib/evolvable/mutation.rb +87 -41
  67. data/lib/evolvable/point_crossover.rb +24 -4
  68. data/lib/evolvable/population.rb +258 -84
  69. data/lib/evolvable/rigid_count_gene.rb +36 -0
  70. data/lib/evolvable/selection.rb +68 -14
  71. data/lib/evolvable/serializer.rb +46 -0
  72. data/lib/evolvable/uniform_crossover.rb +30 -6
  73. data/lib/evolvable/version.rb +2 -1
  74. data/lib/evolvable.rb +268 -107
  75. metadata +57 -36
  76. data/examples/images/diagram.png +0 -0
  77. data/exe/hello +0 -16
  78. data/lib/evolvable/error/undefined_method.rb +0 -7
  79. data/lib/evolvable/search_space.rb +0 -181
data/docs/Evolvable/Gene.html ADDED
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta charset="utf-8">
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ <title>
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+ Module: Evolvable::Gene
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+
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+ &mdash; Documentation by YARD 0.9.37
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+
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+ </title>
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+
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+ <link rel="stylesheet" href="../css/style.css" type="text/css" />
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+
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+ <link rel="stylesheet" href="../css/common.css" type="text/css" />
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+
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+ <script type="text/javascript">
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+ pathId = "Evolvable::Gene";
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+ relpath = '../';
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+ </script>
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+
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+
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+ <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
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+
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+ <script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
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+
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+
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+ </head>
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+ <body>
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+ <div class="nav_wrap">
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+ <iframe id="nav" src="../class_list.html?1"></iframe>
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+ <div id="resizer"></div>
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+ </div>
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+
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+ <div id="main" tabindex="-1">
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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="../_index.html">Index (G)</a> &raquo;
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+ <span class='title'><span class='object_link'><a href="../Evolvable.html" title="Evolvable (module)">Evolvable</a></span></span>
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+ &raquo;
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+ <span class="title">Gene</span>
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+
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+ </div>
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+
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+ <div id="search">
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+
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+ <a class="full_list_link" id="class_list_link"
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+ href="../class_list.html">
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+
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+ <svg width="24" height="24">
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+ <rect x="0" y="4" width="24" height="4" rx="1" ry="1"></rect>
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+ <rect x="0" y="12" width="24" height="4" rx="1" ry="1"></rect>
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+ <rect x="0" y="20" width="24" height="4" rx="1" ry="1"></rect>
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+ </svg>
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+ </a>
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+
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+
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+ <div id="content"><h1>Module: Evolvable::Gene
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+
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+
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+
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+ </h1>
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+ <div class="box_info">
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <dl>
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+ <dt>Included in:</dt>
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+ <dd><span class='object_link'><a href="CountGene.html" title="Evolvable::CountGene (class)">CountGene</a></span>, <span class='object_link'><a href="RigidCountGene.html" title="Evolvable::RigidCountGene (class)">RigidCountGene</a></span></dd>
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+ </dl>
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+
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+
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+
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+ <dl>
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+ <dt>Defined in:</dt>
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+ <dd>lib/evolvable/gene.rb</dd>
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+ </dl>
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+
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+ </div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+ <p>Genes are the building blocks of evolvable objects, encapsulating individual characteristics
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+ that can be combined and mutated during evolution. Each gene represents a trait or behavior
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+ that can influence an evolvable&#39;s performance.</p>
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+
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+ <p><strong>To define a gene class:</strong></p>
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+
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+ <ol>
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+ <li>Include the <code>Evolvable::Gene</code> module</li>
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+ <li>Define how the gene&#39;s value is determined</li>
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+ </ol>
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+
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+ <pre class="code ruby"><code class="ruby"><span class='kw'>class</span> <span class='const'>BehaviorGene</span>
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+ <span class='id identifier rubyid_include'>include</span> <span class='const'><span class='object_link'><a href="../Evolvable.html" title="Evolvable (module)">Evolvable</a></span></span><span class='op'>::</span><span class='const'>Gene</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_value'>value</span>
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+ <span class='ivar'>@value</span> <span class='op'>||=</span> <span class='qwords_beg'>%w[</span><span class='tstring_content'>explore</span><span class='words_sep'> </span><span class='tstring_content'>gather</span><span class='words_sep'> </span><span class='tstring_content'>attack</span><span class='words_sep'> </span><span class='tstring_content'>defend</span><span class='words_sep'> </span><span class='tstring_content'>build</span><span class='tstring_end'>]</span></span><span class='period'>.</span><span class='id identifier rubyid_sample'>sample</span>
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+ <span class='kw'>end</span>
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+ <span class='kw'>end</span>
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+ </code></pre>
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+
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+ <p>Then use it in an evolvable class:</p>
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+
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+ <pre class="code ruby"><code class="ruby"><span class='kw'>class</span> <span class='const'>Robot</span>
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+ <span class='id identifier rubyid_include'>include</span> <span class='const'><span class='object_link'><a href="../Evolvable.html" title="Evolvable (module)">Evolvable</a></span></span>
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+
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+ <span class='id identifier rubyid_gene'>gene</span> <span class='symbol'>:behaviors</span><span class='comma'>,</span> <span class='label'>type:</span> <span class='const'>BehaviorGene</span><span class='comma'>,</span> <span class='label'>count:</span> <span class='int'>3</span><span class='op'>..</span><span class='int'>5</span>
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+ <span class='id identifier rubyid_gene'>gene</span> <span class='symbol'>:speed</span><span class='comma'>,</span> <span class='label'>type:</span> <span class='const'>SpeedGene</span><span class='comma'>,</span> <span class='label'>count:</span> <span class='int'>1</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_fitness'>fitness</span>
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+ <span class='id identifier rubyid_run_simulation'>run_simulation</span><span class='lparen'>(</span><span class='label'>behaviors:</span> <span class='id identifier rubyid_behaviors'>behaviors</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lparen'>(</span><span class='op'>&amp;</span><span class='symbol'>:value</span><span class='rparen'>)</span><span class='comma'>,</span> <span class='label'>speed:</span> <span class='id identifier rubyid_speed'>speed</span><span class='period'>.</span><span class='id identifier rubyid_value'>value</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span>
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+ <span class='kw'>end</span>
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+ </code></pre>
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+
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+ <p><strong>Gene Count</strong></p>
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+
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+ <p>You can control how many copies of a gene are created using the <code>count:</code> parameter:</p>
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+
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+ <ul>
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+ <li><code>count: 1</code> (default) creates a single instance.</li>
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+ <li>A numeric value (e.g. <code>count: 5</code>) creates a fixed number of genes using <code>RigidCountGene</code>.</li>
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+ <li>A range (e.g. <code>count: 2..8</code>) creates a variable number of genes using <code>CountGene</code>, allowing the count to evolve over time.</li>
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+ </ul>
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+
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+ <p>Evolves melody length:</p>
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+
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+ <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_gene'>gene</span> <span class='symbol'>:notes</span><span class='comma'>,</span> <span class='label'>type:</span> <span class='const'>NoteGene</span><span class='comma'>,</span> <span class='label'>count:</span> <span class='int'>4</span><span class='op'>..</span><span class='int'>12</span>
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+ </code></pre>
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+
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+ <p><strong>Custom Combination</strong></p>
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+
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+ <p>By default, the <code>combine</code> method randomly picks one of the two parent genes.
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+ A gene class can implement custom behavior by overriding <code>.combine</code>.</p>
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+
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+ <pre class="code ruby"><code class="ruby"><span class='kw'>class</span> <span class='const'>SpeedGene</span>
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+ <span class='id identifier rubyid_include'>include</span> <span class='const'><span class='object_link'><a href="../Evolvable.html" title="Evolvable (module)">Evolvable</a></span></span><span class='op'>::</span><span class='const'>Gene</span>
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+
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+ <span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_combine'>combine</span><span class='lparen'>(</span><span class='id identifier rubyid_gene_a'>gene_a</span><span class='comma'>,</span> <span class='id identifier rubyid_gene_b'>gene_b</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_new_gene'>new_gene</span> <span class='op'>=</span> <span class='id identifier rubyid_new'>new</span>
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+ <span class='id identifier rubyid_new_gene'>new_gene</span><span class='period'>.</span><span class='id identifier rubyid_value'>value</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_gene_a'>gene_a</span><span class='period'>.</span><span class='id identifier rubyid_value'>value</span> <span class='op'>+</span> <span class='id identifier rubyid_gene_b'>gene_b</span><span class='period'>.</span><span class='id identifier rubyid_value'>value</span><span class='rparen'>)</span> <span class='op'>/</span> <span class='int'>2</span>
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+ <span class='id identifier rubyid_new_gene'>new_gene</span>
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+ <span class='kw'>end</span>
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+
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+ <span class='id identifier rubyid_attr_writer'>attr_writer</span> <span class='symbol'>:value</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_value'>value</span>
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+ <span class='ivar'>@value</span> <span class='op'>||=</span> <span class='id identifier rubyid_rand'>rand</span><span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='int'>100</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span>
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+ <span class='kw'>end</span>
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+ </code></pre>
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+
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+ <p><strong>Design Patterns</strong></p>
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+
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+ <p>Effective gene design typically follows these principles:</p>
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+
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+ <ul>
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+ <li><strong>Immutability</strong>: Cache values after initial sampling (e.g., <code>@value ||= ...</code>)</li>
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+ <li><strong>Self-Contained</strong>: Genes should encapsulate their logic and state</li>
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+ <li><strong>Composable</strong>: You can build complex structures using multiple genes or clusters</li>
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+ <li><strong>Domain-Specific</strong>: Genes should map directly to your problem’s traits or features</li>
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+ </ul>
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+
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+ <p>Genes come in various types, each representing different aspects of a solution.
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+ Common examples include numeric genes for quantities, selection genes for choices
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+ from sets, boolean genes for binary decisions, structural genes for architecture,
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+ and parameter genes for configuration settings.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ <p class="tag_title">See Also:</p>
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+ <ul class="see">
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+
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+ <li><span class='object_link'><a href="GeneSpace.html" title="Evolvable::GeneSpace (class)">GeneSpace</a></span></li>
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+
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+ <li><span class='object_link'><a href="GeneCluster.html" title="Evolvable::GeneCluster (module)">GeneCluster</a></span></li>
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+
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+ <li><span class='object_link'><a href="GeneCombination.html" title="Evolvable::GeneCombination (class)">GeneCombination</a></span></li>
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+
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+ <li><span class='object_link'><a href="CountGene.html" title="Evolvable::CountGene (class)">CountGene</a></span></li>
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+
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+ <li><span class='object_link'><a href="RigidCountGene.html" title="Evolvable::RigidCountGene (class)">RigidCountGene</a></span></li>
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+
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+ </ul>
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+
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+ </div><h2>Defined Under Namespace</h2>
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+ <p class="children">
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+
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+
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+ <strong class="modules">Modules:</strong> <span class='object_link'><a href="Gene/ClassMethods.html" title="Evolvable::Gene::ClassMethods (module)">ClassMethods</a></span>
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+
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+
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+
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+
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+ </p>
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+
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+
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+
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+
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+ <h2>Instance Attribute Summary <small><a href="#" class="summary_toggle">collapse</a></small></h2>
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#evolvable-instance_method" title="#evolvable (instance method)">#<strong>evolvable</strong> &#x21d2; Evolvable </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'><p>The evolvable instance that this gene belongs to.</p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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+
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+
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+ <h2>
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+ Class Method Summary
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+ <small><a href="#" class="summary_toggle">collapse</a></small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#included-class_method" title="included (class method)">.<strong>included</strong>(base) &#x21d2; Object </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'><p>When included in a class, extends the class with ClassMethods.</p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+ <h2>
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+ Instance Method Summary
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+ <small><a href="#" class="summary_toggle">collapse</a></small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#key-instance_method" title="#key (instance method)">#<strong>key</strong> &#x21d2; Symbol </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'><p>Returns the unique key for this gene instance.</p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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+ <div id="instance_attr_details" class="attr_details">
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+ <h2>Instance Attribute Details</h2>
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+
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+
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+ <span id="evolvable=-instance_method"></span>
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+ <div class="method_details first">
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+ <h3 class="signature first" id="evolvable-instance_method">
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+
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+ #<strong>evolvable</strong> &#x21d2; <tt><span class='object_link'><a href="../Evolvable.html" title="Evolvable (module)">Evolvable</a></span></tt>
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <p>The evolvable instance that this gene belongs to.
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+ Used for accessing other genes or evolvable properties.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+ <p class="tag_title">Returns:</p>
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+ <ul class="return">
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+
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+ <li>
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+
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+
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+ <span class='type'>(<tt><span class='object_link'><a href="../Evolvable.html" title="Evolvable (module)">Evolvable</a></span></tt>)</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'><p>The evolvable instance this gene is part of</p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 152
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+ 153
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+ 154</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/evolvable/gene.rb', line 152</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_evolvable'>evolvable</span>
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+ <span class='ivar'>@evolvable</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+
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+ <div id="class_method_details" class="method_details_list">
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+ <h2>Class Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="included-class_method">
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+
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+ .<strong>included</strong>(base) &#x21d2; <tt>Object</tt>
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <p>When included in a class, extends the class with ClassMethods.
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+ Gene classes should include this module to participate in the evolutionary process.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+ <p class="tag_title">Parameters:</p>
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+ <ul class="param">
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+
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+ <li>
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+
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+ <span class='name'>base</span>
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+
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+
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+ <span class='type'>(<tt>Class</tt>)</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'><p>The class that includes the Gene module</p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 103
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+ 104
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+ 105</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/evolvable/gene.rb', line 103</span>
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+
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+ <span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_included'>included</span><span class='lparen'>(</span><span class='id identifier rubyid_base'>base</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_base'>base</span><span class='period'>.</span><span class='id identifier rubyid_extend'>extend</span><span class='lparen'>(</span><span class='const'><span class='object_link'><a href="Gene/ClassMethods.html" title="Evolvable::Gene::ClassMethods (module)">ClassMethods</a></span></span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ <div id="instance_method_details" class="method_details_list">
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+ <h2>Instance Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="key-instance_method">
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+
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+ #<strong>key</strong> &#x21d2; <tt>Symbol</tt>
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <p>Returns the unique key for this gene instance.
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+ Delegates to the class-level key.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+ <p class="tag_title">Returns:</p>
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+ <ul class="return">
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+
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+ <li>
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+
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+
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+ <span class='type'>(<tt>Symbol</tt>)</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'><p>The key that identifies this gene type</p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 160
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+ 161
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+ 162</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/evolvable/gene.rb', line 160</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_key'>key</span>
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+ <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_class'>class</span><span class='period'>.</span><span class='id identifier rubyid_key'>key</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Sat May 10 18:39:22 2025 by
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+ <a href="https://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.9.37 (ruby-3.4.2).
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+ </div>
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+
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+ </div>
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+ </body>
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+ </html>