RubyGems - rubyneat - Versions diffs - 0.3.5.alpha.3 → 0.3.5.alpha.5 - Mend

rubyneat 0.3.5.alpha.3 → 0.3.5.alpha.5

Files changed (252) hide show

checksums.yaml +4 -4
data/.semver +1 -1
data/Gemfile +19 -19
data/Gemfile.lock +39 -33
data/README.md +66 -0
data/Rakefile +19 -2
data/bin/neat +4 -60
data/lib/rubyneat/cli.rb +5 -0
data/lib/rubyneat/cli/generate.rb +131 -0
data/lib/rubyneat/cli/main.rb +54 -0
data/lib/rubyneat/cli/templates/generate/Gemfile.tt +17 -0
data/lib/rubyneat/cli/templates/generate/README.md.tt +1 -0
data/lib/rubyneat/cli/templates/generate/bin/neat.tt +14 -0
data/{neater/xor_neat.rb → lib/rubyneat/cli/templates/generate/neater.tt} +7 -22
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data/doc/NEAT/Critter/Genotype.html DELETED Viewed

@@ -1,1601 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: NEAT::Critter::Genotype
-    &mdash; Documentation by YARD 0.8.7.4
-</title>
-  <link rel="stylesheet" href="../../css/style.css" type="text/css" charset="utf-8" />
-  <link rel="stylesheet" href="../../css/common.css" type="text/css" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '../../';
-  framesUrl = "../../frames.html#!NEAT/Critter/Genotype.html";
-</script>
-  <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="../../js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="../../_index.html">Index (G)</a> &raquo;
-    <span class='title'><span class='object_link'><a href="../../NEAT.html" title="NEAT (module)">NEAT</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../Critter.html" title="NEAT::Critter (class)">Critter</a></span></span>
-     &raquo;
-    <span class="title">Genotype</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="../../class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="../../method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="../../file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: NEAT::Critter::Genotype
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName"><span class='object_link'><a href="../NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next"><span class='object_link'><a href="../NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></li>
-            <li class="next">NEAT::Critter::Genotype</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/rubyneat/critter.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<h1 id="label-Genotype+part+of+the+Critter">Genotype part of the Critter</h1>
-<p>List of connections, basically.</p>
-<p>Also, basic phentypic expression (which may be overriden by the expressor)</p>
-<h1 id="label-Notes">Notes</h1>
-<p>Currently, all lists of neurons and genes are Hashes. The neurons are
-indexed by their own names, and the genes are indexed by their innovation
-numbers.</p>
-  </div>
-</div>
-<div class="tags">
-</div><h2>Defined Under Namespace</h2>
-<p class="children">
-      <strong class="classes">Classes:</strong> <span class='object_link'><a href="Genotype/Gene.html" title="NEAT::Critter::Genotype::Gene (class)">Gene</a></span>
-</p>
-  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
-  <ul class="summary">
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#critter-instance_method" title="#critter (instance method)">- (Object) <strong>critter</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Critter to which we belong.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#dangling_neurons-instance_method" title="#dangling_neurons (instance method)">- (Object) <strong>dangling_neurons</strong> </a>
-      (also: #dangling_neurons?)
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>This will be set to true if there are dangling neurons.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#genes-instance_method" title="#genes (instance method)">- (Object) <strong>genes</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Genes keyed by innovation numbers.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#neural_gene_map-instance_method" title="#neural_gene_map (instance method)">- (Object) <strong>neural_gene_map</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Map neurons to the genes that marks them as output { oneu_name =&gt; [
-gene_1, gene_2,… gene_n], …} Just take the in_neuron name and the weight to
-do the call to that neuron function with the appropriate weights.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#neural_inputs-instance_method" title="#neural_inputs (instance method)">- (Object) <strong>neural_inputs</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Instantiations of neural inputs and outputs.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#neural_outputs-instance_method" title="#neural_outputs (instance method)">- (Object) <strong>neural_outputs</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Instantiations of neural inputs and outputs.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#neurons-instance_method" title="#neurons (instance method)">- (Object) <strong>neurons</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>List of neurons hashed by name.</p>
-</div></span>
-</li>
-  </ul>
-  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="../NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="../NeatOb.html#controller-instance_method" title="NEAT::NeatOb#controller (method)">#controller</a></span>, <span class='object_link'><a href="../NeatOb.html#name-instance_method" title="NEAT::NeatOb#name (method)">#name</a></span></p>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#add_genes-instance_method" title="#add_genes (instance method)">- (Object) <strong>add_genes</strong>(*genes) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Genes added here MUST correspond to pre-existing neurons.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#add_neurons-instance_method" title="#add_neurons (instance method)">- (Object) <strong>add_neurons</strong>(*neus) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Add new neurons to the fold.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#dump_s-instance_method" title="#dump_s (instance method)">- (Object) <strong>dump_s</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#fitness_cost-instance_method" title="#fitness_cost (instance method)">- (Object) <strong>fitness_cost</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Calculate the cost of this genotype.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#forget%21-instance_method" title="#forget! (instance method)">- (Object) <strong>forget!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Make the neurons forget their wiring.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (Genotype) <strong>initialize</strong>(critter, mating = false, &amp;block) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>A new instance of Genotype.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#innervate%21-instance_method" title="#innervate! (instance method)">- (Object) <strong>innervate!</strong>(*hneus) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>We take the neural hashes (presumably from other neurons), and innervate
-them.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#neucleate-instance_method" title="#neucleate (instance method)">- (Object) <strong>neucleate</strong>(clean: true, &amp;block) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>We add genes given here to the genome.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#nuke_redundancies%21-instance_method" title="#nuke_redundancies! (instance method)">- (Object) <strong>nuke_redundancies!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Remove any redundancies in the genome, any genes refering to the same two
-neurons.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#prune%21-instance_method" title="#prune! (instance method)">- (Object) <strong>prune!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Go through the list of neurons and drop any neurons not referenced by the
-genes.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#wire%21-instance_method" title="#wire! (instance method)">- (Object) <strong>wire!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Wire up the neurons based on the genes.</p>
-</div></span>
-</li>
-    </ul>
-  <h3 class="inherited">Methods inherited from <span class='object_link'><a href="../NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="../NeatOb.html#log-instance_method" title="NEAT::NeatOb#log (method)">#log</a></span>, <span class='object_link'><a href="../NeatOb.html#log-class_method" title="NEAT::NeatOb.log (method)">log</a></span>, <span class='object_link'><a href="../NeatOb.html#to_s-instance_method" title="NEAT::NeatOb#to_s (method)">#to_s</a></span></p>
-  <div id="constructor_details" class="method_details_list">
-  <h2>Constructor Details</h2>
-    <div class="method_details first">
-  <h3 class="signature first" id="initialize-instance_method">
-    - (<tt><span class='object_link'><a href="" title="NEAT::Critter::Genotype (class)">Genotype</a></span></tt>) <strong>initialize</strong>(critter, mating = false, &amp;block)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns a new instance of Genotype</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-93
-94
-95
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-100
-101
-102
-103
-104
-105
-106</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 88</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_critter'>critter</span><span class='comma'>,</span> <span class='id identifier rubyid_mating'>mating</span> <span class='op'>=</span> <span class='kw'>false</span><span class='comma'>,</span> <span class='op'>&amp;</span><span class='id identifier rubyid_block'>block</span><span class='rparen'>)</span>
-  <span class='kw'>super</span> <span class='id identifier rubyid_critter'>critter</span><span class='period'>.</span><span class='id identifier rubyid_controller'>controller</span>
-  <span class='ivar'>@critter</span> <span class='op'>=</span> <span class='id identifier rubyid_critter'>critter</span>
-  <span class='comment'># Initialize basic structures
-</span>  <span class='ivar'>@genes</span> <span class='op'>=</span> <span class='kw'>nil</span>
-  <span class='ivar'>@neural_inputs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@critter</span><span class='period'>.</span><span class='id identifier rubyid_population'>population</span><span class='period'>.</span><span class='id identifier rubyid_input_neurons'>input_neurons</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='op'>|</span>
-                          <span class='lbracket'>[</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@controller</span><span class='comma'>,</span> <span class='id identifier rubyid_sym'>sym</span><span class='rparen'>)</span><span class='rbracket'>]</span>
-                        <span class='rbrace'>}</span><span class='rbracket'>]</span>
-  <span class='ivar'>@neural_outputs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@critter</span><span class='period'>.</span><span class='id identifier rubyid_population'>population</span><span class='period'>.</span><span class='id identifier rubyid_output_neurons'>output_neurons</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='op'>|</span>
-                          <span class='lbracket'>[</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@controller</span><span class='comma'>,</span> <span class='id identifier rubyid_sym'>sym</span><span class='rparen'>)</span><span class='rbracket'>]</span>
-                        <span class='rbrace'>}</span><span class='rbracket'>]</span>
-  <span class='ivar'>@neurons</span> <span class='op'>=</span> <span class='ivar'>@neural_inputs</span><span class='period'>.</span><span class='id identifier rubyid_clone'>clone</span> <span class='comment'># this must be a shallow clone!
-</span>  <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_merge!'>merge!</span> <span class='ivar'>@neural_outputs</span>
-  <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_evolver'>evolver</span><span class='period'>.</span><span class='id identifier rubyid_gen_initial_genes!'>gen_initial_genes!</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span> <span class='kw'>unless</span> <span class='id identifier rubyid_mating'>mating</span>
-  <span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span> <span class='kw'>unless</span> <span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-</div>
-  <div id="instance_attr_details" class="attr_details">
-    <h2>Instance Attribute Details</h2>
-      <span id="critter=-instance_method"></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="critter-instance_method">
-    - (<tt>Object</tt>) <strong>critter</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Critter to which we belong</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-67
-68
-69</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 67</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_critter'>critter</span>
-  <span class='ivar'>@critter</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="dangling_neurons=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="dangling_neurons-instance_method">
-    - (<tt>Object</tt>) <strong>dangling_neurons</strong>
-    <span class="aliases">Also known as:
-    <span class="names"><span id='dangling_neurons?-instance_method'>dangling_neurons?</span></span>
-    </span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>This will be set to true if there are dangling neurons.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-79
-80
-81</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 79</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_dangling_neurons'>dangling_neurons</span>
-  <span class='ivar'>@dangling_neurons</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="genes=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="genes-instance_method">
-    - (<tt>Object</tt>) <strong>genes</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Genes keyed by innovation numbers</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-70
-71
-72</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 70</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_genes'>genes</span>
-  <span class='ivar'>@genes</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="neural_gene_map-instance_method">
-    - (<tt>Object</tt>) <strong>neural_gene_map</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Map neurons to the genes that marks them as output { oneu_name =&gt; [
-gene_1, gene_2,… gene_n], …} Just take the in_neuron name and the weight to
-do the call to that neuron function with the appropriate weights</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-86
-87
-88</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 86</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_neural_gene_map'>neural_gene_map</span>
-  <span class='ivar'>@neural_gene_map</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="neural_inputs-instance_method">
-    - (<tt>Object</tt>) <strong>neural_inputs</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Instantiations of neural inputs and outputs</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-76
-77
-78</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 76</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_neural_inputs'>neural_inputs</span>
-  <span class='ivar'>@neural_inputs</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="neural_outputs-instance_method">
-    - (<tt>Object</tt>) <strong>neural_outputs</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Instantiations of neural inputs and outputs</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-76
-77
-78</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 76</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_neural_outputs'>neural_outputs</span>
-  <span class='ivar'>@neural_outputs</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="neurons=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="neurons-instance_method">
-    - (<tt>Object</tt>) <strong>neurons</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>List of neurons hashed by name</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-73
-74
-75</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 73</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_neurons'>neurons</span>
-  <span class='ivar'>@neurons</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="add_genes-instance_method">
-    - (<tt>Object</tt>) <strong>add_genes</strong>(*genes)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Genes added here MUST correspond to pre-existing neurons. Be sure to do
-add_neurons first!!!!</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-163
-164
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-167
-168
-169</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 163</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_add_genes'>add_genes</span><span class='lparen'>(</span><span class='op'>*</span><span class='id identifier rubyid_genes'>genes</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_genes'>genes</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NeatException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Neuron </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='embexpr_end'>}</span><span class='tstring_content'> missing</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>unless</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NeatException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Neuron </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='embexpr_end'>}</span><span class='tstring_content'> missing</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>unless</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span>
-    <span class='ivar'>@genes</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_innovation'>innovation</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_gene'>gene</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="add_neurons-instance_method">
-    - (<tt>Object</tt>) <strong>add_neurons</strong>(*neus)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Add new neurons to the fold</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-155
-156
-157
-158
-159</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 155</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_add_neurons'>add_neurons</span><span class='lparen'>(</span><span class='op'>*</span><span class='id identifier rubyid_neus'>neus</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_neus'>neus</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_neu'>neu</span><span class='op'>|</span>
-    <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_neu'>neu</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_neu'>neu</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="dump_s-instance_method">
-    - (<tt>Object</tt>) <strong>dump_s</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-218
-219
-220
-221
-222</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 218</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_dump_s'>dump_s</span>
-  <span class='id identifier rubyid_to_s'>to_s</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\ngenes:\n</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
-    <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nneurons:\n</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_neu'>neu</span><span class='op'>|</span>
-    <span class='id identifier rubyid_neu'>neu</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="fitness_cost-instance_method">
-    - (<tt>Object</tt>) <strong>fitness_cost</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Calculate the cost of this genotype.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-213
-214
-215
-216</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 213</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_fitness_cost'>fitness_cost</span>
-  <span class='id identifier rubyid_p'>p</span> <span class='op'>=</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_parms'>parms</span>
-  <span class='id identifier rubyid_p'>p</span><span class='period'>.</span><span class='id identifier rubyid_fitness_cost_per_neuron'>fitness_cost_per_neuron</span> <span class='op'>*</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span> <span class='op'>+</span> <span class='id identifier rubyid_p'>p</span><span class='period'>.</span><span class='id identifier rubyid_fitness_cost_per_gene'>fitness_cost_per_gene</span> <span class='op'>*</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="forget!-instance_method">
-    - (<tt>Object</tt>) <strong>forget!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Make the neurons forget their wiring.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-134
-135
-136
-137</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 134</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_forget!'>forget!</span>
-  <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_neu'>neu</span><span class='op'>|</span> <span class='id identifier rubyid_neu'>neu</span><span class='period'>.</span><span class='id identifier rubyid_clear_graph'>clear_graph</span> <span class='rbrace'>}</span>
-  <span class='ivar'>@neural_gene_map</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_h'>h</span><span class='comma'>,</span> <span class='id identifier rubyid_k'>k</span><span class='op'>|</span> <span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span> <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="innervate!-instance_method">
-    - (<tt>Object</tt>) <strong>innervate!</strong>(*hneus)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>We take the neural hashes (presumably from other neurons), and innervate
-them. We do this in distinctions based on the neuron&#39;s names. FIXME We
-need to randomly select a neuron in the case of clashes.</p>
-  </div>
-</div>
-<div class="tags">
-  <p class="tag_title">Parameters:</p>
-<ul class="param">
-    <li>
-        <span class='name'>hneus</span>
-        <span class='type'>(<tt>Hash</tt>)</span>
-        &mdash;
-        <div class='inline'>
-<p>– hashes of neurons to innervate</p>
-</div>
-    </li>
-</ul>
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-175
-176
-177
-178
-179</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 175</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_innervate!'>innervate!</span><span class='lparen'>(</span><span class='op'>*</span><span class='id identifier rubyid_hneus'>hneus</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_hneus'>hneus</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_neus'>neus</span><span class='op'>|</span>
-    <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_merge!'>merge!</span> <span class='id identifier rubyid_neus'>neus</span><span class='period'>.</span><span class='id identifier rubyid_dclone'>dclone</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="neucleate-instance_method">
-    - (<tt>Object</tt>) <strong>neucleate</strong>(clean: true, &amp;block)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>We add genes given here to the genome. An array of genes is returned from
-the block and we simply add them in.</p>
-  </div>
-</div>
-<div class="tags">
-  <p class="tag_title">Parameters:</p>
-<ul class="param">
-    <li>
-        <span class='name'>clean</span>
-        <span class='type'>(<tt>boolean</tt>)</span>
-    </li>
-    <li>
-        <span class='name'>block</span>
-        <span class='type'>(<tt>Proc</tt>)</span>
-    </li>
-</ul>
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-113
-114
-115
-116
-117
-118
-119
-120
-121
-122
-123</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 113</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_neucleate'>neucleate</span><span class='lparen'>(</span><span class='label'>clean:</span> <span class='kw'>true</span><span class='comma'>,</span> <span class='op'>&amp;</span><span class='id identifier rubyid_block'>block</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_genes'>genes</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_g'>g</span><span class='op'>|</span>
-    <span class='id identifier rubyid_g'>g</span><span class='period'>.</span><span class='id identifier rubyid_genotype'>genotype</span> <span class='op'>=</span> <span class='kw'>self</span>
-    <span class='lbracket'>[</span><span class='id identifier rubyid_g'>g</span><span class='period'>.</span><span class='id identifier rubyid_innovation'>innovation</span><span class='comma'>,</span> <span class='id identifier rubyid_g'>g</span><span class='rbracket'>]</span> <span class='rbrace'>}</span><span class='rbracket'>]</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_clean'>clean</span>
-    <span class='ivar'>@genes</span> <span class='op'>=</span> <span class='id identifier rubyid_genes'>genes</span>
-  <span class='kw'>else</span>
-    <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_merge!'>merge!</span> <span class='id identifier rubyid_genes'>genes</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_nuke_redundancies!'>nuke_redundancies!</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="nuke_redundancies!-instance_method">
-    - (<tt>Object</tt>) <strong>nuke_redundancies!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Remove any redundancies in the genome, any genes refering to the same two
-neurons. Simply choose one and delete the rest. TODO: implement
-nuke_redundancies!</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-129
-130
-131</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 129</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_nuke_redundancies!'>nuke_redundancies!</span>
-  <span class='id identifier rubyid_log'>log</span><span class='period'>.</span><span class='id identifier rubyid_warn'>warn</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>nuke_redundancies! NIY</span><span class='tstring_end'>&#39;</span></span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="prune!-instance_method">
-    - (<tt>Object</tt>) <strong>prune!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Go through the list of neurons and drop any neurons not referenced by the
-genes.</p>
-<p>Then go through the genes and drop any that are dangling (i.e. no matching
-neurons)</p>
-<p>Then make sure that @neural_inputs and @neural_outputs reference the actual
-instance neurons in @neurons</p>
-<p>TODO add this circularity check to prune!</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-191
-192
-193
-194
-195
-196
-197
-198
-199
-200
-201
-202
-203
-204
-205
-206
-207
-208
-209
-210</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 191</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_prune!'>prune!</span>
-  <span class='comment'># Take care of dangling neurons
-</span>  <span class='id identifier rubyid_neunames'>neunames</span> <span class='op'>=</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_values'>values</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_g'>g</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_g'>g</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='comma'>,</span> <span class='id identifier rubyid_g'>g</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='period'>.</span><span class='id identifier rubyid_to_set'>to_set</span>
-  <span class='ivar'>@neurons</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_values'>values</span><span class='period'>.</span><span class='id identifier rubyid_reject'>reject</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span>
-    <span class='kw'>not</span> <span class='id identifier rubyid_neunames'>neunames</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span>
-  <span class='kw'>end</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span>
-    <span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='rbracket'>]</span>
-  <span class='kw'>end</span><span class='rbracket'>]</span>
-  <span class='comment'># Take care of dangling genes
-</span>  <span class='ivar'>@genes</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_values'>values</span><span class='period'>.</span><span class='id identifier rubyid_reject'>reject</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
-    <span class='kw'>not</span> <span class='lparen'>(</span><span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='rparen'>)</span> <span class='kw'>and</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rparen'>)</span><span class='rparen'>)</span>
-  <span class='kw'>end</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
-    <span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_gene'>gene</span><span class='rbracket'>]</span>
-  <span class='kw'>end</span><span class='rbracket'>]</span>
-  <span class='comment'># Make sure @neural_inputs and @neural_outputs are consistent
-</span>  <span class='ivar'>@neural_inputs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@neural_inputs</span><span class='period'>.</span><span class='id identifier rubyid_values'>values</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='rbracket'>]</span>
-  <span class='ivar'>@neural_outputs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@neural_outputs</span><span class='period'>.</span><span class='id identifier rubyid_values'>values</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='rbracket'>]</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="wire!-instance_method">
-    - (<tt>Object</tt>) <strong>wire!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Wire up the neurons based on the genes.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-140
-141
-142
-143
-144
-145
-146
-147
-148
-149
-150
-151
-152</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 140</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_wire!'>wire!</span>
-  <span class='id identifier rubyid_forget!'>forget!</span>
-  <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_innov'>innov</span><span class='comma'>,</span> <span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_enabled?'>enabled?</span>
-      <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NeatException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Can&#39;t find </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>if</span> <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-      <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rbracket'>]</span> <span class='op'>&lt;&lt;</span> <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='rbracket'>]</span>
-      <span class='ivar'>@neural_gene_map</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rbracket'>]</span> <span class='op'>&lt;&lt;</span> <span class='id identifier rubyid_gene'>gene</span> <span class='kw'>unless</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span> <span class='kw'>unless</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-  <span class='kw'>if</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-    <span class='gvar'>$log</span><span class='period'>.</span><span class='id identifier rubyid_error'>error</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>Genes Not Present</span><span class='tstring_end'>&#39;</span></span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Sun Apr 13 15:54:02 2014 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.4 (ruby-2.1.1).
-</div>
-  </body>
-</html>