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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GA-module.html">Package GA</a> ::
Module Evolver
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<h1 class="epydoc">Source Code for <a href="Bio.GA.Evolver-module.html">Module Bio.GA.Evolver</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Evolution Strategies for a Population.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">Evolver classes manage a population of individuals, and are responsible</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">for taking care of the transition from one generation to the next.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># standard modules</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="SteadyStateEvolver"></a><div id="SteadyStateEvolver-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="SteadyStateEvolver-toggle" onclick="return toggle('SteadyStateEvolver');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GA.Evolver.SteadyStateEvolver-class.html">SteadyStateEvolver</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SteadyStateEvolver-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="SteadyStateEvolver-expanded"><a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-docstring">"""Evolve a population in place.</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"> This implements a Steady State GA, where the population of individuals</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring"> is evolved in place.</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="SteadyStateEvolver.__init__"></a><div id="SteadyStateEvolver.__init__-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="SteadyStateEvolver.__init__-toggle" onclick="return toggle('SteadyStateEvolver.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Evolver.SteadyStateEvolver-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SteadyStateEvolver.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SteadyStateEvolver.__init__-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"Need to code this."</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> </tt>
<a name="GenerationEvolver"></a><div id="GenerationEvolver-def"><a name="L18"></a><tt class="py-lineno">18</tt> <a class="py-toggle" href="#" id="GenerationEvolver-toggle" onclick="return toggle('GenerationEvolver');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GA.Evolver.GenerationEvolver-class.html">GenerationEvolver</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenerationEvolver-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="GenerationEvolver-expanded"><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-docstring">"""Evolve a population from generation to generation.</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> This implements a Generational GA, in which the population moves from</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> generation to generation.</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="GenerationEvolver.__init__"></a><div id="GenerationEvolver.__init__-def"><a name="L24"></a><tt class="py-lineno">24</tt> <a class="py-toggle" href="#" id="GenerationEvolver.__init__-toggle" onclick="return toggle('GenerationEvolver.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Evolver.GenerationEvolver-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">starting_population</tt><tt class="py-op">,</tt> <tt class="py-param">selector</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenerationEvolver.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="GenerationEvolver.__init__-expanded"><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the evolver.</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"> o starting_population -- An initial set of individuals to begin</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> the evolution process from. This should be a list of Organism</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> objects.</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> o selector -- A Selection object that implements selection, along</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> with mutation and crossover to select a new population from a</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-docstring"> given population.</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt> <tt class="py-op">=</tt> <tt class="py-name">starting_population</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_selector</tt> <tt class="py-op">=</tt> <tt class="py-name">selector</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> </tt>
<a name="GenerationEvolver.evolve"></a><div id="GenerationEvolver.evolve-def"><a name="L40"></a><tt class="py-lineno">40</tt> <a class="py-toggle" href="#" id="GenerationEvolver.evolve-toggle" onclick="return toggle('GenerationEvolver.evolve');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Evolver.GenerationEvolver-class.html#evolve">evolve</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">stopping_criteria</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenerationEvolver.evolve-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="GenerationEvolver.evolve-expanded"><a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-docstring">"""Evolve the population through multiple generations.</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-docstring"> o stoppping_criteria -- A function which, when passed the current</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-docstring"> individuals in the population, will determine when to stop</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-docstring"> the evolution process.</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt class="py-docstring"> Returns:</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-docstring"> o The final evolved population.</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt><tt class="py-op">(</tt><tt id="link-0" class="py-name" targets="Method Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.stopping_criteria()=Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-class.html#stopping_criteria"><a title="Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.stopping_criteria" class="py-name" href="#" onclick="return doclink('link-0', 'stopping_criteria', 'link-0');">stopping_criteria</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-comment"># perform selection, mutation, crossover on the population</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_selector</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.GA.Selection.Abstract.AbstractSelection.select()=Bio.GA.Selection.Abstract.AbstractSelection-class.html#select,Method Bio.GA.Selection.Diversity.DiversitySelection.select()=Bio.GA.Selection.Diversity.DiversitySelection-class.html#select,Method Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.select()=Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html#select,Method Bio.GA.Selection.Tournament.TournamentSelection.select()=Bio.GA.Selection.Tournament.TournamentSelection-class.html#select"><a title="Bio.GA.Selection.Abstract.AbstractSelection.select
Bio.GA.Selection.Diversity.DiversitySelection.select
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.select
Bio.GA.Selection.Tournament.TournamentSelection.select" class="py-name" href="#" onclick="return doclink('link-1', 'select', 'link-1');">select</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-comment"># update the fitness of the new popultation</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-2" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.organism()=Bio.GenBank._FeatureConsumer-class.html#organism,Method Bio.GenBank._RecordConsumer.organism()=Bio.GenBank._RecordConsumer-class.html#organism"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism" class="py-name" href="#" onclick="return doclink('link-2', 'organism', 'link-2');">organism</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt id="link-3" class="py-name"><a title="Bio.GenBank._FeatureConsumer.organism
Bio.GenBank._RecordConsumer.organism" class="py-name" href="#" onclick="return doclink('link-3', 'organism', 'link-2');">organism</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.GA.Organism.Organism.recalculate_fitness()=Bio.GA.Organism.Organism-class.html#recalculate_fitness"><a title="Bio.GA.Organism.Organism.recalculate_fitness" class="py-name" href="#" onclick="return doclink('link-4', 'recalculate_fitness', 'link-4');">recalculate_fitness</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-comment"># dump out all of the organisms for debugging if the</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-comment"># evolution process is broken with a Control-C</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyboardInterrupt</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-comment"># sort the population so we can look at duplicates</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.sort()=Bio.Align.MultipleSeqAlignment-class.html#sort,Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-5', 'sort', 'link-5');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">org</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">org</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_population</tt> </tt>
</div></div><a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> </tt><script type="text/javascript">
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