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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GA-module.html">Package GA</a> ::
<a href="Bio.GA.Selection-module.html">Package Selection</a> ::
Module Abstract
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<h1 class="epydoc">Source Code for <a href="Bio.GA.Selection.Abstract-module.html">Module Bio.GA.Selection.Abstract</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Base selection class from which all Selectors should derive.</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>
<a name="AbstractSelection"></a><div id="AbstractSelection-def"><a name="L4"></a><tt class="py-lineno"> 4</tt> <a class="py-toggle" href="#" id="AbstractSelection-toggle" onclick="return toggle('AbstractSelection');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GA.Selection.Abstract.AbstractSelection-class.html">AbstractSelection</a><tt class="py-op">:</tt> </tt>
</div><div id="AbstractSelection-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="AbstractSelection-expanded"><a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for Selector classes.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"> This classes provides useful functions for different selector classes</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"> and also defines the functions that all selector classes must</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"> implement.</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring"> This class should not be used directly, but rather should be subclassed.</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="AbstractSelection.__init__"></a><div id="AbstractSelection.__init__-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="AbstractSelection.__init__-toggle" onclick="return toggle('AbstractSelection.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Selection.Abstract.AbstractSelection-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">mutator</tt><tt class="py-op">,</tt> <tt class="py-param">crossover</tt><tt class="py-op">,</tt> <tt class="py-param">repairer</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractSelection.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="AbstractSelection.__init__-expanded"><a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize a selector.</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> o mutator -- A Mutation object which will perform mutation</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> on an individual.</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"> o crossover -- A Crossover object which will take two</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> individuals and produce two new individuals which may</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> have had crossover occur.</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> o repairer -- A class which can do repair on rearranged genomes</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> to eliminate infeasible individuals. If set at None, so repair</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> will be done.</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mutator</tt> <tt class="py-op">=</tt> <tt class="py-name">mutator</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover._crossover()=Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover-class.html#_crossover,Method Bio.GA.Crossover.GeneralPoint.InterleaveCrossover._crossover()=Bio.GA.Crossover.GeneralPoint.InterleaveCrossover-class.html#_crossover,Method Bio.GA.Crossover.GeneralPoint.TwoCrossover._crossover()=Bio.GA.Crossover.GeneralPoint.TwoCrossover-class.html#_crossover"><a title="Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover._crossover
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover._crossover
Bio.GA.Crossover.GeneralPoint.TwoCrossover._crossover" class="py-name" href="#" onclick="return doclink('link-0', '_crossover', 'link-0');">_crossover</a></tt> <tt class="py-op">=</tt> <tt class="py-name">crossover</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_repairer</tt> <tt class="py-op">=</tt> <tt class="py-name">repairer</tt> </tt>
</div><a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> </tt>
<a name="AbstractSelection.mutate_and_crossover"></a><div id="AbstractSelection.mutate_and_crossover-def"><a name="L33"></a><tt class="py-lineno">33</tt> <a class="py-toggle" href="#" id="AbstractSelection.mutate_and_crossover-toggle" onclick="return toggle('AbstractSelection.mutate_and_crossover');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Selection.Abstract.AbstractSelection-class.html#mutate_and_crossover">mutate_and_crossover</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">org_1</tt><tt class="py-op">,</tt> <tt class="py-param">org_2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractSelection.mutate_and_crossover-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="AbstractSelection.mutate_and_crossover-expanded"><a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform mutation and crossover on the two organisms.</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-docstring"> This uses the classes mutator and crossover functions to</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-docstring"> perform the manipulations.</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"> If a repair class is available, then the rearranged genomes will</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> be repaired to make them feasible.</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-docstring"> The newly created individuals are returned.</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-comment"># first crossover the two organisms</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cross_org_1</tt><tt class="py-op">,</tt> <tt class="py-name">cross_org_2</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name"><a title="Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover._crossover
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover._crossover
Bio.GA.Crossover.GeneralPoint.TwoCrossover._crossover" class="py-name" href="#" onclick="return doclink('link-1', '_crossover', 'link-0');">_crossover</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.GA.Crossover.General.SafeFitnessCrossover.do_crossover()=Bio.GA.Crossover.General.SafeFitnessCrossover-class.html#do_crossover,Method Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.do_crossover()=Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover-class.html#do_crossover,Method Bio.GA.Crossover.Uniform.UniformCrossover.do_crossover()=Bio.GA.Crossover.Uniform.UniformCrossover-class.html#do_crossover"><a title="Bio.GA.Crossover.General.SafeFitnessCrossover.do_crossover
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.do_crossover
Bio.GA.Crossover.Uniform.UniformCrossover.do_crossover" class="py-name" href="#" onclick="return doclink('link-2', 'do_crossover', 'link-2');">do_crossover</a></tt><tt class="py-op">(</tt><tt class="py-name">org_1</tt><tt class="py-op">,</tt> <tt class="py-name">org_2</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-comment"># now perform mutation on the two organisms</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">final_org_1</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mutator</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.GA.Mutation.General.SafeFitnessMutation.mutate()=Bio.GA.Mutation.General.SafeFitnessMutation-class.html#mutate,Method Bio.GA.Mutation.Simple.ConversionMutation.mutate()=Bio.GA.Mutation.Simple.ConversionMutation-class.html#mutate,Method Bio.GA.Mutation.Simple.SinglePositionMutation.mutate()=Bio.GA.Mutation.Simple.SinglePositionMutation-class.html#mutate"><a title="Bio.GA.Mutation.General.SafeFitnessMutation.mutate
Bio.GA.Mutation.Simple.ConversionMutation.mutate
Bio.GA.Mutation.Simple.SinglePositionMutation.mutate" class="py-name" href="#" onclick="return doclink('link-3', 'mutate', 'link-3');">mutate</a></tt><tt class="py-op">(</tt><tt class="py-name">cross_org_1</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-name">final_org_2</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mutator</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.GA.Mutation.General.SafeFitnessMutation.mutate
Bio.GA.Mutation.Simple.ConversionMutation.mutate
Bio.GA.Mutation.Simple.SinglePositionMutation.mutate" class="py-name" href="#" onclick="return doclink('link-4', 'mutate', 'link-3');">mutate</a></tt><tt class="py-op">(</tt><tt class="py-name">cross_org_2</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-comment"># if we have a repair class, perform repair</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_repairer</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-name">final_org_1</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_repairer</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.GA.Repair.Stabilizing.AmbiguousRepair.repair()=Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html#repair"><a title="Bio.GA.Repair.Stabilizing.AmbiguousRepair.repair" class="py-name" href="#" onclick="return doclink('link-5', 'repair', 'link-5');">repair</a></tt><tt class="py-op">(</tt><tt class="py-name">final_org_1</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-name">final_org_2</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_repairer</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.GA.Repair.Stabilizing.AmbiguousRepair.repair" class="py-name" href="#" onclick="return doclink('link-6', 'repair', 'link-5');">repair</a></tt><tt class="py-op">(</tt><tt class="py-name">final_org_2</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">final_org_1</tt><tt class="py-op">,</tt> <tt class="py-name">final_org_2</tt> </tt>
</div><a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> </tt>
<a name="AbstractSelection.select"></a><div id="AbstractSelection.select-def"><a name="L58"></a><tt class="py-lineno">58</tt> <a class="py-toggle" href="#" id="AbstractSelection.select-toggle" onclick="return toggle('AbstractSelection.select');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Selection.Abstract.AbstractSelection-class.html#select">select</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">population</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractSelection.select-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="AbstractSelection.select-expanded"><a name="L59"></a><tt class="py-lineno">59</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">"Derived classes must implement."</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> </tt><script type="text/javascript">
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