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Module General
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<h1 class="epydoc">Source Code for <a href="Bio.GA.Mutation.General-module.html">Module Bio.GA.Mutation.General</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""General functionality for mutations.</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-comment"># standard library</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># local stuff</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.GA=Bio.GA-module.html"><a title="Bio.GA" class="py-name" href="#" onclick="return doclink('link-1', 'GA', 'link-1');">GA</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.GA.Organism=Bio.GA.Organism-module.html,Class Bio.GA.Organism.Organism=Bio.GA.Organism.Organism-class.html,Class Bio.Graphics.BasicChromosome.Organism=Bio.Graphics.BasicChromosome.Organism-class.html"><a title="Bio.GA.Organism
Bio.GA.Organism.Organism
Bio.Graphics.BasicChromosome.Organism" class="py-name" href="#" onclick="return doclink('link-2', 'Organism', 'link-2');">Organism</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.GA.Organism
Bio.GA.Organism.Organism
Bio.Graphics.BasicChromosome.Organism" class="py-name" href="#" onclick="return doclink('link-3', 'Organism', 'link-2');">Organism</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="SafeFitnessMutation"></a><div id="SafeFitnessMutation-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="SafeFitnessMutation-toggle" onclick="return toggle('SafeFitnessMutation');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GA.Mutation.General.SafeFitnessMutation-class.html">SafeFitnessMutation</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="SafeFitnessMutation-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="SafeFitnessMutation-expanded"><a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform mutations, but do not allow decreases in organism fitness.</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 doesn't actually do any mutation work, but just checks that</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring"> newly create organisms do not have lower fitnesses. </tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="SafeFitnessMutation.__init__"></a><div id="SafeFitnessMutation.__init__-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="SafeFitnessMutation.__init__-toggle" onclick="return toggle('SafeFitnessMutation.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Mutation.General.SafeFitnessMutation-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">actual_mutation</tt><tt class="py-op">,</tt> <tt class="py-param">accept_less</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SafeFitnessMutation.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SafeFitnessMutation.__init__-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize to do safe mutations</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"> Arguments:</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> o actual_mutation - A Mutation class which actually implements</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> mutation. functionality.</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> o accept_less - A probability to accept mutations which</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> generate lower fitness. This allows you to accept some</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> crossovers which reduce fitness, but not all of them.</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mutation</tt> <tt class="py-op">=</tt> <tt class="py-name">actual_mutation</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_accept_less_percent</tt> <tt class="py-op">=</tt> <tt class="py-name">accept_less</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">_accept_less_rand</tt> <tt class="py-op">=</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">Random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> </tt>
<a name="SafeFitnessMutation.mutate"></a><div id="SafeFitnessMutation.mutate-def"><a name="L31"></a><tt class="py-lineno">31</tt> <a class="py-toggle" href="#" id="SafeFitnessMutation.mutate-toggle" onclick="return toggle('SafeFitnessMutation.mutate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Mutation.General.SafeFitnessMutation-class.html#mutate">mutate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">org</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SafeFitnessMutation.mutate-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SafeFitnessMutation.mutate-expanded"><a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform safe mutation of the specified organism.</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">new_org</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_mutation</tt><tt class="py-op">.</tt><tt id="link-4" 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-4', 'mutate', 'link-4');">mutate</a></tt><tt class="py-op">(</tt><tt class="py-name">org</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">new_org</tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'recalculate_fitness', 'link-5');">recalculate_fitness</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">org</tt><tt class="py-op">.</tt><tt class="py-name">fitness</tt> <tt class="py-op">></tt> <tt class="py-name">new_org</tt><tt class="py-op">.</tt><tt class="py-name">fitness</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">accept_less_chance</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_accept_less_rand</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">accept_less_chance</tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_accept_less_percent</tt><tt class="py-op">:</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">new_org</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">org</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">new_org</tt> </tt>
</div></div><a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> </tt><script type="text/javascript">
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