<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.GA.Crossover.Uniform</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.GA-module.html">Package GA</a> :: <a href="Bio.GA.Crossover-module.html">Package Crossover</a> :: Module Uniform </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.GA.Crossover.Uniform-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.GA.Crossover.Uniform-module.html">Module Bio.GA.Crossover.Uniform</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Perform uniform crossovers between the genomes of two organisms.</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"></tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">genome 1 -- A B C D E F G</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-docstring">genome 2 -- a b c d e f g</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">After crossover:</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">new genome 1 -- a B c d E f G</tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">new genome 2 -- A b C D e F g</tt> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring">Uniform Crossover is a standard crossover technique for</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring">rapid mutation-behavior. </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-comment"># standard modules</tt> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> </tt> <a name="UniformCrossover"></a><div id="UniformCrossover-def"><a name="L19"></a><tt class="py-lineno">19</tt> <a class="py-toggle" href="#" id="UniformCrossover-toggle" onclick="return toggle('UniformCrossover');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GA.Crossover.Uniform.UniformCrossover-class.html">UniformCrossover</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="UniformCrossover-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="UniformCrossover-expanded"><a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform single point crossover between genomes at some defined rates.</tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> This performs a single crossover between two genomes at some</tt> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> defined frequency. The location of the crossover is chosen randomly</tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> if the crossover meets the probability to occur.</tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="UniformCrossover.__init__"></a><div id="UniformCrossover.__init__-def"><a name="L26"></a><tt class="py-lineno">26</tt> <a class="py-toggle" href="#" id="UniformCrossover.__init__-toggle" onclick="return toggle('UniformCrossover.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Crossover.Uniform.UniformCrossover-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">crossover_prob</tt> <tt class="py-op">=</tt> <tt class="py-number">.1</tt><tt class="py-op">,</tt> <tt class="py-param">uniform_prob</tt> <tt class="py-op">=</tt> <tt class="py-number">0.7</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="UniformCrossover.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="UniformCrossover.__init__-expanded"><a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize to do uniform crossover at the specified probability and frequency.</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">_crossover_prob</tt> <tt class="py-op">=</tt> <tt class="py-name">crossover_prob</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 class="py-name">_uniform_prob</tt> <tt class="py-op">=</tt> <tt class="py-name">uniform_prob</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> </div><a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> </tt> <a name="UniformCrossover.do_crossover"></a><div id="UniformCrossover.do_crossover-def"><a name="L33"></a><tt class="py-lineno">33</tt> <a class="py-toggle" href="#" id="UniformCrossover.do_crossover-toggle" onclick="return toggle('UniformCrossover.do_crossover');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Crossover.Uniform.UniformCrossover-class.html#do_crossover">do_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="UniformCrossover.do_crossover-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="UniformCrossover.do_crossover-expanded"><a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-docstring">"""Potentially do a crossover between 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-name">new_org_1</tt> <tt class="py-op">=</tt> <tt class="py-name">org_1</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.SeqIO._index._IndexedSeqFileDict.copy()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#copy"><a title="Bio.Crystal.Crystal.copy Bio.GA.Organism.Organism.copy Bio.PDB.Vector'.Vector.copy Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-0', 'copy', 'link-0');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">new_org_2</tt> <tt class="py-op">=</tt> <tt class="py-name">org_2</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name"><a title="Bio.Crystal.Crystal.copy Bio.GA.Organism.Organism.copy Bio.PDB.Vector'.Vector.copy Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-1', 'copy', 'link-0');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt> <a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-comment"># determine if we have a crossover</tt> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">crossover_chance</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> <a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">crossover_chance</tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_crossover_prob</tt><tt class="py-op">:</tt> </tt> <a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-name">minlen</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">new_org_1</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">new_org_2</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-2" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-2', 'i', 'link-2');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-3" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range Bio.Graphics.GenomeDiagram._Graph.GraphData.range Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-3', 'range', 'link-3');">range</a></tt><tt class="py-op">(</tt> <tt class="py-name">minlen</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">uniform_chance</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> <a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">uniform_chance</tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_uniform_prob</tt><tt class="py-op">:</tt> </tt> <a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-comment"># cycle element</tt> </tt> <a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">temp</tt> <tt class="py-op">=</tt> <tt class="py-name">new_org_1</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">[</tt><tt id="link-4" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-4', 'i', 'link-2');">i</a></tt><tt class="py-op">]</tt> </tt> <a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-name">new_org_1</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">[</tt><tt id="link-5" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-5', 'i', 'link-2');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">new_org_2</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">[</tt><tt id="link-6" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-6', 'i', 'link-2');">i</a></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">new_org_2</tt><tt class="py-op">.</tt><tt class="py-name">genome</tt><tt class="py-op">[</tt><tt id="link-7" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-7', 'i', 'link-2');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">temp</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-keyword">return</tt> <tt class="py-name">new_org_1</tt><tt class="py-op">,</tt> <tt class="py-name">new_org_2</tt> </tt> </div></div><a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Thu Aug 18 18:22:25 2011 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" 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