<?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.Selection.RouletteWheel</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.Selection-module.html">Package Selection</a> :: Module RouletteWheel </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.Selection.RouletteWheel-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.GA.Selection.RouletteWheel-module.html">Module Bio.GA.Selection.RouletteWheel</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Implement Roulette Wheel selection on 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">This implements Roulette Wheel selection in which individuals are</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">selected from a population randomly, with their proportion of selection</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">based on their relative fitness in the population.</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-comment"># standard modules</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</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.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy Bio.GA.Organism.Organism.copy Bio.GenBank.NCBIDictionary.copy Bio.PDB.Vector'.Vector.copy Bio.Prosite.ExPASyDictionary.copy Bio.Prosite.Pattern.PrositeTerm.copy Bio.Prosite.Prodoc.ExPASyDictionary.copy Bio.PubMed.Dictionary.copy Bio.SwissProt.SProt.ExPASyDictionary.copy Martel.Expression.Any.copy Martel.Expression.AnyEol.copy Martel.Expression.Assert.copy Martel.Expression.AtBeginning.copy Martel.Expression.AtEnd.copy Martel.Expression.Debug.copy Martel.Expression.Dot.copy Martel.Expression.Expression.copy Martel.Expression.ExpressionList.copy Martel.Expression.FastFeature.copy Martel.Expression.Group.copy Martel.Expression.GroupRef.copy Martel.Expression.HeaderFooter.copy Martel.Expression.Literal.copy Martel.Expression.MaxRepeat.copy Martel.Expression.NullOp.copy Martel.Expression.ParseRecords.copy Martel.Expression.PassThrough.copy Martel.Expression.Str.copy Martel.IterParser.IterHeaderFooter.copy Martel.IterParser.IterRecords.copy Martel.Iterator.IteratorRecords.copy Martel.Parser.HeaderFooterParser.copy Martel.Parser.Parser.copy Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-0', 'copy', 'link-0');">copy</a></tt> </tt> <a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"># local modules</tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Module Bio.GA.Selection.Abstract=Bio.GA.Selection.Abstract-module.html"><a title="Bio.GA.Selection.Abstract" class="py-name" href="#" onclick="return doclink('link-1', 'Abstract', 'link-1');">Abstract</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Class Bio.GA.Selection.Abstract.AbstractSelection=Bio.GA.Selection.Abstract.AbstractSelection-class.html"><a title="Bio.GA.Selection.Abstract.AbstractSelection" class="py-name" href="#" onclick="return doclink('link-2', 'AbstractSelection', 'link-2');">AbstractSelection</a></tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt> <a name="RouletteWheelSelection"></a><div id="RouletteWheelSelection-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="RouletteWheelSelection-toggle" onclick="return toggle('RouletteWheelSelection');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html">RouletteWheelSelection</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractSelection</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RouletteWheelSelection-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RouletteWheelSelection-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-docstring">"""Roulette wheel selection proportional to individuals fitness.</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> The implements a roulette wheel selector that selects individuals</tt> </tt> <a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> from the population, and performs mutation and crossover on</tt> </tt> <a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> the selected individuals.</tt> </tt> <a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="RouletteWheelSelection.__init__"></a><div id="RouletteWheelSelection.__init__-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="RouletteWheelSelection.__init__-toggle" onclick="return toggle('RouletteWheelSelection.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-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="RouletteWheelSelection.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RouletteWheelSelection.__init__-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the selector.</tt> </tt> <a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> o mutator -- A Mutation object which will perform mutation</tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> on an individual.</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 crossover -- A Crossover object which will take two</tt> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> individuals and produce two new individuals which may</tt> </tt> <a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> have had crossover occur.</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 repairer -- A class which can do repair on rearranged genomes</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> to eliminate infeasible individuals. If set at None, so repair</tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> will be done.</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 id="link-3" class="py-name"><a title="Bio.GA.Selection.Abstract.AbstractSelection" class="py-name" href="#" onclick="return doclink('link-3', 'AbstractSelection', 'link-2');">AbstractSelection</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method 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Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method 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Bio.SwissProt.KeyWList._Scanner.__init__ Bio.SwissProt.SProt.Dictionary.__init__ Bio.SwissProt.SProt.ExPASyDictionary.__init__ Bio.SwissProt.SProt.Iterator.__init__ Bio.SwissProt.SProt.Record.__init__ Bio.SwissProt.SProt.RecordParser.__init__ Bio.SwissProt.SProt.Reference.__init__ Bio.SwissProt.SProt.SequenceParser.__init__ Bio.SwissProt.SProt._RecordConsumer.__init__ Bio.SwissProt.SProt._SequenceConsumer.__init__ Bio.Transcribe.Transcribe.__init__ Bio.Translate.Translator.__init__ Bio.UniGene.Iterator.__init__ Bio.UniGene.RecordParser.__init__ Bio.UniGene.UnigeneProtsimRecord.__init__ Bio.UniGene.UnigeneRecord.__init__ Bio.UniGene.UnigeneSTSRecord.__init__ Bio.UniGene.UnigeneSequenceRecord.__init__ Bio.UniGene._RecordConsumer.__init__ Bio.WWW.RequestLimiter.__init__ Bio.Wise.dnal.Statistics.__init__ Bio.Wise.psw.AlignmentColumn.__init__ Bio.Wise.psw.ColumnUnit.__init__ Bio.Writer.Writer.__init__ Bio.biblio.Biblio.__init__ Bio.biblio.BiblioCollection.__init__ Bio.builders.Search.search.BuildSearch.__init__ Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__ Bio.config.DBRegistry.BioCorbaDB.__init__ Bio.config.DBRegistry.BioSQLDB.__init__ Bio.config.DBRegistry.CGIDB.__init__ Bio.config.DBRegistry.DBGroup.__init__ Bio.config.DBRegistry.DBObject.__init__ Bio.config.DBRegistry.DBRegistry.__init__ Bio.config.DBRegistry.EUtilsDB.__init__ Bio.config.DBRegistry.IndexedFileDB.__init__ Bio.config.FormatRegistry.FormatGroup.__init__ Bio.config.FormatRegistry.FormatObject.__init__ Bio.config.FormatRegistry.FormatRegistry.__init__ Bio.config.Registry.RegisterableGroup.__init__ Bio.config.Registry.RegisterableObject.__init__ Bio.config.Registry.Registry.__init__ Bio.config.SeqDBRegistry.SeqDBRegistry.__init__ Bio.config._stanzaformat.Stanza.__init__ Bio.config._stanzaformat.StanzaFormat.__init__ Bio.config._support.make_cached_expression.__init__ Bio.config._support.make_rate_limited_function.__init__ Bio.kNN.kNN.__init__ Bio.pairwise2.affine_penalty.__init__ Bio.pairwise2.dictionary_match.__init__ Bio.pairwise2.identity_match.__init__ Bio.writers.SeqRecord.embl.WriteEmbl.__init__ Bio.writers.SeqRecord.fasta.WriteFasta.__init__ BioSQL.BioSeq.DBSeq.__init__ BioSQL.BioSeq.DBSeqRecord.__init__ BioSQL.BioSeqDatabase.Adaptor.__init__ BioSQL.BioSeqDatabase.BioSeqDatabase.__init__ BioSQL.BioSeqDatabase.DBServer.__init__ BioSQL.DBUtils.Generic_dbutils.__init__ BioSQL.Loader.DatabaseLoader.__init__ BioSQL.Loader.DatabaseRemover.__init__ Martel.Dispatch.Callback.__init__ Martel.Dispatch.DispatchHandler.__init__ Martel.Dispatch.Dispatcher.__init__ Martel.Dispatch.Multicall.__init__ Martel.Dispatch.RemapEnd.__init__ Martel.Dispatch.RemapStart.__init__ Martel.Expression.Alt.__init__ Martel.Expression.Any.__init__ Martel.Expression.Assert.__init__ Martel.Expression.Debug.__init__ Martel.Expression.FastFeature.__init__ Martel.Expression.Group.__init__ Martel.Expression.GroupRef.__init__ Martel.Expression.HeaderFooter.__init__ Martel.Expression.Literal.__init__ Martel.Expression.MaxRepeat.__init__ Martel.Expression.NullOp.__init__ Martel.Expression.ParseRecords.__init__ Martel.Expression.PassThrough.__init__ Martel.Expression.Seq.__init__ Martel.Expression.Str.__init__ Martel.Generate.CheckAssert.__init__ Martel.Generate.CheckAssertNot.__init__ Martel.Generate.CheckGroupRef.__init__ Martel.Generate.GeneratorState.__init__ Martel.Generate.HandleRepeatCount.__init__ Martel.Generate.SetGroupValue.__init__ Martel.Generate._call_call.__init__ Martel.Generate._call_calltag.__init__ Martel.Generate.print_debug.__init__ Martel.Generate.print_info.__init__ Martel.IterParser.IterHeaderFooter.__init__ Martel.IterParser.IterRecords.__init__ Martel.Iterator.EventStream.__init__ Martel.Iterator.HeaderFooterEventStream.__init__ Martel.Iterator.Iterate.__init__ Martel.Iterator.Iterator.__init__ Martel.Iterator.IteratorHeaderFooter.__init__ Martel.Iterator.IteratorRecords.__init__ Martel.Iterator.RecordEventStream.__init__ Martel.Iterator.StoreEvents.__init__ Martel.LAX.ElementInfo.__init__ Martel.LAX.LAX.__init__ Martel.Parser.HeaderFooterParser.__init__ Martel.Parser.Parser.__init__ Martel.Parser.ParserIncompleteException.__init__ Martel.Parser.ParserPositionException.__init__ Martel.Parser.RecordParser.__init__ Martel.RecordReader.CountLines.__init__ Martel.RecordReader.EndsWith.__init__ Martel.RecordReader.Everything.__init__ Martel.RecordReader.Nothing.__init__ Martel.RecordReader.RecordReader.__init__ Martel.RecordReader.StartsWith.__init__ Martel.RecordReader.Until.__init__ Martel.convert_re.GroupNames.__init__ Martel.msre_parse.Pattern.__init__ Martel.msre_parse.SubPattern.__init__ Martel.msre_parse.Tokenizer.__init__ Martel.test.support.CheckGood.__init__ Martel.test.support.Dump.__init__ Martel.test.support.Storage.__init__ Martel.test.test_Parser.CountErrors.__init__ Martel.test.test_Parser.CountRecords.__init__ Martel.test.test_delimiter.CatchFields.__init__ Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-4', '__init__', 'link-4');">__init__</a></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 class="py-name">crossover</tt><tt class="py-op">,</tt> <tt class="py-name">repairer</tt><tt class="py-op">)</tt> </tt> </div><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt> <a name="RouletteWheelSelection.select"></a><div id="RouletteWheelSelection.select-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="RouletteWheelSelection.select-toggle" onclick="return toggle('RouletteWheelSelection.select');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-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="RouletteWheelSelection.select-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RouletteWheelSelection.select-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform selection on the population based using a Roulette model.</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"> Arguments:</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-docstring"> o population -- A population of organisms on which we will perform</tt> </tt> <a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> selection. The individuals are assumed to have fitness values which</tt> </tt> <a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> are due to their current genome.</tt> </tt> <a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-comment"># set up the current probabilities for selecting organisms</tt> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># from the population</tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">prob_wheel</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.GA.Selection.RouletteWheel.RouletteWheelSelection._set_up_wheel()=Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html#_set_up_wheel"><a title="Bio.GA.Selection.RouletteWheel.RouletteWheelSelection._set_up_wheel" class="py-name" href="#" onclick="return doclink('link-5', '_set_up_wheel', 'link-5');">_set_up_wheel</a></tt><tt class="py-op">(</tt><tt class="py-name">population</tt><tt class="py-op">)</tt> </tt> <a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">probs</tt> <tt class="py-op">=</tt> <tt class="py-name">prob_wheel</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-6', 'keys', 'link-6');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">probs</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="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.PDB.Residue.DisorderedResidue.sort Bio.PDB.Residue.Residue.sort Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-7', 'sort', 'link-7');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt> <a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-comment"># now create the new population with the same size as the original</tt> </tt> <a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">new_population</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt> <a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pair_spin</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</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-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-comment"># select two individuals using roulette wheel selection</tt> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">choice_num_1</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="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">choice_num_2</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="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"># now grab the two organisms from the probabilities</tt> </tt> <a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">chosen_org_1</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">chosen_org_2</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">prev_prob</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">cur_prob</tt> <tt class="py-keyword">in</tt> <tt class="py-name">probs</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">if</tt> <tt class="py-name">choice_num_1</tt> <tt class="py-op">></tt> <tt class="py-name">prev_prob</tt> <tt class="py-keyword">and</tt> <tt class="py-name">choice_num_1</tt> <tt class="py-op"><=</tt> <tt class="py-name">cur_prob</tt><tt class="py-op">:</tt> </tt> <a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">chosen_org_1</tt> <tt class="py-op">=</tt> <tt class="py-name">prob_wheel</tt><tt class="py-op">[</tt><tt class="py-name">cur_prob</tt><tt class="py-op">]</tt> </tt> <a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">choice_num_2</tt> <tt class="py-op">></tt> <tt class="py-name">prev_prob</tt> <tt class="py-keyword">and</tt> <tt class="py-name">choice_num_2</tt> <tt class="py-op"><=</tt> <tt class="py-name">cur_prob</tt><tt class="py-op">:</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">chosen_org_2</tt> <tt class="py-op">=</tt> <tt class="py-name">prob_wheel</tt><tt class="py-op">[</tt><tt class="py-name">cur_prob</tt><tt class="py-op">]</tt> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt> <a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">prev_prob</tt> <tt class="py-op">=</tt> <tt class="py-name">cur_prob</tt> </tt> <a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt> <a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">chosen_org_1</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 class="py-string">"Didn't select organism one"</tt> </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">chosen_org_2</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 class="py-string">"Didn't select organism two"</tt> </tt> <a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt> <a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-comment"># do mutation and crossover to get the new organisms</tt> </tt> <a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">new_org_1</tt><tt class="py-op">,</tt> <tt class="py-name">new_org_2</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.GA.Selection.Abstract.AbstractSelection.mutate_and_crossover()=Bio.GA.Selection.Abstract.AbstractSelection-class.html#mutate_and_crossover"><a title="Bio.GA.Selection.Abstract.AbstractSelection.mutate_and_crossover" class="py-name" href="#" onclick="return doclink('link-8', 'mutate_and_crossover', 'link-8');">mutate_and_crossover</a></tt><tt class="py-op">(</tt><tt class="py-name">chosen_org_1</tt><tt class="py-op">,</tt> </tt> <a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">chosen_org_2</tt><tt class="py-op">)</tt> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">new_population</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend Bio.SCOP.Raf.SeqMap.extend Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-9', 'extend', 'link-9');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">new_org_1</tt><tt class="py-op">,</tt> <tt class="py-name">new_org_2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">new_population</tt> </tt> </div><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt> <a name="RouletteWheelSelection._set_up_wheel"></a><div id="RouletteWheelSelection._set_up_wheel-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="RouletteWheelSelection._set_up_wheel-toggle" onclick="return toggle('RouletteWheelSelection._set_up_wheel');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html#_set_up_wheel">_set_up_wheel</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="RouletteWheelSelection._set_up_wheel-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RouletteWheelSelection._set_up_wheel-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-docstring">"""Set up the roulette wheel based on the fitnesses.</tt> </tt> <a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> This creates a fitness proportional 'wheel' that will be used for</tt> </tt> <a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> selecting based on random numbers.</tt> </tt> <a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> Returns:</tt> </tt> <a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt> <a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> o A dictionary where the keys are the 'high' value that an</tt> </tt> <a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> individual will be selected. The low value is determined by</tt> </tt> <a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> the previous key in a sorted list of keys. For instance, if we</tt> </tt> <a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> have a sorted list of keys like:</tt> </tt> <a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> [.1, .3, .7, 1]</tt> </tt> <a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> Then the individual whose key is .1 will be selected if a number</tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> between 0 and .1 is chosen, the individual whose key is .3 will</tt> </tt> <a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> be selected if the number is between .1 and .3, and so on.</tt> </tt> <a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> The values of the dictionary are the organism instances.</tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-comment"># first sum up the total fitness in the population</tt> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">total_fitness</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L108"></a><tt class="py-lineno">108</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">population</tt><tt class="py-op">:</tt> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">total_fitness</tt> <tt class="py-op">+=</tt> <tt class="py-name">org</tt><tt class="py-op">.</tt><tt class="py-name">fitness</tt> </tt> <a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt> <a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-comment"># now create the wheel dictionary for all of the individuals</tt> </tt> <a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">wheel_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">total_percentage</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L114"></a><tt class="py-lineno">114</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">population</tt><tt class="py-op">:</tt> </tt> <a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">org_percentage</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</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-op">/</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">total_fitness</tt><tt class="py-op">)</tt> </tt> <a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt> <a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-comment"># the organisms chance of being picked goes from the previous</tt> </tt> <a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># percentage (total_percentage) to the previous percentage</tt> </tt> <a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># plus the organisms specific fitness percentage</tt> </tt> <a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">wheel_dict</tt><tt class="py-op">[</tt><tt class="py-name">total_percentage</tt> <tt class="py-op">+</tt> <tt class="py-name">org_percentage</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.Crystal.Crystal.copy Bio.GA.Organism.Organism.copy Bio.GenBank.NCBIDictionary.copy Bio.PDB.Vector'.Vector.copy Bio.Prosite.ExPASyDictionary.copy Bio.Prosite.Pattern.PrositeTerm.copy Bio.Prosite.Prodoc.ExPASyDictionary.copy Bio.PubMed.Dictionary.copy Bio.SwissProt.SProt.ExPASyDictionary.copy Martel.Expression.Any.copy Martel.Expression.AnyEol.copy Martel.Expression.Assert.copy Martel.Expression.AtBeginning.copy Martel.Expression.AtEnd.copy Martel.Expression.Debug.copy Martel.Expression.Dot.copy Martel.Expression.Expression.copy Martel.Expression.ExpressionList.copy Martel.Expression.FastFeature.copy Martel.Expression.Group.copy Martel.Expression.GroupRef.copy Martel.Expression.HeaderFooter.copy Martel.Expression.Literal.copy Martel.Expression.MaxRepeat.copy Martel.Expression.NullOp.copy Martel.Expression.ParseRecords.copy Martel.Expression.PassThrough.copy Martel.Expression.Str.copy Martel.IterParser.IterHeaderFooter.copy Martel.IterParser.IterRecords.copy Martel.Iterator.IteratorRecords.copy Martel.Parser.HeaderFooterParser.copy Martel.Parser.Parser.copy Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-10', 'copy', 'link-0');">copy</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Crystal.Crystal.copy Bio.GA.Organism.Organism.copy Bio.GenBank.NCBIDictionary.copy Bio.PDB.Vector'.Vector.copy Bio.Prosite.ExPASyDictionary.copy Bio.Prosite.Pattern.PrositeTerm.copy Bio.Prosite.Prodoc.ExPASyDictionary.copy Bio.PubMed.Dictionary.copy Bio.SwissProt.SProt.ExPASyDictionary.copy Martel.Expression.Any.copy Martel.Expression.AnyEol.copy Martel.Expression.Assert.copy Martel.Expression.AtBeginning.copy Martel.Expression.AtEnd.copy Martel.Expression.Debug.copy Martel.Expression.Dot.copy Martel.Expression.Expression.copy Martel.Expression.ExpressionList.copy Martel.Expression.FastFeature.copy Martel.Expression.Group.copy Martel.Expression.GroupRef.copy Martel.Expression.HeaderFooter.copy Martel.Expression.Literal.copy Martel.Expression.MaxRepeat.copy Martel.Expression.NullOp.copy Martel.Expression.ParseRecords.copy Martel.Expression.PassThrough.copy Martel.Expression.Str.copy Martel.IterParser.IterHeaderFooter.copy Martel.IterParser.IterRecords.copy Martel.Iterator.IteratorRecords.copy Martel.Parser.HeaderFooterParser.copy Martel.Parser.Parser.copy Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-11', 'copy', 'link-0');">copy</a></tt><tt class="py-op">(</tt><tt class="py-name">org</tt><tt class="py-op">)</tt> </tt> <a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt> <a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-comment"># keep a running total of where we are at in the percentages</tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">total_percentage</tt> <tt class="py-op">+=</tt> <tt class="py-name">org_percentage</tt> </tt> <a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt> <a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">wheel_dict</tt> </tt> </div></div><a name="L126"></a><tt class="py-lineno">126</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 Mon Sep 15 09:26:59 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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