<?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.triefind</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> :: Module triefind </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.triefind-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.triefind-module.html">Module Bio.triefind</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">Given a trie, find all occurrences of a word in the trie in a string.</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">Like searching a string for a substring, except that the substring is</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">any word in a trie.</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">Functions:</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">match Find longest key in a trie matching the beginning of the string.</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">match_all Find all keys in a trie matching the beginning of the string.</tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">find Find keys in a trie matching anywhere in a string.</tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">find_words Find keys in a trie matching whole words in a string.</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">"""</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt> <a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt> <a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt> <a name="match"></a><div id="match-def"><a name="L17"></a><tt class="py-lineno">17</tt> <a class="py-toggle" href="#" id="match-toggle" onclick="return toggle('match');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.triefind-module.html#match">match</a><tt class="py-op">(</tt><tt class="py-param">string</tt><tt class="py-op">,</tt> <tt class="py-param">trie</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="match-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="match-expanded"><a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-docstring">"""match(string, trie) -> longest key or None</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"> Find the longest key in the trie that matches the beginning of the</tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> string.</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"> """</tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">longest</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-0" 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-0', 'i', 'link-0');">i</a></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">string</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">substr</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-1" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-1', 'i', 'link-0');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt> <a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">trie</tt><tt class="py-op">.</tt><tt class="py-name">has_prefix</tt><tt class="py-op">(</tt><tt class="py-name">substr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt> <a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">trie</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key Bio.EUtils.POM.ElementNode.has_key Bio.GenBank.NCBIDictionary.has_key Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key Bio.PDB.FragmentMapper'.FragmentMapper.has_key Bio.Prosite.ExPASyDictionary.has_key Bio.Prosite.Prodoc.ExPASyDictionary.has_key Bio.PubMed.Dictionary.has_key Bio.SwissProt.SProt.ExPASyDictionary.has_key Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-2', 'has_key', 'link-2');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">substr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">longest</tt> <tt class="py-op">=</tt> <tt class="py-name">substr</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">longest</tt> </tt> </div><a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> </tt> <a name="match_all"></a><div id="match_all-def"><a name="L33"></a><tt class="py-lineno">33</tt> <a class="py-toggle" href="#" id="match_all-toggle" onclick="return toggle('match_all');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.triefind-module.html#match_all">match_all</a><tt class="py-op">(</tt><tt class="py-param">string</tt><tt class="py-op">,</tt> <tt class="py-param">trie</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="match_all-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="match_all-expanded"><a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-docstring">"""match_all(string, trie) -> list of keys</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"> Find all the keys in the trie that matches the beginning of the</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-docstring"> string.</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"> """</tt> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">matches</tt> <tt class="py-op">=</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">for</tt> <tt id="link-3" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-3', 'i', 'link-0');">i</a></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">string</tt><tt class="py-op">)</tt><tt class="py-op">)</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">substr</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">[</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-0');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">trie</tt><tt class="py-op">.</tt><tt class="py-name">has_prefix</tt><tt class="py-op">(</tt><tt class="py-name">substr</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-keyword">break</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">trie</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Crystal.Crystal.has_key Bio.EUtils.POM.ElementNode.has_key Bio.GenBank.NCBIDictionary.has_key Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key Bio.PDB.FragmentMapper'.FragmentMapper.has_key Bio.Prosite.ExPASyDictionary.has_key Bio.Prosite.Prodoc.ExPASyDictionary.has_key Bio.PubMed.Dictionary.has_key Bio.SwissProt.SProt.ExPASyDictionary.has_key Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-5', 'has_key', 'link-2');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">substr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-name">matches</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append Bio.EUtils.POM.ElementNode.append Bio.EUtils.sourcegen.SourceFile.append Bio.SCOP.Raf.SeqMap.append Bio.Seq.MutableSeq.append Bio.Wise.psw.Alignment.append Bio.Wise.psw.AlignmentColumn.append Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-6', 'append', 'link-6');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">substr</tt><tt class="py-op">)</tt> </tt> <a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">matches</tt> </tt> </div><a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt> <a name="find"></a><div id="find-def"><a name="L49"></a><tt class="py-lineno">49</tt> <a class="py-toggle" href="#" id="find-toggle" onclick="return toggle('find');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.triefind-module.html#find">find</a><tt class="py-op">(</tt><tt class="py-param">string</tt><tt class="py-op">,</tt> <tt class="py-param">trie</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="find-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="find-expanded"><a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-docstring">"""find(string, trie) -> list of tuples (key, start, end)</tt> </tt> <a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-docstring"> Find all the keys in the trie that match anywhere in the string.</tt> </tt> <a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">results</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 id="link-7" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-7', 'start', 'link-7');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># index to start the search</tt> </tt> <a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-8" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-8', 'start', 'link-7');">start</a></tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">string</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"># Look for a match.</tt> </tt> <a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-9" 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-9', 'keys', 'link-9');">keys</a></tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name" targets="Function Bio.triefind.match_all()=Bio.triefind-module.html#match_all"><a title="Bio.triefind.match_all" class="py-name" href="#" onclick="return doclink('link-10', 'match_all', 'link-10');">match_all</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">[</tt><tt id="link-11" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-11', 'start', 'link-7');">start</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">trie</tt><tt class="py-op">)</tt> </tt> <a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-12" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-12', 'key', 'link-12');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-13" class="py-name"><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-13', 'keys', 'link-9');">keys</a></tt><tt class="py-op">:</tt> </tt> <a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Crystal.Chain.append Bio.EUtils.POM.ElementNode.append Bio.EUtils.sourcegen.SourceFile.append Bio.SCOP.Raf.SeqMap.append Bio.Seq.MutableSeq.append Bio.Wise.psw.Alignment.append Bio.Wise.psw.AlignmentColumn.append Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-14', 'append', 'link-6');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-15', 'key', 'link-12');">key</a></tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-16', 'start', 'link-7');">start</a></tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-17', 'start', 'link-7');">start</a></tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-18', 'key', 'link-12');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-19', 'start', 'link-7');">start</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">results</tt> </tt> </div><a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> </tt> <a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"><tt id="link-20" class="py-name" targets="Variable Bio.triefind.DEFAULT_BOUNDARY_CHARS=Bio.triefind-module.html#DEFAULT_BOUNDARY_CHARS"><a title="Bio.triefind.DEFAULT_BOUNDARY_CHARS" class="py-name" href="#" onclick="return doclink('link-20', 'DEFAULT_BOUNDARY_CHARS', 'link-20');">DEFAULT_BOUNDARY_CHARS</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">punctuation</tt> <tt class="py-op">+</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Variable Bio.expressions.embl.embl65.whitespace=Bio.expressions.embl.embl65-module.html#whitespace"><a title="Bio.expressions.embl.embl65.whitespace" class="py-name" href="#" onclick="return doclink('link-21', 'whitespace', 'link-21');">whitespace</a></tt> </tt> <a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> </tt> <a name="find_words"></a><div id="find_words-def"><a name="L67"></a><tt class="py-lineno">67</tt> <a class="py-toggle" href="#" id="find_words-toggle" onclick="return toggle('find_words');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.triefind-module.html#find_words">find_words</a><tt class="py-op">(</tt><tt class="py-param">string</tt><tt class="py-op">,</tt> <tt class="py-param">trie</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="find_words-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="find_words-expanded"><a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-docstring">"""find_words(string, trie) -> list of tuples (key, start, end)</tt> </tt> <a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"><tt class="py-docstring"> Find all the keys in the trie that match full words in the string.</tt> </tt> <a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"><tt class="py-docstring"> Word boundaries are defined as any punctuation or whitespace.</tt> </tt> <a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-name">_boundary_re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-22', 'compile', 'link-22');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"[%s]+"</tt> <tt class="py-op">%</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Function Martel.Dispatch.escape()=Martel.Dispatch-module.html#escape,Function Martel.Expression.escape()=Martel.Expression-module.html#escape"><a title="Martel.Dispatch.escape Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-23', 'escape', 'link-23');">escape</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.triefind.DEFAULT_BOUNDARY_CHARS" class="py-name" href="#" onclick="return doclink('link-24', 'DEFAULT_BOUNDARY_CHARS', 'link-20');">DEFAULT_BOUNDARY_CHARS</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> </tt> <a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt id="link-25" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-25', 'start', 'link-7');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># index of word boundary</tt> </tt> <a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-26" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-26', 'start', 'link-7');">start</a></tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> <tt class="py-comment"># Look for a match.</tt> </tt> <a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-27" class="py-name"><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-27', 'keys', 'link-9');">keys</a></tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.triefind.match_all" class="py-name" href="#" onclick="return doclink('link-28', 'match_all', 'link-10');">match_all</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">[</tt><tt id="link-29" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-29', 'start', 'link-7');">start</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">trie</tt><tt class="py-op">)</tt> </tt> <a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-30" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-30', 'key', 'link-12');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-31" class="py-name"><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-31', 'keys', 'link-9');">keys</a></tt><tt class="py-op">:</tt> </tt> <a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-32', 'key', 'link-12');">key</a></tt><tt class="py-op">)</tt> </tt> <a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> <tt class="py-comment"># Make sure it ends at a boundary.</tt> </tt> <a name="L84"></a><tt class="py-lineno">84</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-33" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-33', 'start', 'link-7');">start</a></tt><tt class="py-op">+</tt><tt class="py-name">l</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-name">_boundary_re</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match Bio.Prosite.Pattern.Prosite.match Bio.triefind.match Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-34', 'match', 'link-34');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">[</tt><tt id="link-35" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-35', 'start', 'link-7');">start</a></tt><tt class="py-op">+</tt><tt class="py-name">l</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L86"></a><tt class="py-lineno">86</tt> <tt class="py-line"> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Crystal.Chain.append Bio.EUtils.POM.ElementNode.append Bio.EUtils.sourcegen.SourceFile.append Bio.SCOP.Raf.SeqMap.append Bio.Seq.MutableSeq.append Bio.Wise.psw.Alignment.append Bio.Wise.psw.AlignmentColumn.append Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-36', 'append', 'link-6');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-37', 'key', 'link-12');">key</a></tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-38', 'start', 'link-7');">start</a></tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-39', 'start', 'link-7');">start</a></tt><tt class="py-op">+</tt><tt class="py-name">l</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L87"></a><tt class="py-lineno">87</tt> <tt class="py-line"> <tt class="py-comment"># Move forward to the next boundary.</tt> </tt> <a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">_boundary_re</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search Bio.EUtils.HistoryClient.HistoryClient.search Bio.KDTree.KDTree.KDTree.search Bio.PDB.NeighborSearch.NeighborSearch.search Bio.Prosite.Pattern.Prosite.search Bio.Restriction.Restriction.AbstractCut.search Bio.Restriction.Restriction.RestrictionBatch.search Bio.SCOP.search Bio.builders.Search.search Bio.formatdefs.search Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-40', 'search', 'link-40');">search</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">,</tt> <tt id="link-41" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-41', 'start', 'link-7');">start</a></tt><tt class="py-op">)</tt> </tt> <a name="L89"></a><tt class="py-lineno">89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt> <a name="L90"></a><tt class="py-lineno">90</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt> <a name="L91"></a><tt class="py-lineno">91</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Bio.GFF.easy.Location.start Bio.Prosite.Pattern.PrositeMatch.start Bio.Restriction._Update.RestrictionCompiler.start Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-42', 'start', 'link-7');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end Bio.Prosite.Pattern.PrositeMatch.end Bio.expressions.blocks.end Bio.expressions.embl.embl65.end Bio.expressions.swissprot.sprot38.end Martel.LAX.LAX.end Martel.test.test_swissprot38.end Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-43', 'end', 'link-43');">end</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L92"></a><tt class="py-lineno">92</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">results</tt> </tt> </div><a name="L93"></a><tt class="py-lineno">93</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 09:28:14 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script 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