<?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.SCOP.FileIndex</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.SCOP-module.html">Package SCOP</a> :: Module FileIndex </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.SCOP.FileIndex-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.SCOP.FileIndex-module.html">Module Bio.SCOP.FileIndex</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2001 by Gavin E. Crooks. All rights reserved.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># This functionality may be of general use, in which case this module should</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># be moved out of the SCOP package.</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.SCOP.FileIndex was deprecated, as it does not seem to have any users. If you do use this module, please contact the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module"</tt><tt class="py-op">)</tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt> <a name="defaultdict"></a><div id="defaultdict-def"><a name="L14"></a><tt class="py-lineno">14</tt> <a class="py-toggle" href="#" id="defaultdict-toggle" onclick="return toggle('defaultdict');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.FileIndex.defaultdict-class.html">defaultdict</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="defaultdict-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="defaultdict-expanded"><a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> </tt> <a name="defaultdict.__init__"></a><div id="defaultdict.__init__-def"><a name="L16"></a><tt class="py-lineno">16</tt> <a class="py-toggle" href="#" id="defaultdict.__init__-toggle" onclick="return toggle('defaultdict.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.FileIndex.defaultdict-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">default</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="defaultdict.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="defaultdict.__init__-expanded"><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method 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Martel.Parser.MartelAttributeList.__getitem__ Martel.msre_parse.SubPattern.__getitem__ Martel.test.support.Storage.__getitem__" class="py-name" href="#" onclick="return doclink('link-3', '__getitem__', 'link-3');">__getitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-4" 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-4', 'key', 'link-4');">key</a></tt><tt class="py-op">)</tt> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-5', 'default', 'link-1');">default</a></tt> </tt> </div></div><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt> <a name="FileIndex"></a><div id="FileIndex-def"><a name="L26"></a><tt class="py-lineno">26</tt> <a class="py-toggle" href="#" id="FileIndex-toggle" onclick="return toggle('FileIndex');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.FileIndex.FileIndex-class.html">FileIndex</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="FileIndex-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="FileIndex-expanded"><a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-docstring">""" An in memory index that allows rapid random access into a file.</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"> The class can be used to turn a file into a read-only</tt> </tt> <a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> database.</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="FileIndex.__init__"></a><div id="FileIndex.__init__-def"><a name="L32"></a><tt class="py-lineno">32</tt> <a class="py-toggle" href="#" id="FileIndex.__init__-toggle" onclick="return toggle('FileIndex.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.FileIndex.FileIndex-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">filename</tt><tt class="py-op">,</tt> <tt class="py-param">iterator_gen</tt><tt class="py-op">,</tt> <tt class="py-param">key_gen</tt> <tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="FileIndex.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FileIndex.__init__-expanded"><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</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"> filename -- The file to index</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-docstring"> iterator_gen -- A function that eats a file handle, and returns</tt> </tt> <a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"> a file iterator. 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class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-keyword">try</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">loc</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt id="link-8" 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-8', 'i', 'link-8');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">iterator_gen</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt> <a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt> <tt class="py-op">:</tt> </tt> <a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">next_thing</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-9', 'i', 'link-8');">i</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next Bio.AlignIO.EmbossIO.EmbossIterator.next Bio.AlignIO.FastaIO.FastaM10Iterator.next Bio.AlignIO.Interfaces.AlignmentIterator.next Bio.AlignIO.PhylipIO.PhylipIterator.next Bio.AlignIO.StockholmIO.StockholmIterator.next Bio.Blast.NCBIStandalone.Iterator.next Bio.Blast.ParseBlastTable.BlastTableReader.next Bio.CDD.Iterator.next Bio.Compass.Iterator.next Bio.DocSQL.IterationCursor.next Bio.ECell.Iterator.next Bio.Enzyme.Iterator.next Bio.Fasta.Iterator.next Bio.GenBank.Iterator.next Bio.Gobase.Iterator.next Bio.IntelliGenetics.IntelliGeneticsReader.next Bio.IntelliGenetics.Iterator.next Bio.LocusLink.Iterator.next Bio.Medline.Iterator.next Bio.MetaTool.Iterator.next Bio.NBRF.Iterator.next Bio.Nexus.Nexus.CharBuffer.next Bio.Prosite.Iterator.next Bio.Prosite.Prodoc.Iterator.next Bio.Rebase.Iterator.next Bio.SCOP.Cla.Iterator.next Bio.SCOP.Des.Iterator.next Bio.SCOP.Dom.Iterator.next Bio.SCOP.Hie.Iterator.next Bio.SCOP.Raf.Iterator.next Bio.Saf.Iterator.next Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next Bio.SeqIO.Interfaces.SequenceIterator.next Bio.Sequencing.Ace.Iterator.next Bio.Sequencing.Phd.Iterator.next Bio.SwissProt.SProt.Iterator.next Bio.UniGene.Iterator.next Martel.Iterator.EventStream.next Martel.Iterator.HeaderFooterEventStream.next Martel.Iterator.Iterate.next Martel.Iterator.RecordEventStream.next Martel.RecordReader.CountLines.next Martel.RecordReader.EndsWith.next Martel.RecordReader.Everything.next Martel.RecordReader.Nothing.next Martel.RecordReader.RecordReader.next Martel.RecordReader.StartsWith.next Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-10', 'next', 'link-10');">next</a></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 class="py-keyword">if</tt> <tt class="py-name">next_thing</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt> <a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-11', 'key', 'link-4');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">key_gen</tt><tt class="py-op">(</tt><tt class="py-name">next_thing</tt><tt class="py-op">)</tt> </tt> <a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-12" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-12', 'key', 'link-4');">key</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt> <a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-13" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-13', 'key', 'link-4');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">loc</tt> </tt> <a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-name">loc</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.tell()=Bio.EUtils.ReseekFile.ReseekFile-class.html#tell,Method Bio.File.UndoHandle.tell()=Bio.File.UndoHandle-class.html#tell,Method Martel.msre_parse.Tokenizer.tell()=Martel.msre_parse.Tokenizer-class.html#tell"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell Bio.File.UndoHandle.tell Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-14', 'tell', 'link-14');">tell</a></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 class="py-keyword">finally</tt> <tt class="py-op">:</tt> </tt> <a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-15', 'close', 'link-15');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> </tt> <a name="FileIndex.__getitem__"></a><div id="FileIndex.__getitem__-def"><a name="L64"></a><tt class="py-lineno">64</tt> <a class="py-toggle" href="#" id="FileIndex.__getitem__-toggle" onclick="return toggle('FileIndex.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.FileIndex.FileIndex-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="FileIndex.__getitem__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="FileIndex.__getitem__-expanded"><a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-docstring">""" Return an item from the indexed file. """</tt> </tt> <a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-name">loc</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Align.AlignInfo.PSSM.__getitem__ Bio.Crystal.Chain.__getitem__ Bio.Crystal.Crystal.__getitem__ Bio.DBXRef.BioformatDBName.__getitem__ Bio.DBXRef.UnknownDBName.__getitem__ Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__ Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__getitem__ Bio.EUtils.Datatypes.DBIds.__getitem__ Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__getitem__ Bio.EUtils.MultiDict._BaseMultiDict.__getitem__ Bio.EUtils.POM.ElementNode.__getitem__ Bio.FSSP.fssp_rec.fff_rec.__getitem__ Bio.GFF.GenericTools.ForgivingDictionary.__getitem__ Bio.GFF.easy.FeatureDict.__getitem__ Bio.GenBank.NCBIDictionary.__getitem__ Bio.Gobase.Dictionary.__getitem__ Bio.Mindy.BaseDB.DictLookup.__getitem__ Bio.Mindy.BaseDB.OpenDB.__getitem__ Bio.Mindy.BerkeleyDB.BerkeleyDB.__getitem__ Bio.Mindy.BerkeleyDB.PrimaryNamespace.__getitem__ Bio.Mindy.BerkeleyDB.SecondaryNamespace.__getitem__ Bio.Mindy.FlatDB.BisectFile.__getitem__ Bio.Mindy.FlatDB.DiskFlatDB.__getitem__ Bio.Mindy.FlatDB.MemoryFlatDB.__getitem__ Bio.Mindy.FlatDB.PrimaryNamespace.__getitem__ Bio.Mindy.FlatDB.PrimaryTable.__getitem__ Bio.Mindy.FlatDB.SecondaryNamespace.__getitem__ Bio.Mindy.FlatDB.SecondaryTable.__getitem__ Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__ Bio.PDB.Chain.Chain.__getitem__ Bio.PDB.Entity.Entity.__getitem__ Bio.PDB.FragmentMapper'.FragmentMapper.__getitem__ Bio.PDB.MMCIF2Dict.MMCIF2Dict.__getitem__ Bio.PDB.Vector'.Vector.__getitem__ Bio.PropertyManager.CreateDict.__getitem__ Bio.Prosite.Dictionary.__getitem__ Bio.Prosite.ExPASyDictionary.__getitem__ Bio.Prosite.Pattern.Prosite.__getitem__ Bio.Prosite.Pattern.PrositeMatch.__getitem__ Bio.Prosite.Prodoc.Dictionary.__getitem__ Bio.Prosite.Prodoc.ExPASyDictionary.__getitem__ Bio.PubMed.Dictionary.__getitem__ Bio.Rebase.Dictionary.__getitem__ Bio.Restriction.Restriction.FormattedSeq.__getitem__ Bio.SCOP.Cla.Index.__getitem__ Bio.SCOP.FileIndex.FileIndex.__getitem__ Bio.SCOP.FileIndex.defaultdict.__getitem__ Bio.SCOP.Raf.SeqMapIndex.__getitem__ Bio.Seq.MutableSeq.__getitem__ Bio.Seq.Seq.__getitem__ Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__getitem__ Bio.SeqIO.StockholmIO.StockholmIterator.__getitem__ Bio.SwissProt.SProt.Dictionary.__getitem__ Bio.SwissProt.SProt.ExPASyDictionary.__getitem__ Bio.config.DBRegistry.DBGroup.__getitem__ Bio.config.DBRegistry.DBObject.__getitem__ Bio.config.Registry.Registry.__getitem__ Bio.config.SeqDBRegistry.SeqDBRegistry.__getitem__ BioSQL.BioSeq.DBSeq.__getitem__ BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__ BioSQL.BioSeqDatabase.DBServer.__getitem__ Martel.Iterator.Iterate.__getitem__ Martel.Parser.MartelAttributeList.__getitem__ Martel.msre_parse.SubPattern.__getitem__ Martel.test.support.Storage.__getitem__" class="py-name" href="#" onclick="return doclink('link-16', '__getitem__', 'link-3');">__getitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt id="link-17" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-17', 'key', 'link-4');">key</a></tt><tt class="py-op">)</tt> </tt> <a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> </tt> <a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-18', 'open', 'link-7');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</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">try</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">f</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek Bio.File.UndoHandle.seek Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-19', 'seek', 'link-19');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">loc</tt><tt class="py-op">)</tt> </tt> <a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-name">thing</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">iterator_gen</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next Bio.AlignIO.EmbossIO.EmbossIterator.next Bio.AlignIO.FastaIO.FastaM10Iterator.next Bio.AlignIO.Interfaces.AlignmentIterator.next Bio.AlignIO.PhylipIO.PhylipIterator.next Bio.AlignIO.StockholmIO.StockholmIterator.next Bio.Blast.NCBIStandalone.Iterator.next Bio.Blast.ParseBlastTable.BlastTableReader.next Bio.CDD.Iterator.next Bio.Compass.Iterator.next Bio.DocSQL.IterationCursor.next Bio.ECell.Iterator.next Bio.Enzyme.Iterator.next Bio.Fasta.Iterator.next Bio.GenBank.Iterator.next Bio.Gobase.Iterator.next Bio.IntelliGenetics.IntelliGeneticsReader.next Bio.IntelliGenetics.Iterator.next Bio.LocusLink.Iterator.next Bio.Medline.Iterator.next Bio.MetaTool.Iterator.next Bio.NBRF.Iterator.next Bio.Nexus.Nexus.CharBuffer.next Bio.Prosite.Iterator.next Bio.Prosite.Prodoc.Iterator.next Bio.Rebase.Iterator.next Bio.SCOP.Cla.Iterator.next Bio.SCOP.Des.Iterator.next Bio.SCOP.Dom.Iterator.next Bio.SCOP.Hie.Iterator.next Bio.SCOP.Raf.Iterator.next Bio.Saf.Iterator.next Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next Bio.SeqIO.Interfaces.SequenceIterator.next Bio.Sequencing.Ace.Iterator.next Bio.Sequencing.Phd.Iterator.next Bio.SwissProt.SProt.Iterator.next Bio.UniGene.Iterator.next Martel.Iterator.EventStream.next Martel.Iterator.HeaderFooterEventStream.next Martel.Iterator.Iterate.next Martel.Iterator.RecordEventStream.next Martel.RecordReader.CountLines.next Martel.RecordReader.EndsWith.next Martel.RecordReader.Everything.next Martel.RecordReader.Nothing.next Martel.RecordReader.RecordReader.next Martel.RecordReader.StartsWith.next Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-20', 'next', 'link-10');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt> <a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-21', 'close', 'link-15');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">thing</tt> </tt> </div></div><a name="L75"></a><tt class="py-lineno">75</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" 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