<?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.Index</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 Index
</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.Index-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Index-module.html">Module Bio.Index</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 1999 by Jeffrey Chang. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><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"># 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"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Index.py</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This module provides a way to create indexes to text files.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Index Dictionary-like class used to store index information.</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">_ShelveIndex An Index class based on the shelve module.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">_InMemoryIndex An in-memory Index class.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">array</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">cPickle</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">shelve</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="_ShelveIndex"></a><div id="_ShelveIndex-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="_ShelveIndex-toggle" onclick="return toggle('_ShelveIndex');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Index._ShelveIndex-class.html">_ShelveIndex</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="_ShelveIndex-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_ShelveIndex-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-docstring">"""An index file wrapped around shelve.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"></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-comment"># Without a good dbm module installed, this is pretty slow and</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-comment"># generates large files. When generating an index on a FASTA-</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-comment"># formatted file with 82000 sequences (37Mb), the </tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-comment"># index 'dat' file is 42Mb and 'dir' file is 8Mb.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Variable Bio.Index._InMemoryIndex.__version=Bio.Index._InMemoryIndex-class.html#__version,Variable Bio.Index._ShelveIndex.__version=Bio.Index._ShelveIndex-class.html#__version"><a title="Bio.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-0', '__version', 'link-0');">__version</a></tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt id="link-1" class="py-name" targets="Variable Bio.Index._InMemoryIndex.__version_key=Bio.Index._InMemoryIndex-class.html#__version_key,Variable Bio.Index._ShelveIndex.__version_key=Bio.Index._ShelveIndex-class.html#__version_key"><a title="Bio.Index._InMemoryIndex.__version_key
Bio.Index._ShelveIndex.__version_key" class="py-name" href="#" onclick="return doclink('link-1', '__version_key', 'link-1');">__version_key</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'__version'</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="_ShelveIndex.__init__"></a><div id="_ShelveIndex.__init__-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="_ShelveIndex.__init__-toggle" onclick="return toggle('_ShelveIndex.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._ShelveIndex-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">indexname</tt><tt class="py-op">,</tt> <tt class="py-param">truncate</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="_ShelveIndex.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_ShelveIndex.__init__-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-2" 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.Affy.CelFile.CelScanner.__init__()=Bio.Affy.CelFile.CelScanner-class.html#__init__,Method Bio.Affy.CelFile.Record.__init__()=Bio.Affy.CelFile.Record-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__()=Bio.Align.Applications._Clustalw.ClustalwCommandline-class.html#__init__,Method Bio.Align.Applications._Dialign.DialignCommandline.__init__()=Bio.Align.Applications._Dialign.DialignCommandline-class.html#__init__,Method Bio.Align.Applications._Mafft.MafftCommandline.__init__()=Bio.Align.Applications._Mafft.MafftCommandline-class.html#__init__,Method Bio.Align.Applications._Muscle.MuscleCommandline.__init__()=Bio.Align.Applications._Muscle.MuscleCommandline-class.html#__init__,Method Bio.Align.Applications._Prank.PrankCommandline.__init__()=Bio.Align.Applications._Prank.PrankCommandline-class.html#__init__,Method Bio.Align.Applications._Probcons.ProbconsCommandline.__init__()=Bio.Align.Applications._Probcons.ProbconsCommandline-class.html#__init__,Method Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__()=Bio.Align.Applications._TCoffee.TCoffeeCommandline-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.Align.MultipleSeqAlignment.__init__()=Bio.Align.MultipleSeqAlignment-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 Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationError.__init__()=Bio.Application.ApplicationError-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Application._Argument.__init__()=Bio.Application._Argument-class.html#__init__,Method Bio.Application._Option.__init__()=Bio.Application._Option-class.html#__init__,Method Bio.Application._Switch.__init__()=Bio.Application._Switch-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.BlastpgpCommandline.__init__()=Bio.Blast.Applications.BlastpgpCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastformatterCommandline.__init__()=Bio.Blast.Applications.NcbiblastformatterCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastnCommandline.__init__()=Bio.Blast.Applications.NcbiblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastpCommandline.__init__()=Bio.Blast.Applications.NcbiblastpCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbiblastxCommandline.__init__()=Bio.Blast.Applications.NcbiblastxCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbipsiblastCommandline.__init__()=Bio.Blast.Applications.NcbipsiblastCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbirpsblastCommandline.__init__()=Bio.Blast.Applications.NcbirpsblastCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbirpstblastnCommandline.__init__()=Bio.Blast.Applications.NcbirpstblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbitblastnCommandline.__init__()=Bio.Blast.Applications.NcbitblastnCommandline-class.html#__init__,Method Bio.Blast.Applications.NcbitblastxCommandline.__init__()=Bio.Blast.Applications.NcbitblastxCommandline-class.html#__init__,Method Bio.Blast.Applications.RpsBlastCommandline.__init__()=Bio.Blast.Applications.RpsBlastCommandline-class.html#__init__,Method Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__()=Bio.Blast.Applications._BlastAllOrPgpCommandLine-class.html#__init__,Method Bio.Blast.Applications._BlastCommandLine.__init__()=Bio.Blast.Applications._BlastCommandLine-class.html#__init__,Method Bio.Blast.Applications._NcbibaseblastCommandline.__init__()=Bio.Blast.Applications._NcbibaseblastCommandline-class.html#__init__,Method Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__()=Bio.Blast.Applications._Ncbiblast2SeqCommandline-class.html#__init__,Method Bio.Blast.Applications._NcbiblastCommandline.__init__()=Bio.Blast.Applications._NcbiblastCommandline-class.html#__init__,Method Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__()=Bio.Blast.Applications._NcbiblastMain2SeqCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method Bio.Compass.Iterator.__init__()=Bio.Compass.Iterator-class.html#__init__,Method Bio.Compass.Record.__init__()=Bio.Compass.Record-class.html#__init__,Method Bio.Compass.RecordParser.__init__()=Bio.Compass.RecordParser-class.html#__init__,Method Bio.Compass._Consumer.__init__()=Bio.Compass._Consumer-class.html#__init__,Method Bio.Compass._Scanner.__init__()=Bio.Compass._Scanner-class.html#__init__,Method Bio.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousCodonTable.__init__()=Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__init__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__init__,Method Bio.Data.CodonTable.CodonTable.__init__()=Bio.Data.CodonTable.CodonTable-class.html#__init__,Method Bio.Data.CodonTable.NCBICodonTable.__init__()=Bio.Data.CodonTable.NCBICodonTable-class.html#__init__,Method Bio.DocSQL.Create.__init__()=Bio.DocSQL.Create-class.html#__init__,Method Bio.DocSQL.Insert.__init__()=Bio.DocSQL.Insert-class.html#__init__,Method Bio.DocSQL.IterationCursor.__init__()=Bio.DocSQL.IterationCursor-class.html#__init__,Method Bio.DocSQL.Query.__init__()=Bio.DocSQL.Query-class.html#__init__,Method Bio.DocSQL.QueryAll.__init__()=Bio.DocSQL.QueryAll-class.html#__init__,Method Bio.DocSQL.QueryGeneric.__init__()=Bio.DocSQL.QueryGeneric-class.html#__init__,Method Bio.DocSQL.QueryRow.__init__()=Bio.DocSQL.QueryRow-class.html#__init__,Method Bio.DocSQL.QuerySingle.__init__()=Bio.DocSQL.QuerySingle-class.html#__init__,Method Bio.Emboss.Applications.DiffseqCommandline.__init__()=Bio.Emboss.Applications.DiffseqCommandline-class.html#__init__,Method Bio.Emboss.Applications.EInvertedCommandline.__init__()=Bio.Emboss.Applications.EInvertedCommandline-class.html#__init__,Method Bio.Emboss.Applications.ETandemCommandline.__init__()=Bio.Emboss.Applications.ETandemCommandline-class.html#__init__,Method Bio.Emboss.Applications.Est2GenomeCommandline.__init__()=Bio.Emboss.Applications.Est2GenomeCommandline-class.html#__init__,Method Bio.Emboss.Applications.FConsenseCommandline.__init__()=Bio.Emboss.Applications.FConsenseCommandline-class.html#__init__,Method Bio.Emboss.Applications.FDNADistCommandline.__init__()=Bio.Emboss.Applications.FDNADistCommandline-class.html#__init__,Method Bio.Emboss.Applications.FDNAParsCommandline.__init__()=Bio.Emboss.Applications.FDNAParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.FNeighborCommandline.__init__()=Bio.Emboss.Applications.FNeighborCommandline-class.html#__init__,Method Bio.Emboss.Applications.FProtDistCommandline.__init__()=Bio.Emboss.Applications.FProtDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.FProtParsCommandline.__init__()=Bio.Emboss.Applications.FProtParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.FSeqBootCommandline.__init__()=Bio.Emboss.Applications.FSeqBootCommandline-class.html#__init__,Method Bio.Emboss.Applications.FTreeDistCommandline.__init__()=Bio.Emboss.Applications.FTreeDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.FuzznucCommandline.__init__()=Bio.Emboss.Applications.FuzznucCommandline-class.html#__init__,Method Bio.Emboss.Applications.IepCommandline.__init__()=Bio.Emboss.Applications.IepCommandline-class.html#__init__,Method Bio.Emboss.Applications.NeedleCommandline.__init__()=Bio.Emboss.Applications.NeedleCommandline-class.html#__init__,Method Bio.Emboss.Applications.PalindromeCommandline.__init__()=Bio.Emboss.Applications.PalindromeCommandline-class.html#__init__,Method Bio.Emboss.Applications.Primer3Commandline.__init__()=Bio.Emboss.Applications.Primer3Commandline-class.html#__init__,Method Bio.Emboss.Applications.PrimerSearchCommandline.__init__()=Bio.Emboss.Applications.PrimerSearchCommandline-class.html#__init__,Method Bio.Emboss.Applications.SeqmatchallCommandline.__init__()=Bio.Emboss.Applications.SeqmatchallCommandline-class.html#__init__,Method Bio.Emboss.Applications.SeqretCommandline.__init__()=Bio.Emboss.Applications.SeqretCommandline-class.html#__init__,Method Bio.Emboss.Applications.TranalignCommandline.__init__()=Bio.Emboss.Applications.TranalignCommandline-class.html#__init__,Method Bio.Emboss.Applications.WaterCommandline.__init__()=Bio.Emboss.Applications.WaterCommandline-class.html#__init__,Method Bio.Emboss.Applications._EmbossCommandLine.__init__()=Bio.Emboss.Applications._EmbossCommandLine-class.html#__init__,Method Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__()=Bio.Emboss.Applications._EmbossMinimalCommandLine-class.html#__init__,Method Bio.Emboss.Primer3.Primers.__init__()=Bio.Emboss.Primer3.Primers-class.html#__init__,Method Bio.Emboss.Primer3.Record.__init__()=Bio.Emboss.Primer3.Record-class.html#__init__,Method Bio.Emboss.PrimerSearch.Amplifier.__init__()=Bio.Emboss.PrimerSearch.Amplifier-class.html#__init__,Method Bio.Emboss.PrimerSearch.InputRecord.__init__()=Bio.Emboss.PrimerSearch.InputRecord-class.html#__init__,Method Bio.Emboss.PrimerSearch.OutputRecord.__init__()=Bio.Emboss.PrimerSearch.OutputRecord-class.html#__init__,Method Bio.Entrez.Parser.CorruptedXMLError.__init__()=Bio.Entrez.Parser.CorruptedXMLError-class.html#__init__,Method Bio.Entrez.Parser.DataHandler.__init__()=Bio.Entrez.Parser.DataHandler-class.html#__init__,Method Bio.Entrez.Parser.NotXMLError.__init__()=Bio.Entrez.Parser.NotXMLError-class.html#__init__,Method Bio.Entrez.Parser.StructureElement.__init__()=Bio.Entrez.Parser.StructureElement-class.html#__init__,Method Bio.Entrez.Parser.ValidationError.__init__()=Bio.Entrez.Parser.ValidationError-class.html#__init__,Method Bio.ExPASy.Enzyme.Record.__init__()=Bio.ExPASy.Enzyme.Record-class.html#__init__,Method Bio.ExPASy.Prodoc.Record.__init__()=Bio.ExPASy.Prodoc.Record-class.html#__init__,Method Bio.ExPASy.Prodoc.Reference.__init__()=Bio.ExPASy.Prodoc.Reference-class.html#__init__,Method Bio.ExPASy.Prosite.Record.__init__()=Bio.ExPASy.Prosite.Record-class.html#__init__,Method Bio.ExPASy.ScanProsite.ContentHandler.__init__()=Bio.ExPASy.ScanProsite.ContentHandler-class.html#__init__,Method Bio.ExPASy.ScanProsite.Parser.__init__()=Bio.ExPASy.ScanProsite.Parser-class.html#__init__,Method Bio.ExPASy.ScanProsite.Record.__init__()=Bio.ExPASy.ScanProsite.Record-class.html#__init__,Method Bio.FSSP.FSSPAlignDict.__init__()=Bio.FSSP.FSSPAlignDict-class.html#__init__,Method Bio.FSSP.FSSPAlignRec.__init__()=Bio.FSSP.FSSPAlignRec-class.html#__init__,Method Bio.FSSP.FSSPHeader.__init__()=Bio.FSSP.FSSPHeader-class.html#__init__,Method Bio.FSSP.FSSPSumRec.__init__()=Bio.FSSP.FSSPSumRec-class.html#__init__,Method Bio.FSSP.FSSPTools.FSSPMultAlign.__init__()=Bio.FSSP.FSSPTools.FSSPMultAlign-class.html#__init__,Method Bio.FSSP.PosAlign.__init__()=Bio.FSSP.PosAlign-class.html#__init__,Method Bio.FSSP.fssp_rec.fff_rec.__init__()=Bio.FSSP.fssp_rec.fff_rec-class.html#__init__,Method Bio.File.SGMLStripper.MyParser.__init__()=Bio.File.SGMLStripper.MyParser-class.html#__init__,Method Bio.File.SGMLStripper.__init__()=Bio.File.SGMLStripper-class.html#__init__,Method Bio.File.UndoHandle.__init__()=Bio.File.UndoHandle-class.html#__init__,Method Bio.GA.Crossover.General.SafeFitnessCrossover.__init__()=Bio.GA.Crossover.General.SafeFitnessCrossover-class.html#__init__,Method Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__()=Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover-class.html#__init__,Method Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__()=Bio.GA.Crossover.GeneralPoint.InterleaveCrossover-class.html#__init__,Method Bio.GA.Crossover.Point.SinglePointCrossover.__init__()=Bio.GA.Crossover.Point.SinglePointCrossover-class.html#__init__,Method Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__()=Bio.GA.Crossover.TwoPoint.TwoPointCrossover-class.html#__init__,Method Bio.GA.Crossover.Uniform.UniformCrossover.__init__()=Bio.GA.Crossover.Uniform.UniformCrossover-class.html#__init__,Method Bio.GA.Evolver.GenerationEvolver.__init__()=Bio.GA.Evolver.GenerationEvolver-class.html#__init__,Method Bio.GA.Evolver.SteadyStateEvolver.__init__()=Bio.GA.Evolver.SteadyStateEvolver-class.html#__init__,Method Bio.GA.Mutation.General.SafeFitnessMutation.__init__()=Bio.GA.Mutation.General.SafeFitnessMutation-class.html#__init__,Method Bio.GA.Mutation.Simple.ConversionMutation.__init__()=Bio.GA.Mutation.Simple.ConversionMutation-class.html#__init__,Method Bio.GA.Mutation.Simple.SinglePositionMutation.__init__()=Bio.GA.Mutation.Simple.SinglePositionMutation-class.html#__init__,Method Bio.GA.Organism.Organism.__init__()=Bio.GA.Organism.Organism-class.html#__init__,Method Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__()=Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html#__init__,Method Bio.GA.Selection.Abstract.AbstractSelection.__init__()=Bio.GA.Selection.Abstract.AbstractSelection-class.html#__init__,Method Bio.GA.Selection.Diversity.DiversitySelection.__init__()=Bio.GA.Selection.Diversity.DiversitySelection-class.html#__init__,Method Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__()=Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html#__init__,Method Bio.GA.Selection.Tournament.TournamentSelection.__init__()=Bio.GA.Selection.Tournament.TournamentSelection-class.html#__init__,Method Bio.GenBank.FeatureParser.__init__()=Bio.GenBank.FeatureParser-class.html#__init__,Method Bio.GenBank.Iterator.__init__()=Bio.GenBank.Iterator-class.html#__init__,Method Bio.GenBank.LocationParser.AbsoluteLocation.__init__()=Bio.GenBank.LocationParser.AbsoluteLocation-class.html#__init__,Method Bio.GenBank.LocationParser.Between.__init__()=Bio.GenBank.LocationParser.Between-class.html#__init__,Method Bio.GenBank.LocationParser.FeatureName.__init__()=Bio.GenBank.LocationParser.FeatureName-class.html#__init__,Method Bio.GenBank.LocationParser.Function.__init__()=Bio.GenBank.LocationParser.Function-class.html#__init__,Method Bio.GenBank.LocationParser.HighBound.__init__()=Bio.GenBank.LocationParser.HighBound-class.html#__init__,Method Bio.GenBank.LocationParser.Integer.__init__()=Bio.GenBank.LocationParser.Integer-class.html#__init__,Method Bio.GenBank.LocationParser.LocationParser.__init__()=Bio.GenBank.LocationParser.LocationParser-class.html#__init__,Method Bio.GenBank.LocationParser.LocationScanner.__init__()=Bio.GenBank.LocationParser.LocationScanner-class.html#__init__,Method Bio.GenBank.LocationParser.LowBound.__init__()=Bio.GenBank.LocationParser.LowBound-class.html#__init__,Method Bio.GenBank.LocationParser.Path.__init__()=Bio.GenBank.LocationParser.Path-class.html#__init__,Method Bio.GenBank.LocationParser.Range.__init__()=Bio.GenBank.LocationParser.Range-class.html#__init__,Method Bio.GenBank.LocationParser.Symbol.__init__()=Bio.GenBank.LocationParser.Symbol-class.html#__init__,Method Bio.GenBank.LocationParser.Token.__init__()=Bio.GenBank.LocationParser.Token-class.html#__init__,Method Bio.GenBank.LocationParser.TwoBound.__init__()=Bio.GenBank.LocationParser.TwoBound-class.html#__init__,Method Bio.GenBank.Record.Feature.__init__()=Bio.GenBank.Record.Feature-class.html#__init__,Method Bio.GenBank.Record.Qualifier.__init__()=Bio.GenBank.Record.Qualifier-class.html#__init__,Method Bio.GenBank.Record.Record.__init__()=Bio.GenBank.Record.Record-class.html#__init__,Method Bio.GenBank.Record.Reference.__init__()=Bio.GenBank.Record.Reference-class.html#__init__,Method Bio.GenBank.RecordParser.__init__()=Bio.GenBank.RecordParser-class.html#__init__,Method Bio.GenBank.Scanner.InsdcScanner.__init__()=Bio.GenBank.Scanner.InsdcScanner-class.html#__init__,Method Bio.GenBank._BaseGenBankConsumer.__init__()=Bio.GenBank._BaseGenBankConsumer-class.html#__init__,Method Bio.GenBank._FeatureConsumer.__init__()=Bio.GenBank._FeatureConsumer-class.html#__init__,Method Bio.GenBank._RecordConsumer.__init__()=Bio.GenBank._RecordConsumer-class.html#__init__,Method Bio.GenBank.utils.FeatureValueCleaner.__init__()=Bio.GenBank.utils.FeatureValueCleaner-class.html#__init__,Method Bio.Geo.Record.Record.__init__()=Bio.Geo.Record.Record-class.html#__init__,Method Bio.Graphics.BasicChromosome.Chromosome.__init__()=Bio.Graphics.BasicChromosome.Chromosome-class.html#__init__,Method Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__()=Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html#__init__,Method Bio.Graphics.BasicChromosome.Organism.__init__()=Bio.Graphics.BasicChromosome.Organism-class.html#__init__,Method Bio.Graphics.BasicChromosome.TelomereSegment.__init__()=Bio.Graphics.BasicChromosome.TelomereSegment-class.html#__init__,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#__init__,Method Bio.Graphics.Comparative.ComparativeScatterPlot.__init__()=Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#__init__,Method Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__()=Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#__init__,Method Bio.Graphics.Distribution.BarChartDistribution.__init__()=Bio.Graphics.Distribution.BarChartDistribution-class.html#__init__,Method Bio.Graphics.Distribution.DistributionPage.__init__()=Bio.Graphics.Distribution.DistributionPage-class.html#__init__,Method Bio.Graphics.Distribution.LineDistribution.__init__()=Bio.Graphics.Distribution.LineDistribution-class.html#__init__,Method Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__()=Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#__init__,Method Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__()=Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer-class.html#__init__,Method Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__()=Bio.Graphics.GenomeDiagram._Colors.ColorTranslator-class.html#__init__,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#__init__,Method Bio.Graphics.GenomeDiagram._Feature.Feature.__init__()=Bio.Graphics.GenomeDiagram._Feature.Feature-class.html#__init__,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#__init__,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#__init__,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#__init__,Method Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__()=Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#__init__,Method Bio.Graphics.GenomeDiagram._Track.Track.__init__()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#__init__,Method Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#__init__,Method Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.LogDPAlgorithms-class.html#__init__,Method Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#__init__,Method Bio.HMM.MarkovModel.HiddenMarkovModel.__init__()=Bio.HMM.MarkovModel.HiddenMarkovModel-class.html#__init__,Method Bio.HMM.MarkovModel.MarkovModelBuilder.__init__()=Bio.HMM.MarkovModel.MarkovModelBuilder-class.html#__init__,Method Bio.HMM.Trainer.AbstractTrainer.__init__()=Bio.HMM.Trainer.AbstractTrainer-class.html#__init__,Method Bio.HMM.Trainer.BaumWelchTrainer.__init__()=Bio.HMM.Trainer.BaumWelchTrainer-class.html#__init__,Method Bio.HMM.Trainer.KnownStateTrainer.__init__()=Bio.HMM.Trainer.KnownStateTrainer-class.html#__init__,Method Bio.HMM.Trainer.TrainingSequence.__init__()=Bio.HMM.Trainer.TrainingSequence-class.html#__init__,Method Bio.HotRand.HotCache.__init__()=Bio.HotRand.HotCache-class.html#__init__,Method Bio.HotRand.HotRandom.__init__()=Bio.HotRand.HotRandom-class.html#__init__,Method Bio.Index._InMemoryIndex.__init__()=Bio.Index._InMemoryIndex-class.html#__init__,Method Bio.Index._ShelveIndex.__init__()=Bio.Index._ShelveIndex-class.html#__init__,Method Bio.KDTree.KDTree.KDTree.__init__()=Bio.KDTree.KDTree.KDTree-class.html#__init__,Method Bio.KEGG.Compound.Record.__init__()=Bio.KEGG.Compound.Record-class.html#__init__,Method Bio.KEGG.Enzyme.Record.__init__()=Bio.KEGG.Enzyme.Record-class.html#__init__,Method Bio.LogisticRegression.LogisticRegression.__init__()=Bio.LogisticRegression.LogisticRegression-class.html#__init__,Method Bio.MarkovModel.MarkovModel.__init__()=Bio.MarkovModel.MarkovModel-class.html#__init__,Method Bio.MaxEntropy.MaxEntropy.__init__()=Bio.MaxEntropy.MaxEntropy-class.html#__init__,Method Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__()=Bio.Motif.Applications._AlignAce.AlignAceCommandline-class.html#__init__,Method Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__()=Bio.Motif.Applications._AlignAce.CompareAceCommandline-class.html#__init__,Method Bio.Motif.Parsers.AlignAce.Record.__init__()=Bio.Motif.Parsers.AlignAce.Record-class.html#__init__,Method Bio.Motif.Parsers.MAST.Record.__init__()=Bio.Motif.Parsers.MAST.Record-class.html#__init__,Method Bio.Motif.Parsers.MEME.MEMEInstance.__init__()=Bio.Motif.Parsers.MEME.MEMEInstance-class.html#__init__,Method Bio.Motif.Parsers.MEME.MEMEMotif.__init__()=Bio.Motif.Parsers.MEME.MEMEMotif-class.html#__init__,Method Bio.Motif.Parsers.MEME.MEMERecord.__init__()=Bio.Motif.Parsers.MEME.MEMERecord-class.html#__init__,Method Bio.Motif.Thresholds.ScoreDistribution.__init__()=Bio.Motif.Thresholds.ScoreDistribution-class.html#__init__,Method Bio.Motif._Motif.Motif.__init__()=Bio.Motif._Motif.Motif-class.html#__init__,Method Bio.NMR.xpktools.Peaklist.__init__()=Bio.NMR.xpktools.Peaklist-class.html#__init__,Method Bio.NMR.xpktools.XpkEntry.__init__()=Bio.NMR.xpktools.XpkEntry-class.html#__init__,Method Bio.NaiveBayes.NaiveBayes.__init__()=Bio.NaiveBayes.NaiveBayes-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__()=Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork-class.html#__init__,Method Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__()=Bio.NeuralNetwork.Gene.Motif.MotifCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#__init__,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__()=Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__()=Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__()=Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__()=Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.Schema.__init__()=Bio.NeuralNetwork.Gene.Schema.Schema-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaFactory-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__()=Bio.NeuralNetwork.Gene.Schema.SimpleFinisher-class.html#__init__,Method Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__()=Bio.NeuralNetwork.Gene.Signature.SignatureCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#__init__,Method Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__()=Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-class.html#__init__,Method Bio.NeuralNetwork.Training.ExampleManager.__init__()=Bio.NeuralNetwork.Training.ExampleManager-class.html#__init__,Method Bio.NeuralNetwork.Training.TrainingExample.__init__()=Bio.NeuralNetwork.Training.TrainingExample-class.html#__init__,Method Bio.Nexus.Nexus.Block.__init__()=Bio.Nexus.Nexus.Block-class.html#__init__,Method Bio.Nexus.Nexus.CharBuffer.__init__()=Bio.Nexus.Nexus.CharBuffer-class.html#__init__,Method Bio.Nexus.Nexus.Commandline.__init__()=Bio.Nexus.Nexus.Commandline-class.html#__init__,Method Bio.Nexus.Nexus.Nexus.__init__()=Bio.Nexus.Nexus.Nexus-class.html#__init__,Method Bio.Nexus.Nexus.StepMatrix.__init__()=Bio.Nexus.Nexus.StepMatrix-class.html#__init__,Method Bio.Nexus.Nodes.Chain.__init__()=Bio.Nexus.Nodes.Chain-class.html#__init__,Method Bio.Nexus.Nodes.Node.__init__()=Bio.Nexus.Nodes.Node-class.html#__init__,Method Bio.Nexus.Trees.NodeData.__init__()=Bio.Nexus.Trees.NodeData-class.html#__init__,Method Bio.Nexus.Trees.Tree.__init__()=Bio.Nexus.Trees.Tree-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap-class.html#__init__,Method Bio.PDB.Atom.Atom.__init__()=Bio.PDB.Atom.Atom-class.html#__init__,Method Bio.PDB.Atom.DisorderedAtom.__init__()=Bio.PDB.Atom.DisorderedAtom-class.html#__init__,Method Bio.PDB.Chain.Chain.__init__()=Bio.PDB.Chain.Chain-class.html#__init__,Method Bio.PDB.DSSP'.DSSP.__init__()=Bio.PDB.DSSP%27.DSSP-class.html#__init__,Method Bio.PDB.Dice.ChainSelector.__init__()=Bio.PDB.Dice.ChainSelector-class.html#__init__,Method Bio.PDB.Entity.DisorderedEntityWrapper.__init__()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__init__,Method Bio.PDB.Entity.Entity.__init__()=Bio.PDB.Entity.Entity-class.html#__init__,Method Bio.PDB.FragmentMapper'.Fragment.__init__()=Bio.PDB.FragmentMapper%27.Fragment-class.html#__init__,Method Bio.PDB.FragmentMapper'.FragmentMapper.__init__()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#__init__,Method Bio.PDB.HSExposure.ExposureCN.__init__()=Bio.PDB.HSExposure.ExposureCN-class.html#__init__,Method Bio.PDB.HSExposure.HSExposureCA.__init__()=Bio.PDB.HSExposure.HSExposureCA-class.html#__init__,Method Bio.PDB.HSExposure.HSExposureCB.__init__()=Bio.PDB.HSExposure.HSExposureCB-class.html#__init__,Method Bio.PDB.HSExposure._AbstractHSExposure.__init__()=Bio.PDB.HSExposure._AbstractHSExposure-class.html#__init__,Method Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__()=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#__init__,Method Bio.PDB.Model.Model.__init__()=Bio.PDB.Model.Model-class.html#__init__,Method Bio.PDB.NACCESS.NACCESS.__init__()=Bio.PDB.NACCESS.NACCESS-class.html#__init__,Method Bio.PDB.NACCESS.NACCESS_atomic.__init__()=Bio.PDB.NACCESS.NACCESS_atomic-class.html#__init__,Method Bio.PDB.NeighborSearch.NeighborSearch.__init__()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#__init__,Method Bio.PDB.PDBIO'.PDBIO.__init__()=Bio.PDB.PDBIO%27.PDBIO-class.html#__init__,Method Bio.PDB.PDBList'.PDBList.__init__()=Bio.PDB.PDBList%27.PDBList-class.html#__init__,Method Bio.PDB.PDBParser'.PDBParser.__init__()=Bio.PDB.PDBParser%27.PDBParser-class.html#__init__,Method Bio.PDB.PSEA.PSEA.__init__()=Bio.PDB.PSEA.PSEA-class.html#__init__,Method Bio.PDB.Polypeptide.CaPPBuilder.__init__()=Bio.PDB.Polypeptide.CaPPBuilder-class.html#__init__,Method Bio.PDB.Polypeptide.PPBuilder.__init__()=Bio.PDB.Polypeptide.PPBuilder-class.html#__init__,Method Bio.PDB.Polypeptide._PPBuilder.__init__()=Bio.PDB.Polypeptide._PPBuilder-class.html#__init__,Method Bio.PDB.Residue.DisorderedResidue.__init__()=Bio.PDB.Residue.DisorderedResidue-class.html#__init__,Method Bio.PDB.Residue.Residue.__init__()=Bio.PDB.Residue.Residue-class.html#__init__,Method Bio.PDB.ResidueDepth'.ResidueDepth.__init__()=Bio.PDB.ResidueDepth%27.ResidueDepth-class.html#__init__,Method Bio.PDB.Structure.Structure.__init__()=Bio.PDB.Structure.Structure-class.html#__init__,Method Bio.PDB.StructureAlignment'.StructureAlignment.__init__()=Bio.PDB.StructureAlignment%27.StructureAlignment-class.html#__init__,Method Bio.PDB.StructureBuilder.StructureBuilder.__init__()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#__init__,Method Bio.PDB.Superimposer'.Superimposer.__init__()=Bio.PDB.Superimposer%27.Superimposer-class.html#__init__,Method Bio.PDB.Vector'.Vector.__init__()=Bio.PDB.Vector%27.Vector-class.html#__init__,Method Bio.ParserSupport.EventGenerator.__init__()=Bio.ParserSupport.EventGenerator-class.html#__init__,Method Bio.ParserSupport.SGMLStrippingConsumer.__init__()=Bio.ParserSupport.SGMLStrippingConsumer-class.html#__init__,Method Bio.ParserSupport.TaggingConsumer.__init__()=Bio.ParserSupport.TaggingConsumer-class.html#__init__,Method Bio.Parsers.spark.GenericASTBuilder.__init__()=Bio.Parsers.spark.GenericASTBuilder-class.html#__init__,Method Bio.Parsers.spark.GenericASTMatcher.__init__()=Bio.Parsers.spark.GenericASTMatcher-class.html#__init__,Method Bio.Parsers.spark.GenericASTTraversal.__init__()=Bio.Parsers.spark.GenericASTTraversal-class.html#__init__,Method Bio.Parsers.spark.GenericParser.__init__()=Bio.Parsers.spark.GenericParser-class.html#__init__,Method Bio.Parsers.spark.GenericScanner.__init__()=Bio.Parsers.spark.GenericScanner-class.html#__init__,Method Bio.Pathway.Network.__init__()=Bio.Pathway.Network-class.html#__init__,Method Bio.Pathway.Reaction.__init__()=Bio.Pathway.Reaction-class.html#__init__,Method Bio.Pathway.Rep.Graph.Graph.__init__()=Bio.Pathway.Rep.Graph.Graph-class.html#__init__,Method Bio.Pathway.Rep.HashSet.HashSet.__init__()=Bio.Pathway.Rep.HashSet.HashSet-class.html#__init__,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__init__,Method Bio.Pathway.System.__init__()=Bio.Pathway.System-class.html#__init__,Method Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__()=Bio.Phylo.Applications._Phyml.PhymlCommandline-class.html#__init__,Method Bio.Phylo.BaseTree.Clade.__init__()=Bio.Phylo.BaseTree.Clade-class.html#__init__,Method Bio.Phylo.BaseTree.Tree.__init__()=Bio.Phylo.BaseTree.Tree-class.html#__init__,Method Bio.Phylo.Newick.Clade.__init__()=Bio.Phylo.Newick.Clade-class.html#__init__,Method Bio.Phylo.Newick.Tree.__init__()=Bio.Phylo.Newick.Tree-class.html#__init__,Method Bio.Phylo.NewickIO.Parser.__init__()=Bio.Phylo.NewickIO.Parser-class.html#__init__,Method Bio.Phylo.NewickIO.Writer.__init__()=Bio.Phylo.NewickIO.Writer-class.html#__init__,Method Bio.Phylo.PAML._paml.Paml.__init__()=Bio.Phylo.PAML._paml.Paml-class.html#__init__,Method Bio.Phylo.PAML.baseml.Baseml.__init__()=Bio.Phylo.PAML.baseml.Baseml-class.html#__init__,Method Bio.Phylo.PAML.codeml.Codeml.__init__()=Bio.Phylo.PAML.codeml.Codeml-class.html#__init__,Method Bio.Phylo.PAML.yn00.Yn00.__init__()=Bio.Phylo.PAML.yn00.Yn00-class.html#__init__,Method Bio.Phylo.PhyloXML.Accession.__init__()=Bio.Phylo.PhyloXML.Accession-class.html#__init__,Method Bio.Phylo.PhyloXML.Annotation.__init__()=Bio.Phylo.PhyloXML.Annotation-class.html#__init__,Method Bio.Phylo.PhyloXML.BinaryCharacters.__init__()=Bio.Phylo.PhyloXML.BinaryCharacters-class.html#__init__,Method Bio.Phylo.PhyloXML.BranchColor.__init__()=Bio.Phylo.PhyloXML.BranchColor-class.html#__init__,Method Bio.Phylo.PhyloXML.Clade.__init__()=Bio.Phylo.PhyloXML.Clade-class.html#__init__,Method Bio.Phylo.PhyloXML.CladeRelation.__init__()=Bio.Phylo.PhyloXML.CladeRelation-class.html#__init__,Method Bio.Phylo.PhyloXML.Confidence.__init__()=Bio.Phylo.PhyloXML.Confidence-class.html#__init__,Method Bio.Phylo.PhyloXML.Date.__init__()=Bio.Phylo.PhyloXML.Date-class.html#__init__,Method Bio.Phylo.PhyloXML.Distribution.__init__()=Bio.Phylo.PhyloXML.Distribution-class.html#__init__,Method Bio.Phylo.PhyloXML.DomainArchitecture.__init__()=Bio.Phylo.PhyloXML.DomainArchitecture-class.html#__init__,Method Bio.Phylo.PhyloXML.Events.__init__()=Bio.Phylo.PhyloXML.Events-class.html#__init__,Method Bio.Phylo.PhyloXML.Id.__init__()=Bio.Phylo.PhyloXML.Id-class.html#__init__,Method Bio.Phylo.PhyloXML.MolSeq.__init__()=Bio.Phylo.PhyloXML.MolSeq-class.html#__init__,Method Bio.Phylo.PhyloXML.Other.__init__()=Bio.Phylo.PhyloXML.Other-class.html#__init__,Method Bio.Phylo.PhyloXML.Phylogeny.__init__()=Bio.Phylo.PhyloXML.Phylogeny-class.html#__init__,Method Bio.Phylo.PhyloXML.Phyloxml.__init__()=Bio.Phylo.PhyloXML.Phyloxml-class.html#__init__,Method Bio.Phylo.PhyloXML.Point.__init__()=Bio.Phylo.PhyloXML.Point-class.html#__init__,Method Bio.Phylo.PhyloXML.Polygon.__init__()=Bio.Phylo.PhyloXML.Polygon-class.html#__init__,Method Bio.Phylo.PhyloXML.Property.__init__()=Bio.Phylo.PhyloXML.Property-class.html#__init__,Method Bio.Phylo.PhyloXML.ProteinDomain.__init__()=Bio.Phylo.PhyloXML.ProteinDomain-class.html#__init__,Method Bio.Phylo.PhyloXML.Reference.__init__()=Bio.Phylo.PhyloXML.Reference-class.html#__init__,Method Bio.Phylo.PhyloXML.Sequence.__init__()=Bio.Phylo.PhyloXML.Sequence-class.html#__init__,Method Bio.Phylo.PhyloXML.SequenceRelation.__init__()=Bio.Phylo.PhyloXML.SequenceRelation-class.html#__init__,Method Bio.Phylo.PhyloXML.Taxonomy.__init__()=Bio.Phylo.PhyloXML.Taxonomy-class.html#__init__,Method Bio.Phylo.PhyloXML.Uri.__init__()=Bio.Phylo.PhyloXML.Uri-class.html#__init__,Method Bio.Phylo.PhyloXMLIO.Parser.__init__()=Bio.Phylo.PhyloXMLIO.Parser-class.html#__init__,Method Bio.Phylo.PhyloXMLIO.Writer.__init__()=Bio.Phylo.PhyloXMLIO.Writer-class.html#__init__,Method Bio.PopGen.Async.Async.__init__()=Bio.PopGen.Async.Async-class.html#__init__,Method Bio.PopGen.Async.DirectoryRetriever.__init__()=Bio.PopGen.Async.DirectoryRetriever-class.html#__init__,Method Bio.PopGen.Async.FileRetriever.__init__()=Bio.PopGen.Async.FileRetriever-class.html#__init__,Method Bio.PopGen.Async.Local.Local.__init__()=Bio.PopGen.Async.Local.Local-class.html#__init__,Method Bio.PopGen.FDist.Async.FDistAsync.__init__()=Bio.PopGen.FDist.Async.FDistAsync-class.html#__init__,Method Bio.PopGen.FDist.Async.SplitFDist.__init__()=Bio.PopGen.FDist.Async.SplitFDist-class.html#__init__,Method Bio.PopGen.FDist.Controller.FDistController.__init__()=Bio.PopGen.FDist.Controller.FDistController-class.html#__init__,Method Bio.PopGen.FDist.Record.__init__()=Bio.PopGen.FDist.Record-class.html#__init__,Method Bio.PopGen.GenePop.Controller.GenePopController.__init__()=Bio.PopGen.GenePop.Controller.GenePopController-class.html#__init__,Method Bio.PopGen.GenePop.Controller._FileIterator.__init__()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#__init__,Method Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__()=Bio.PopGen.GenePop.Controller._GenePopCommandline-class.html#__init__,Method Bio.PopGen.GenePop.EasyController.EasyController.__init__()=Bio.PopGen.GenePop.EasyController.EasyController-class.html#__init__,Method Bio.PopGen.GenePop.FileParser.FileRecord.__init__()=Bio.PopGen.GenePop.FileParser.FileRecord-class.html#__init__,Method Bio.PopGen.GenePop.LargeFileParser.Record.__init__()=Bio.PopGen.GenePop.LargeFileParser.Record-class.html#__init__,Method Bio.PopGen.GenePop.Record.__init__()=Bio.PopGen.GenePop.Record-class.html#__init__,Method Bio.PopGen.SimCoal.Async.SimCoalCache.__init__()=Bio.PopGen.SimCoal.Async.SimCoalCache-class.html#__init__,Method Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__()=Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html#__init__,Method Bio.PopGen.SimCoal.Controller.SimCoalController.__init__()=Bio.PopGen.SimCoal.Controller.SimCoalController-class.html#__init__,Method Bio.Restriction.PrintFormat.PrintFormat.__init__()=Bio.Restriction.PrintFormat.PrintFormat-class.html#__init__,Method Bio.Restriction.Restriction.Analysis.__init__()=Bio.Restriction.Restriction.Analysis-class.html#__init__,Method Bio.Restriction.Restriction.FormattedSeq.__init__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__init__,Method Bio.Restriction.Restriction.RestrictionBatch.__init__()=Bio.Restriction.Restriction.RestrictionBatch-class.html#__init__,Method Bio.Restriction.Restriction.RestrictionType.__init__()=Bio.Restriction.Restriction.RestrictionType-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__()=Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__()=Bio.Restriction._Update.RestrictionCompiler.newenzyme-class.html#__init__,Method Bio.Restriction._Update.Update.ConnectionError.__init__()=Bio.Restriction._Update.Update.ConnectionError-class.html#__init__,Method Bio.Restriction._Update.Update.FtpNameError.__init__()=Bio.Restriction._Update.Update.FtpNameError-class.html#__init__,Method Bio.Restriction._Update.Update.FtpPasswordError.__init__()=Bio.Restriction._Update.Update.FtpPasswordError-class.html#__init__,Method Bio.Restriction._Update.Update.RebaseUpdate.__init__()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#__init__,Method Bio.SCOP.Astral.__init__()=Bio.SCOP.Astral-class.html#__init__,Method Bio.SCOP.Cla.Index.__init__()=Bio.SCOP.Cla.Index-class.html#__init__,Method Bio.SCOP.Cla.Record.__init__()=Bio.SCOP.Cla.Record-class.html#__init__,Method Bio.SCOP.Des.Record.__init__()=Bio.SCOP.Des.Record-class.html#__init__,Method Bio.SCOP.Dom.Record.__init__()=Bio.SCOP.Dom.Record-class.html#__init__,Method Bio.SCOP.Domain.__init__()=Bio.SCOP.Domain-class.html#__init__,Method Bio.SCOP.Hie.Record.__init__()=Bio.SCOP.Hie.Record-class.html#__init__,Method Bio.SCOP.Node.__init__()=Bio.SCOP.Node-class.html#__init__,Method Bio.SCOP.Raf.Res.__init__()=Bio.SCOP.Raf.Res-class.html#__init__,Method Bio.SCOP.Raf.SeqMap.__init__()=Bio.SCOP.Raf.SeqMap-class.html#__init__,Method Bio.SCOP.Raf.SeqMapIndex.__init__()=Bio.SCOP.Raf.SeqMapIndex-class.html#__init__,Method Bio.SCOP.Residues'.Residues.__init__()=Bio.SCOP.Residues%27.Residues-class.html#__init__,Method Bio.SCOP.Scop.__init__()=Bio.SCOP.Scop-class.html#__init__,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#__init__,Method Bio.Search.Algorithm.__init__()=Bio.Search.Algorithm-class.html#__init__,Method Bio.Search.Database.__init__()=Bio.Search.Database-class.html#__init__,Method Bio.Search.HSP.__init__()=Bio.Search.HSP-class.html#__init__,Method Bio.Search.HSPSeq.__init__()=Bio.Search.HSPSeq-class.html#__init__,Method Bio.Search.Hit.__init__()=Bio.Search.Hit-class.html#__init__,Method Bio.Search.HomologySeq.__init__()=Bio.Search.HomologySeq-class.html#__init__,Method Bio.Search.Query.__init__()=Bio.Search.Query-class.html#__init__,Method Bio.Search.Search.__init__()=Bio.Search.Search-class.html#__init__,Method Bio.Search.TableInfo.__init__()=Bio.Search.TableInfo-class.html#__init__,Method Bio.Search._SeqLength.__init__()=Bio.Search._SeqLength-class.html#__init__,Method Bio.Seq.MutableSeq.__init__()=Bio.Seq.MutableSeq-class.html#__init__,Method Bio.Seq.Seq.__init__()=Bio.Seq.Seq-class.html#__init__,Method Bio.Seq.UnknownSeq.__init__()=Bio.Seq.UnknownSeq-class.html#__init__,Method Bio.SeqFeature.AbstractPosition.__init__()=Bio.SeqFeature.AbstractPosition-class.html#__init__,Method Bio.SeqFeature.AfterPosition.__init__()=Bio.SeqFeature.AfterPosition-class.html#__init__,Method Bio.SeqFeature.BeforePosition.__init__()=Bio.SeqFeature.BeforePosition-class.html#__init__,Method Bio.SeqFeature.BetweenPosition.__init__()=Bio.SeqFeature.BetweenPosition-class.html#__init__,Method Bio.SeqFeature.ExactPosition.__init__()=Bio.SeqFeature.ExactPosition-class.html#__init__,Method Bio.SeqFeature.FeatureLocation.__init__()=Bio.SeqFeature.FeatureLocation-class.html#__init__,Method Bio.SeqFeature.OneOfPosition.__init__()=Bio.SeqFeature.OneOfPosition-class.html#__init__,Method Bio.SeqFeature.PositionGap.__init__()=Bio.SeqFeature.PositionGap-class.html#__init__,Method Bio.SeqFeature.Reference.__init__()=Bio.SeqFeature.Reference-class.html#__init__,Method Bio.SeqFeature.SeqFeature.__init__()=Bio.SeqFeature.SeqFeature-class.html#__init__,Method Bio.SeqFeature.UnknownPosition.__init__()=Bio.SeqFeature.UnknownPosition-class.html#__init__,Method Bio.SeqFeature.WithinPosition.__init__()=Bio.SeqFeature.WithinPosition-class.html#__init__,Method Bio.SeqIO.FastaIO.FastaWriter.__init__()=Bio.SeqIO.FastaIO.FastaWriter-class.html#__init__,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__init__,Method Bio.SeqIO.Interfaces.SequenceIterator.__init__()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#__init__,Method Bio.SeqIO.Interfaces.SequenceWriter.__init__()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#__init__,Method Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__()=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#__init__,Method Bio.SeqIO.PhdIO.PhdWriter.__init__()=Bio.SeqIO.PhdIO.PhdWriter-class.html#__init__,Method Bio.SeqIO.QualityIO.QualPhredWriter.__init__()=Bio.SeqIO.QualityIO.QualPhredWriter-class.html#__init__,Method Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__()=Bio.SeqIO.SeqXmlIO.SeqXmlIterator-class.html#__init__,Method Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__()=Bio.SeqIO.SeqXmlIO.SeqXmlWriter-class.html#__init__,Method Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__()=Bio.SeqIO.SeqXmlIO.XMLRecordIterator-class.html#__init__,Method Bio.SeqIO.SffIO.SffWriter.__init__()=Bio.SeqIO.SffIO.SffWriter-class.html#__init__,Method Bio.SeqIO.SffIO._AddTellHandle.__init__()=Bio.SeqIO.SffIO._AddTellHandle-class.html#__init__,Method Bio.SeqIO.UniprotIO.Parser.__init__()=Bio.SeqIO.UniprotIO.Parser-class.html#__init__,Method Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__()=Bio.SeqIO._index.IntelliGeneticsRandomAccess-class.html#__init__,Method Bio.SeqIO._index.SeqFileRandomAccess.__init__()=Bio.SeqIO._index.SeqFileRandomAccess-class.html#__init__,Method Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__()=Bio.SeqIO._index.SequentialSeqFileRandomAccess-class.html#__init__,Method Bio.SeqIO._index.SffRandomAccess.__init__()=Bio.SeqIO._index.SffRandomAccess-class.html#__init__,Method Bio.SeqIO._index._IndexedSeqFileDict.__init__()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#__init__,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__init__,Method Bio.SeqRecord.SeqRecord.__init__()=Bio.SeqRecord.SeqRecord-class.html#__init__,Method Bio.SeqRecord._RestrictedDict.__init__()=Bio.SeqRecord._RestrictedDict-class.html#__init__,Method Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__()=Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#__init__,Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#__init__,Method Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__()=Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#__init__,Method Bio.Sequencing.Ace.ACEFileRecord.__init__()=Bio.Sequencing.Ace.ACEFileRecord-class.html#__init__,Method Bio.Sequencing.Ace.Contig.__init__()=Bio.Sequencing.Ace.Contig-class.html#__init__,Method Bio.Sequencing.Ace.Reads.__init__()=Bio.Sequencing.Ace.Reads-class.html#__init__,Method Bio.Sequencing.Ace.af.__init__()=Bio.Sequencing.Ace.af-class.html#__init__,Method Bio.Sequencing.Ace.bs.__init__()=Bio.Sequencing.Ace.bs-class.html#__init__,Method Bio.Sequencing.Ace.ct.__init__()=Bio.Sequencing.Ace.ct-class.html#__init__,Method Bio.Sequencing.Ace.ds.__init__()=Bio.Sequencing.Ace.ds-class.html#__init__,Method Bio.Sequencing.Ace.qa.__init__()=Bio.Sequencing.Ace.qa-class.html#__init__,Method Bio.Sequencing.Ace.rd.__init__()=Bio.Sequencing.Ace.rd-class.html#__init__,Method Bio.Sequencing.Ace.rt.__init__()=Bio.Sequencing.Ace.rt-class.html#__init__,Method Bio.Sequencing.Ace.wa.__init__()=Bio.Sequencing.Ace.wa-class.html#__init__,Method Bio.Sequencing.Ace.wr.__init__()=Bio.Sequencing.Ace.wr-class.html#__init__,Method Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__()=Bio.Sequencing.Applications._Novoalign.NovoalignCommandline-class.html#__init__,Method Bio.Sequencing.Phd.Record.__init__()=Bio.Sequencing.Phd.Record-class.html#__init__,Method Bio.SubsMat.FreqTable.FreqTable.__init__()=Bio.SubsMat.FreqTable.FreqTable-class.html#__init__,Method Bio.SubsMat.SeqMat.__init__()=Bio.SubsMat.SeqMat-class.html#__init__,Method Bio.SwissProt.KeyWList.Record.__init__()=Bio.SwissProt.KeyWList.Record-class.html#__init__,Method Bio.SwissProt.Record.__init__()=Bio.SwissProt.Record-class.html#__init__,Method Bio.SwissProt.Reference.__init__()=Bio.SwissProt.Reference-class.html#__init__,Method Bio.UniGene.Iterator.__init__()=Bio.UniGene.Iterator-class.html#__init__,Method Bio.UniGene.ProtsimLine.__init__()=Bio.UniGene.ProtsimLine-class.html#__init__,Method Bio.UniGene.Record.__init__()=Bio.UniGene.Record-class.html#__init__,Method Bio.UniGene.RecordParser.__init__()=Bio.UniGene.RecordParser-class.html#__init__,Method Bio.UniGene.STSLine.__init__()=Bio.UniGene.STSLine-class.html#__init__,Method Bio.UniGene.SequenceLine.__init__()=Bio.UniGene.SequenceLine-class.html#__init__,Method Bio.UniGene.UnigeneProtsimRecord.__init__()=Bio.UniGene.UnigeneProtsimRecord-class.html#__init__,Method Bio.UniGene.UnigeneRecord.__init__()=Bio.UniGene.UnigeneRecord-class.html#__init__,Method Bio.UniGene.UnigeneSTSRecord.__init__()=Bio.UniGene.UnigeneSTSRecord-class.html#__init__,Method Bio.UniGene.UnigeneSequenceRecord.__init__()=Bio.UniGene.UnigeneSequenceRecord-class.html#__init__,Method Bio.UniGene._RecordConsumer.__init__()=Bio.UniGene._RecordConsumer-class.html#__init__,Method Bio.UniGene._Scanner.__init__()=Bio.UniGene._Scanner-class.html#__init__,Method Bio.Wise.dnal.Statistics.__init__()=Bio.Wise.dnal.Statistics-class.html#__init__,Method Bio.Wise.psw.AlignmentColumn.__init__()=Bio.Wise.psw.AlignmentColumn-class.html#__init__,Method Bio.Wise.psw.ColumnUnit.__init__()=Bio.Wise.psw.ColumnUnit-class.html#__init__,Method Bio.kNN.kNN.__init__()=Bio.kNN.kNN-class.html#__init__,Method Bio.pairwise2.affine_penalty.__init__()=Bio.pairwise2.affine_penalty-class.html#__init__,Method Bio.pairwise2.dictionary_match.__init__()=Bio.pairwise2.dictionary_match-class.html#__init__,Method Bio.pairwise2.identity_match.__init__()=Bio.pairwise2.identity_match-class.html#__init__,Method BioSQL.BioSeq.DBSeq.__init__()=BioSQL.BioSeq.DBSeq-class.html#__init__,Method BioSQL.BioSeq.DBSeqRecord.__init__()=BioSQL.BioSeq.DBSeqRecord-class.html#__init__,Method BioSQL.BioSeqDatabase.Adaptor.__init__()=BioSQL.BioSeqDatabase.Adaptor-class.html#__init__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__init__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__init__,Method BioSQL.BioSeqDatabase.DBServer.__init__()=BioSQL.BioSeqDatabase.DBServer-class.html#__init__,Method BioSQL.DBUtils.Generic_dbutils.__init__()=BioSQL.DBUtils.Generic_dbutils-class.html#__init__,Method BioSQL.Loader.DatabaseLoader.__init__()=BioSQL.Loader.DatabaseLoader-class.html#__init__,Method BioSQL.Loader.DatabaseRemover.__init__()=BioSQL.Loader.DatabaseRemover-class.html#__init__"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Affy.CelFile.CelScanner.__init__
Bio.Affy.CelFile.Record.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__
Bio.Align.Applications._Dialign.DialignCommandline.__init__
Bio.Align.Applications._Mafft.MafftCommandline.__init__
Bio.Align.Applications._Muscle.MuscleCommandline.__init__
Bio.Align.Applications._Prank.PrankCommandline.__init__
Bio.Align.Applications._Probcons.ProbconsCommandline.__init__
Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__
Bio.Align.Generic.Alignment.__init__
Bio.Align.MultipleSeqAlignment.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationError.__init__
Bio.Application._AbstractParameter.__init__
Bio.Application._Argument.__init__
Bio.Application._Option.__init__
Bio.Application._Switch.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.BlastpgpCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.Applications.NcbiblastformatterCommandline.__init__
Bio.Blast.Applications.NcbiblastnCommandline.__init__
Bio.Blast.Applications.NcbiblastpCommandline.__init__
Bio.Blast.Applications.NcbiblastxCommandline.__init__
Bio.Blast.Applications.NcbipsiblastCommandline.__init__
Bio.Blast.Applications.NcbirpsblastCommandline.__init__
Bio.Blast.Applications.NcbirpstblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastxCommandline.__init__
Bio.Blast.Applications.RpsBlastCommandline.__init__
Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__
Bio.Blast.Applications._BlastCommandLine.__init__
Bio.Blast.Applications._NcbibaseblastCommandline.__init__
Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__
Bio.Blast.Applications._NcbiblastCommandline.__init__
Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Compass._Scanner.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.Hetero.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.Emboss.Applications.DiffseqCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FConsenseCommandline.__init__
Bio.Emboss.Applications.FDNADistCommandline.__init__
Bio.Emboss.Applications.FDNAParsCommandline.__init__
Bio.Emboss.Applications.FNeighborCommandline.__init__
Bio.Emboss.Applications.FProtDistCommandline.__init__
Bio.Emboss.Applications.FProtParsCommandline.__init__
Bio.Emboss.Applications.FSeqBootCommandline.__init__
Bio.Emboss.Applications.FTreeDistCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.IepCommandline.__init__
Bio.Emboss.Applications.NeedleCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.SeqmatchallCommandline.__init__
Bio.Emboss.Applications.SeqretCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Applications._EmbossCommandLine.__init__
Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__
Bio.Emboss.Primer3.Primers.__init__
Bio.Emboss.Primer3.Record.__init__
Bio.Emboss.PrimerSearch.Amplifier.__init__
Bio.Emboss.PrimerSearch.InputRecord.__init__
Bio.Emboss.PrimerSearch.OutputRecord.__init__
Bio.Entrez.Parser.CorruptedXMLError.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.NotXMLError.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Entrez.Parser.ValidationError.__init__
Bio.ExPASy.Enzyme.Record.__init__
Bio.ExPASy.Prodoc.Record.__init__
Bio.ExPASy.Prodoc.Reference.__init__
Bio.ExPASy.Prosite.Record.__init__
Bio.ExPASy.ScanProsite.ContentHandler.__init__
Bio.ExPASy.ScanProsite.Parser.__init__
Bio.ExPASy.ScanProsite.Record.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__
Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__
Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__
Bio.Graphics.GenomeDiagram._Feature.Feature.__init__
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__
Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__
Bio.Graphics.GenomeDiagram._Track.Track.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__
Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__
Bio.Motif.Parsers.AlignAce.Record.__init__
Bio.Motif.Parsers.MAST.Record.__init__
Bio.Motif.Parsers.MEME.MEMEInstance.__init__
Bio.Motif.Parsers.MEME.MEMEMotif.__init__
Bio.Motif.Parsers.MEME.MEMERecord.__init__
Bio.Motif.Thresholds.ScoreDistribution.__init__
Bio.Motif._Motif.Motif.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__
Bio.Phylo.BaseTree.Clade.__init__
Bio.Phylo.BaseTree.Tree.__init__
Bio.Phylo.Newick.Clade.__init__
Bio.Phylo.Newick.Tree.__init__
Bio.Phylo.NewickIO.Parser.__init__
Bio.Phylo.NewickIO.Writer.__init__
Bio.Phylo.PAML._paml.Paml.__init__
Bio.Phylo.PAML.baseml.Baseml.__init__
Bio.Phylo.PAML.codeml.Codeml.__init__
Bio.Phylo.PAML.yn00.Yn00.__init__
Bio.Phylo.PhyloXML.Accession.__init__
Bio.Phylo.PhyloXML.Annotation.__init__
Bio.Phylo.PhyloXML.BinaryCharacters.__init__
Bio.Phylo.PhyloXML.BranchColor.__init__
Bio.Phylo.PhyloXML.Clade.__init__
Bio.Phylo.PhyloXML.CladeRelation.__init__
Bio.Phylo.PhyloXML.Confidence.__init__
Bio.Phylo.PhyloXML.Date.__init__
Bio.Phylo.PhyloXML.Distribution.__init__
Bio.Phylo.PhyloXML.DomainArchitecture.__init__
Bio.Phylo.PhyloXML.Events.__init__
Bio.Phylo.PhyloXML.Id.__init__
Bio.Phylo.PhyloXML.MolSeq.__init__
Bio.Phylo.PhyloXML.Other.__init__
Bio.Phylo.PhyloXML.Phylogeny.__init__
Bio.Phylo.PhyloXML.Phyloxml.__init__
Bio.Phylo.PhyloXML.Point.__init__
Bio.Phylo.PhyloXML.Polygon.__init__
Bio.Phylo.PhyloXML.Property.__init__
Bio.Phylo.PhyloXML.ProteinDomain.__init__
Bio.Phylo.PhyloXML.Reference.__init__
Bio.Phylo.PhyloXML.Sequence.__init__
Bio.Phylo.PhyloXML.SequenceRelation.__init__
Bio.Phylo.PhyloXML.Taxonomy.__init__
Bio.Phylo.PhyloXML.Uri.__init__
Bio.Phylo.PhyloXMLIO.Parser.__init__
Bio.Phylo.PhyloXMLIO.Writer.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.GenePop.Controller.GenePopController.__init__
Bio.PopGen.GenePop.Controller._FileIterator.__init__
Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__
Bio.PopGen.GenePop.EasyController.EasyController.__init__
Bio.PopGen.GenePop.FileParser.FileRecord.__init__
Bio.PopGen.GenePop.LargeFileParser.Record.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__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__" class="py-name" href="#" onclick="return doclink('link-2', '__init__', 'link-2');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">truncate</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-comment"># In python 1.52 and before, dumbdbm (under shelve)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-comment"># doesn't clear the old database.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">files</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">indexname</tt> <tt class="py-op">+</tt> <tt class="py-string">'.dir'</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">indexname</tt> <tt class="py-op">+</tt> <tt class="py-string">'.dat'</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">indexname</tt> <tt class="py-op">+</tt> <tt class="py-string">'.bak'</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-op">]</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">files</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-name">file</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">os</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.unlink()=Bio.Nexus.Nodes.Chain-class.html#unlink"><a title="Bio.Nexus.Nodes.Chain.unlink" class="py-name" href="#" onclick="return doclink('link-3', 'unlink', 'link-3');">unlink</a></tt><tt class="py-op">(</tt><tt class="py-name">file</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">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">(</tt><tt class="py-string">"open a new shelf"</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Variable Bio.Seq.Seq.data=Bio.Seq.Seq-class.html#data,Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-4', 'data', 'link-4');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">shelve</tt><tt class="py-op">.</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">indexname</tt><tt class="py-op">,</tt> <tt class="py-name">flag</tt><tt class="py-op">=</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-comment"># No database exists.</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-5', 'data', 'link-4');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">shelve</tt><tt class="py-op">.</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">indexname</tt><tt class="py-op">,</tt> <tt class="py-name">flag</tt><tt class="py-op">=</tt><tt class="py-string">'n'</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">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-6', 'data', 'link-4');">data</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Index._InMemoryIndex.__version_key
Bio.Index._ShelveIndex.__version_key" class="py-name" href="#" onclick="return doclink('link-7', '__version_key', 'link-1');">__version_key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-8', '__version', 'link-0');">__version</a></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-comment"># Check to make sure the database is the correct version.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt id="link-9" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-9', 'version', 'link-9');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-10', 'data', 'link-4');">data</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqIO._index.SeqFileRandomAccess.get()=Bio.SeqIO._index.SeqFileRandomAccess-class.html#get,Method Bio.SeqIO._index.SffRandomAccess.get()=Bio.SeqIO._index.SffRandomAccess-class.html#get,Method Bio.SeqIO._index.SffTrimedRandomAccess.get()=Bio.SeqIO._index.SffTrimedRandomAccess-class.html#get,Method Bio.SeqIO._index.UniprotRandomAccess.get()=Bio.SeqIO._index.UniprotRandomAccess-class.html#get,Method Bio.SeqIO._index._IndexedSeqFileDict.get()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#get,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.get()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-11', 'get', 'link-11');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Index._InMemoryIndex.__version_key
Bio.Index._ShelveIndex.__version_key" class="py-name" href="#" onclick="return doclink('link-12', '__version_key', 'link-1');">__version_key</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</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 id="link-13" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-13', 'version', 'link-9');">version</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">(</tt><tt class="py-string">"Unrecognized index format"</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">elif</tt> <tt id="link-14" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-14', 'version', 'link-9');">version</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-15', '__version', 'link-0');">__version</a></tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">(</tt><tt class="py-string">"Version %s doesn't match my version %s"</tt> \ </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-16', 'version', 'link-9');">version</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.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-17', '__version', 'link-0');">__version</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="_ShelveIndex.__del__"></a><div id="_ShelveIndex.__del__-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="_ShelveIndex.__del__-toggle" onclick="return toggle('_ShelveIndex.__del__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._ShelveIndex-class.html#__del__">__del__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_ShelveIndex.__del__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_ShelveIndex.__del__-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-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"><a title="Bio.Crystal.Crystal.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key" class="py-name" href="#" onclick="return doclink('link-18', 'has_key', 'link-18');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">'data'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-19', 'data', 'link-4');">data</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.SeqIO.SffIO._AddTellHandle.close()=Bio.SeqIO.SffIO._AddTellHandle-class.html#close,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.close()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method BioSQL.BioSeqDatabase.DBServer.close()=BioSQL.BioSeqDatabase.DBServer-class.html#close"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-20', 'close', 'link-20');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="_InMemoryIndex"></a><div id="_InMemoryIndex-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="_InMemoryIndex-toggle" onclick="return toggle('_InMemoryIndex');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html">_InMemoryIndex</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="_InMemoryIndex-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_InMemoryIndex-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-docstring">"""This creates an in-memory index file.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"></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-comment"># File Format:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-comment"># version</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment"># key value</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># [...]</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt id="link-21" class="py-name"><a title="Bio.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-21', '__version', 'link-0');">__version</a></tt> <tt class="py-op">=</tt> <tt class="py-number">3</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.Index._InMemoryIndex.__version_key
Bio.Index._ShelveIndex.__version_key" class="py-name" href="#" onclick="return doclink('link-22', '__version_key', 'link-1');">__version_key</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'__version'</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="_InMemoryIndex.__init__"></a><div id="_InMemoryIndex.__init__-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="_InMemoryIndex.__init__-toggle" onclick="return toggle('_InMemoryIndex.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-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">indexname</tt><tt class="py-op">,</tt> <tt class="py-param">truncate</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="_InMemoryIndex.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex.__init__-expanded"><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_indexname</tt> <tt class="py-op">=</tt> <tt class="py-name">indexname</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Affy.CelFile.CelScanner.__init__
Bio.Affy.CelFile.Record.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__
Bio.Align.Applications._Dialign.DialignCommandline.__init__
Bio.Align.Applications._Mafft.MafftCommandline.__init__
Bio.Align.Applications._Muscle.MuscleCommandline.__init__
Bio.Align.Applications._Prank.PrankCommandline.__init__
Bio.Align.Applications._Probcons.ProbconsCommandline.__init__
Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__
Bio.Align.Generic.Alignment.__init__
Bio.Align.MultipleSeqAlignment.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationError.__init__
Bio.Application._AbstractParameter.__init__
Bio.Application._Argument.__init__
Bio.Application._Option.__init__
Bio.Application._Switch.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.BlastpgpCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.Applications.NcbiblastformatterCommandline.__init__
Bio.Blast.Applications.NcbiblastnCommandline.__init__
Bio.Blast.Applications.NcbiblastpCommandline.__init__
Bio.Blast.Applications.NcbiblastxCommandline.__init__
Bio.Blast.Applications.NcbipsiblastCommandline.__init__
Bio.Blast.Applications.NcbirpsblastCommandline.__init__
Bio.Blast.Applications.NcbirpstblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastxCommandline.__init__
Bio.Blast.Applications.RpsBlastCommandline.__init__
Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__
Bio.Blast.Applications._BlastCommandLine.__init__
Bio.Blast.Applications._NcbibaseblastCommandline.__init__
Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__
Bio.Blast.Applications._NcbiblastCommandline.__init__
Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Compass._Scanner.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.Hetero.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.Emboss.Applications.DiffseqCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FConsenseCommandline.__init__
Bio.Emboss.Applications.FDNADistCommandline.__init__
Bio.Emboss.Applications.FDNAParsCommandline.__init__
Bio.Emboss.Applications.FNeighborCommandline.__init__
Bio.Emboss.Applications.FProtDistCommandline.__init__
Bio.Emboss.Applications.FProtParsCommandline.__init__
Bio.Emboss.Applications.FSeqBootCommandline.__init__
Bio.Emboss.Applications.FTreeDistCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.IepCommandline.__init__
Bio.Emboss.Applications.NeedleCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.SeqmatchallCommandline.__init__
Bio.Emboss.Applications.SeqretCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Applications._EmbossCommandLine.__init__
Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__
Bio.Emboss.Primer3.Primers.__init__
Bio.Emboss.Primer3.Record.__init__
Bio.Emboss.PrimerSearch.Amplifier.__init__
Bio.Emboss.PrimerSearch.InputRecord.__init__
Bio.Emboss.PrimerSearch.OutputRecord.__init__
Bio.Entrez.Parser.CorruptedXMLError.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.NotXMLError.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Entrez.Parser.ValidationError.__init__
Bio.ExPASy.Enzyme.Record.__init__
Bio.ExPASy.Prodoc.Record.__init__
Bio.ExPASy.Prodoc.Reference.__init__
Bio.ExPASy.Prosite.Record.__init__
Bio.ExPASy.ScanProsite.ContentHandler.__init__
Bio.ExPASy.ScanProsite.Parser.__init__
Bio.ExPASy.ScanProsite.Record.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__
Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__
Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__
Bio.Graphics.GenomeDiagram._Feature.Feature.__init__
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__
Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__
Bio.Graphics.GenomeDiagram._Track.Track.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__
Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__
Bio.Motif.Parsers.AlignAce.Record.__init__
Bio.Motif.Parsers.MAST.Record.__init__
Bio.Motif.Parsers.MEME.MEMEInstance.__init__
Bio.Motif.Parsers.MEME.MEMEMotif.__init__
Bio.Motif.Parsers.MEME.MEMERecord.__init__
Bio.Motif.Thresholds.ScoreDistribution.__init__
Bio.Motif._Motif.Motif.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__
Bio.Phylo.BaseTree.Clade.__init__
Bio.Phylo.BaseTree.Tree.__init__
Bio.Phylo.Newick.Clade.__init__
Bio.Phylo.Newick.Tree.__init__
Bio.Phylo.NewickIO.Parser.__init__
Bio.Phylo.NewickIO.Writer.__init__
Bio.Phylo.PAML._paml.Paml.__init__
Bio.Phylo.PAML.baseml.Baseml.__init__
Bio.Phylo.PAML.codeml.Codeml.__init__
Bio.Phylo.PAML.yn00.Yn00.__init__
Bio.Phylo.PhyloXML.Accession.__init__
Bio.Phylo.PhyloXML.Annotation.__init__
Bio.Phylo.PhyloXML.BinaryCharacters.__init__
Bio.Phylo.PhyloXML.BranchColor.__init__
Bio.Phylo.PhyloXML.Clade.__init__
Bio.Phylo.PhyloXML.CladeRelation.__init__
Bio.Phylo.PhyloXML.Confidence.__init__
Bio.Phylo.PhyloXML.Date.__init__
Bio.Phylo.PhyloXML.Distribution.__init__
Bio.Phylo.PhyloXML.DomainArchitecture.__init__
Bio.Phylo.PhyloXML.Events.__init__
Bio.Phylo.PhyloXML.Id.__init__
Bio.Phylo.PhyloXML.MolSeq.__init__
Bio.Phylo.PhyloXML.Other.__init__
Bio.Phylo.PhyloXML.Phylogeny.__init__
Bio.Phylo.PhyloXML.Phyloxml.__init__
Bio.Phylo.PhyloXML.Point.__init__
Bio.Phylo.PhyloXML.Polygon.__init__
Bio.Phylo.PhyloXML.Property.__init__
Bio.Phylo.PhyloXML.ProteinDomain.__init__
Bio.Phylo.PhyloXML.Reference.__init__
Bio.Phylo.PhyloXML.Sequence.__init__
Bio.Phylo.PhyloXML.SequenceRelation.__init__
Bio.Phylo.PhyloXML.Taxonomy.__init__
Bio.Phylo.PhyloXML.Uri.__init__
Bio.Phylo.PhyloXMLIO.Parser.__init__
Bio.Phylo.PhyloXMLIO.Writer.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.GenePop.Controller.GenePopController.__init__
Bio.PopGen.GenePop.Controller._FileIterator.__init__
Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__
Bio.PopGen.GenePop.EasyController.EasyController.__init__
Bio.PopGen.GenePop.FileParser.FileRecord.__init__
Bio.PopGen.GenePop.LargeFileParser.Record.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__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__" class="py-name" href="#" onclick="return doclink('link-23', '__init__', 'link-2');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># the index hasn't changed</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-comment"># Remove the database if truncate is true.</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">truncate</tt> <tt class="py-keyword">and</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-name">indexname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Nexus.Nodes.Chain.unlink" class="py-name" href="#" onclick="return doclink('link-24', 'unlink', 'link-3');">unlink</a></tt><tt class="py-op">(</tt><tt class="py-name">indexname</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">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-comment"># Load the database if it exists</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">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt class="py-name">indexname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt id="link-25" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-25', 'handle', 'link-25');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">indexname</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-26', 'version', 'link-9');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.Index._InMemoryIndex._toobj()=Bio.Index._InMemoryIndex-class.html#_toobj"><a title="Bio.Index._InMemoryIndex._toobj" class="py-name" href="#" onclick="return doclink('link-27', '_toobj', 'link-27');">_toobj</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-28', 'handle', 'link-25');">handle</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-29', 'readline', 'link-29');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.Seq.Seq.rstrip()=Bio.Seq.Seq-class.html#rstrip"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-30', 'rstrip', 'link-30');">rstrip</a></tt><tt class="py-op">(</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">if</tt> <tt id="link-31" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-31', 'version', 'link-9');">version</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-32', '__version', 'link-0');">__version</a></tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">(</tt><tt class="py-string">"Version %s doesn't match my version %s"</tt> \ </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-33', 'version', 'link-9');">version</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-34', '__version', 'link-0');">__version</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-35" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-35', 'handle', 'link-25');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-36', 'value', 'link-36');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-37', 'split', 'link-37');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-38', 'value', 'link-36');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Index._InMemoryIndex._toobj" class="py-name" href="#" onclick="return doclink('link-39', '_toobj', 'link-27');">_toobj</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Index._InMemoryIndex._toobj" class="py-name" href="#" onclick="return doclink('link-40', '_toobj', 'link-27');">_toobj</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-41', 'value', 'link-36');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-42', 'value', 'link-36');">value</a></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="_InMemoryIndex.update"></a><div id="_InMemoryIndex.update-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="_InMemoryIndex.update-toggle" onclick="return toggle('_InMemoryIndex.update');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html#update">update</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_InMemoryIndex.update-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex.update-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SeqIO._index._IndexedSeqFileDict.update()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#update,Method Bio.SeqRecord._RestrictedDict.update()=Bio.SeqRecord._RestrictedDict-class.html#update"><a title="Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SeqIO._index._IndexedSeqFileDict.update
Bio.SeqRecord._RestrictedDict.update" class="py-name" href="#" onclick="return doclink('link-43', 'update', 'link-43');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">)</tt> </tt>
</div><a name="_InMemoryIndex.__setitem__"></a><div id="_InMemoryIndex.__setitem__-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="_InMemoryIndex.__setitem__-toggle" onclick="return toggle('_InMemoryIndex.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html#__setitem__">__setitem__</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-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_InMemoryIndex.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex.__setitem__-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Crystal.Chain.__setitem__()=Bio.Crystal.Chain-class.html#__setitem__,Method Bio.Crystal.Crystal.__setitem__()=Bio.Crystal.Crystal-class.html#__setitem__,Method Bio.Entrez.Parser.StructureElement.__setitem__()=Bio.Entrez.Parser.StructureElement-class.html#__setitem__,Method Bio.Index._InMemoryIndex.__setitem__()=Bio.Index._InMemoryIndex-class.html#__setitem__,Method Bio.PDB.Entity.DisorderedEntityWrapper.__setitem__()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__setitem__,Method Bio.PDB.Vector'.Vector.__setitem__()=Bio.PDB.Vector%27.Vector-class.html#__setitem__,Method Bio.Phylo.PhyloXML.Events.__setitem__()=Bio.Phylo.PhyloXML.Events-class.html#__setitem__,Method Bio.Seq.MutableSeq.__setitem__()=Bio.Seq.MutableSeq-class.html#__setitem__,Method Bio.SeqIO._index._IndexedSeqFileDict.__setitem__()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#__setitem__,Method Bio.SeqRecord._RestrictedDict.__setitem__()=Bio.SeqRecord._RestrictedDict-class.html#__setitem__"><a title="Bio.Crystal.Chain.__setitem__
Bio.Crystal.Crystal.__setitem__
Bio.Entrez.Parser.StructureElement.__setitem__
Bio.Index._InMemoryIndex.__setitem__
Bio.PDB.Entity.DisorderedEntityWrapper.__setitem__
Bio.PDB.Vector'.Vector.__setitem__
Bio.Phylo.PhyloXML.Events.__setitem__
Bio.Seq.MutableSeq.__setitem__
Bio.SeqIO._index._IndexedSeqFileDict.__setitem__
Bio.SeqRecord._RestrictedDict.__setitem__" class="py-name" href="#" onclick="return doclink('link-44', '__setitem__', 'link-44');">__setitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-45" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-45', 'value', 'link-36');">value</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="_InMemoryIndex.__delitem__"></a><div id="_InMemoryIndex.__delitem__-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="_InMemoryIndex.__delitem__-toggle" onclick="return toggle('_InMemoryIndex.__delitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html#__delitem__">__delitem__</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="_InMemoryIndex.__delitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex.__delitem__-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.Crystal.Chain.__delitem__()=Bio.Crystal.Chain-class.html#__delitem__,Method Bio.Crystal.Crystal.__delitem__()=Bio.Crystal.Crystal-class.html#__delitem__,Method Bio.Index._InMemoryIndex.__delitem__()=Bio.Index._InMemoryIndex-class.html#__delitem__,Method Bio.PDB.Chain.Chain.__delitem__()=Bio.PDB.Chain.Chain-class.html#__delitem__,Method Bio.PDB.Entity.Entity.__delitem__()=Bio.PDB.Entity.Entity-class.html#__delitem__,Method Bio.Phylo.PhyloXML.Events.__delitem__()=Bio.Phylo.PhyloXML.Events-class.html#__delitem__,Method Bio.Seq.MutableSeq.__delitem__()=Bio.Seq.MutableSeq-class.html#__delitem__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__delitem__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__delitem__,Method BioSQL.BioSeqDatabase.DBServer.__delitem__()=BioSQL.BioSeqDatabase.DBServer-class.html#__delitem__"><a title="Bio.Crystal.Chain.__delitem__
Bio.Crystal.Crystal.__delitem__
Bio.Index._InMemoryIndex.__delitem__
Bio.PDB.Chain.Chain.__delitem__
Bio.PDB.Entity.Entity.__delitem__
Bio.Phylo.PhyloXML.Events.__delitem__
Bio.Seq.MutableSeq.__delitem__
BioSQL.BioSeqDatabase.BioSeqDatabase.__delitem__
BioSQL.BioSeqDatabase.DBServer.__delitem__" class="py-name" href="#" onclick="return doclink('link-46', '__delitem__', 'link-46');">__delitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">key</tt><tt class="py-op">)</tt> </tt>
</div><a name="_InMemoryIndex.clear"></a><div id="_InMemoryIndex.clear-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="_InMemoryIndex.clear-toggle" onclick="return toggle('_InMemoryIndex.clear');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html#clear">clear</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_InMemoryIndex.clear-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex.clear-expanded"><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.Crystal.Crystal.clear()=Bio.Crystal.Crystal-class.html#clear,Method Bio.Index._InMemoryIndex.clear()=Bio.Index._InMemoryIndex-class.html#clear,Method Bio.SeqIO._index._IndexedSeqFileDict.clear()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#clear"><a title="Bio.Crystal.Crystal.clear
Bio.Index._InMemoryIndex.clear
Bio.SeqIO._index._IndexedSeqFileDict.clear" class="py-name" href="#" onclick="return doclink('link-47', 'clear', 'link-47');">clear</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="_InMemoryIndex.__del__"></a><div id="_InMemoryIndex.__del__-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="_InMemoryIndex.__del__-toggle" onclick="return toggle('_InMemoryIndex.__del__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html#__del__">__del__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_InMemoryIndex.__del__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex.__del__-expanded"><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__changed</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-48', 'handle', 'link-25');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_indexname</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-49', 'handle', 'link-25');">handle</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-50', 'write', 'link-50');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.Index._InMemoryIndex._tostr()=Bio.Index._InMemoryIndex-class.html#_tostr"><a title="Bio.Index._InMemoryIndex._tostr" class="py-name" href="#" onclick="return doclink('link-51', '_tostr', 'link-51');">_tostr</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.Index._InMemoryIndex.__version
Bio.Index._ShelveIndex.__version" class="py-name" href="#" onclick="return doclink('link-52', '__version', 'link-0');">__version</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-53', 'value', 'link-36');">value</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.Phylo.PhyloXML.Events.items()=Bio.Phylo.PhyloXML.Events-class.html#items,Method Bio.SeqIO._index._IndexedSeqFileDict.items()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.Phylo.PhyloXML.Events.items
Bio.SeqIO._index._IndexedSeqFileDict.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items" class="py-name" href="#" onclick="return doclink('link-54', 'items', 'link-54');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-55" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-55', 'handle', 'link-25');">handle</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-56', 'write', 'link-50');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s %s\n"</tt> <tt class="py-op">%</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Index._InMemoryIndex._tostr" class="py-name" href="#" onclick="return doclink('link-57', '_tostr', 'link-51');">_tostr</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Index._InMemoryIndex._tostr" class="py-name" href="#" onclick="return doclink('link-58', '_tostr', 'link-51');">_tostr</a></tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-59', 'value', 'link-36');">value</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-60', 'handle', 'link-25');">handle</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-61', 'close', 'link-20');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="_InMemoryIndex._tostr"></a><div id="_InMemoryIndex._tostr-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="_InMemoryIndex._tostr-toggle" onclick="return toggle('_InMemoryIndex._tostr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html#_tostr">_tostr</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_InMemoryIndex._tostr-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex._tostr-expanded"><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment"># I need a representation of the object that's saveable to</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment"># a file that uses whitespace as delimiters. Thus, I'm</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment"># going to pickle the object, and then convert each character of</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-comment"># the string to its ASCII integer value. Then, I'm going to convert</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-comment"># the integers into strings and join them together with commas. </tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-comment"># It's not the most efficient way of storing things, but it's</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-comment"># relatively fast.</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">cPickle</tt><tt class="py-op">.</tt><tt class="py-name">dumps</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">intlist</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt> <tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">strlist</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">intlist</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">','</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">strlist</tt><tt class="py-op">)</tt> </tt>
</div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="_InMemoryIndex._toobj"></a><div id="_InMemoryIndex._toobj-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="_InMemoryIndex._toobj-toggle" onclick="return toggle('_InMemoryIndex._toobj');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Index._InMemoryIndex-class.html#_toobj">_toobj</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_InMemoryIndex._toobj-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_InMemoryIndex._toobj-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">intlist</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-62', 'split', 'link-37');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">','</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">intlist</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt> <tt class="py-name">intlist</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">strlist</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">chr</tt><tt class="py-op">,</tt> <tt class="py-name">intlist</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cPickle</tt><tt class="py-op">.</tt><tt class="py-name">loads</tt><tt class="py-op">(</tt><tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">strlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt id="link-63" class="py-name" targets="Module Bio.Index=Bio.Index-module.html,Class Bio.SCOP.Cla.Index=Bio.SCOP.Cla.Index-class.html"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-63', 'Index', 'link-63');">Index</a></tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name" targets="Class Bio.Index._InMemoryIndex=Bio.Index._InMemoryIndex-class.html"><a title="Bio.Index._InMemoryIndex" class="py-name" href="#" onclick="return doclink('link-64', '_InMemoryIndex', 'link-64');">_InMemoryIndex</a></tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Thu Aug 18 18:22:59 2011
</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. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
