Sophie: biopython-doc-1.47-2mdv2008.1 x86

biopython-doc-1.47-2mdv2008.1.x86_64.rpm

<?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.Mindy.FlatDB</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>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</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&nbsp;Bio</a> ::
        <a href="Bio.Mindy-module.html">Package&nbsp;Mindy</a> ::
        Module&nbsp;FlatDB
      </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&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="Bio.Mindy.FlatDB-pysrc.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Mindy.FlatDB-module.html">Module Bio.Mindy.FlatDB</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">bisect</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.Mindy.BaseDB=Bio.Mindy.BaseDB-module.html"><a title="Bio.Mindy.BaseDB" class="py-name" href="#" onclick="return doclink('link-0', 'BaseDB', 'link-0');">BaseDB</a></tt><tt class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Class Bio.GFF.easy.Location=Bio.GFF.easy.Location-class.html,Module Bio.Mindy.Location=Bio.Mindy.Location-module.html,Class Bio.Mindy.Location.Location=Bio.Mindy.Location.Location-class.html"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-1', 'Location', 'link-1');">Location</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-2');">Bio</a></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 id="link-3" class="py-name" targets="Function Bio.Entrez._open()=Bio.Entrez-module.html#_open,Function Bio.Mindy.BerkeleyDB._open()=Bio.Mindy.BerkeleyDB-module.html#_open,Function Bio.SCOP._open()=Bio.SCOP-module.html#_open,Function Bio.WWW.ExPASy._open()=Bio.WWW.ExPASy-module.html#_open,Function Bio.WWW.NCBI._open()=Bio.WWW.NCBI-module.html#_open"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-3', '_open', 'link-3');">_open</a></tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-4', 'open', 'link-4');">open</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable Bio.Mindy.BerkeleyDB.INDEX_TYPE=Bio.Mindy.BerkeleyDB-module.html#INDEX_TYPE,Variable Bio.Mindy.FlatDB.INDEX_TYPE=Bio.Mindy.FlatDB-module.html#INDEX_TYPE"><a title="Bio.Mindy.BerkeleyDB.INDEX_TYPE
Bio.Mindy.FlatDB.INDEX_TYPE" class="py-name" href="#" onclick="return doclink('link-5', 'INDEX_TYPE', 'link-5');">INDEX_TYPE</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"flat/1"</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"> </tt>
<a name="_parse_primary_table_entry"></a><div id="_parse_primary_table_entry-def"><a name="L9"></a><tt class="py-lineno">  9</tt> <a class="py-toggle" href="#" id="_parse_primary_table_entry-toggle" onclick="return toggle('_parse_primary_table_entry');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_parse_primary_table_entry">_parse_primary_table_entry</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse_primary_table_entry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse_primary_table_entry-expanded"><a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line">    <tt id="link-6" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-6', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">filetag</tt><tt class="py-op">,</tt> <tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-7', 'length', 'link-7');">length</a></tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-8', 's', 'link-8');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-9', 'split', 'link-9');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">filetag</tt><tt class="py-op">,</tt> <tt class="py-name">long</tt><tt class="py-op">(</tt><tt class="py-name">startpos</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">long</tt><tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-11', 'length', 'link-7');">length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"> </tt>
<a name="_read_primary_table"></a><div id="_read_primary_table-def"><a name="L13"></a><tt class="py-lineno"> 13</tt> <a class="py-toggle" href="#" id="_read_primary_table-toggle" onclick="return toggle('_read_primary_table');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_read_primary_table">_read_primary_table</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_read_primary_table-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_read_primary_table-expanded"><a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line">    <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-12', '_open', 'link-3');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">    <tt id="link-13" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-13', 'size', 'link-13');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-14', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt id="link-15" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-15', 'table', 'link-15');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">        <tt id="link-16" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-16', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-17', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-18', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-19" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-19', 's', 'link-8');">s</a></tt><tt class="py-op">:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">            <tt class="py-keyword">break</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-20', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-21" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-21', 'size', 'link-13');">size</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-22', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-23', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">        <tt id="link-24" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-24', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">filetag</tt><tt class="py-op">,</tt> <tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt id="link-25" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-25', 'length', 'link-7');">length</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name" targets="Function Bio.Mindy.FlatDB._parse_primary_table_entry()=Bio.Mindy.FlatDB-module.html#_parse_primary_table_entry"><a title="Bio.Mindy.FlatDB._parse_primary_table_entry" class="py-name" href="#" onclick="return doclink('link-26', '_parse_primary_table_entry', 'link-26');">_parse_primary_table_entry</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-27', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">        <tt id="link-28" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-28', 'table', 'link-15');">table</a></tt><tt class="py-op">[</tt><tt id="link-29" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-29', 'name', 'link-6');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">filetag</tt><tt class="py-op">,</tt> <tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt id="link-30" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-30', 'length', 'link-7');">length</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-31" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-31', 'table', 'link-15');">table</a></tt> </tt>
</div><a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"> </tt>
<a name="_write_primary_table"></a><div id="_write_primary_table-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="_write_primary_table-toggle" onclick="return toggle('_write_primary_table');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_write_primary_table">_write_primary_table</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">primary_table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_write_primary_table-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_write_primary_table-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">    <tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt class="py-name">primary_table</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-32', 'items', 'link-32');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-name">info</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-33', 'sort', 'link-33');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-34', 'v', 'link-34');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">info</tt><tt class="py-op">:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-comment"># Find the longest width</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt id="link-35" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-35', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s\t%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-36', 'v', 'link-34');">v</a></tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-37', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">            <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-38', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">9999</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">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">                    <tt class="py-string">"Primary index record too large for format spec! "</tt> <tt class="py-op">+</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">                    <tt class="py-string">" %s bytes in %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-39', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-40', '_open', 'link-3');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"wb"</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-41', 'write', 'link-41');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%04d"</tt> <tt class="py-op">%</tt> <tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-42', 'v', 'link-34');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">info</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">        <tt id="link-43" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-43', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s\t%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-44', 'v', 'link-34');">v</a></tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-45', 'write', 'link-41');">write</a></tt><tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-46', 's', 'link-8');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-47', 'close', 'link-47');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"> </tt>
<a name="_parse_secondary_table_entry"></a><div id="_parse_secondary_table_entry-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="_parse_secondary_table_entry-toggle" onclick="return toggle('_parse_secondary_table_entry');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_parse_secondary_table_entry">_parse_secondary_table_entry</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse_secondary_table_entry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse_secondary_table_entry-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-48" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-48', 's', 'link-8');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-49', 'split', 'link-9');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"> </tt>
<a name="_read_secondary_table"></a><div id="_read_secondary_table-def"><a name="L49"></a><tt class="py-lineno"> 49</tt> <a class="py-toggle" href="#" id="_read_secondary_table-toggle" onclick="return toggle('_read_secondary_table');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_read_secondary_table">_read_secondary_table</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_read_secondary_table-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_read_secondary_table-expanded"><a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-50', '_open', 'link-3');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt id="link-51" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-51', 'size', 'link-13');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-52', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">    <tt id="link-53" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-53', 'table', 'link-15');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">        <tt id="link-54" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-54', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-55', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-56', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-57" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-57', 's', 'link-8');">s</a></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">break</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-58', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-59" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-59', 'size', 'link-13');">size</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-60', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-61', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">        <tt class="py-name">alias</tt><tt class="py-op">,</tt> <tt id="link-62" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-62', 'name', 'link-6');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name" targets="Function Bio.Mindy.FlatDB._parse_secondary_table_entry()=Bio.Mindy.FlatDB-module.html#_parse_secondary_table_entry"><a title="Bio.Mindy.FlatDB._parse_secondary_table_entry" class="py-name" href="#" onclick="return doclink('link-63', '_parse_secondary_table_entry', 'link-63');">_parse_secondary_table_entry</a></tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-64', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">        <tt id="link-65" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-65', 'table', 'link-15');">table</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Method Bio.Crystal.Crystal.setdefault()=Bio.Crystal.Crystal-class.html#setdefault"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-66', 'setdefault', 'link-66');">setdefault</a></tt><tt class="py-op">(</tt><tt class="py-name">alias</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-67', 'append', 'link-67');">append</a></tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-68', 'name', 'link-6');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-69', 'close', 'link-47');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-70" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-70', 'table', 'link-15');">table</a></tt> </tt>
</div><a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"> </tt>
<a name="_write_secondary_table"></a><div id="_write_secondary_table-def"><a name="L63"></a><tt class="py-lineno"> 63</tt> <a class="py-toggle" href="#" id="_write_secondary_table-toggle" onclick="return toggle('_write_secondary_table');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_write_secondary_table">_write_secondary_table</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_write_secondary_table-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_write_secondary_table-expanded"><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">    <tt id="link-71" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-71', 'items', 'link-32');">items</a></tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-72', 'table', 'link-15');">table</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-73', 'items', 'link-32');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-74', 'items', 'link-32');">items</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-75', 'sort', 'link-33');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-comment"># Find the largest field</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-76" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-76', 'v', 'link-34');">v</a></tt> <tt class="py-keyword">in</tt> <tt id="link-77" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-77', 'items', 'link-32');">items</a></tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-78" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-78', 'x', 'link-78');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-79" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-79', 'v', 'link-34');">v</a></tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">            <tt id="link-80" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-80', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s\t%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-81', 'x', 'link-78');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-82', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">                <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-83', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">9999</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">                    <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">               <tt class="py-string">"Secondary index record too large for format spec! "</tt> <tt class="py-op">+</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">               <tt class="py-string">" %s bytes in %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt id="link-84" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-84', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt class="py-comment"># And write the output</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt id="link-85" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-85', '_open', 'link-3');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"wb"</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-86', 'write', 'link-41');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%04d"</tt> <tt class="py-op">%</tt> <tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-87" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-87', 'v', 'link-34');">v</a></tt> <tt class="py-keyword">in</tt> <tt id="link-88" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-88', 'items', 'link-32');">items</a></tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-89" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-89', 'x', 'link-78');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-90" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-90', 'v', 'link-34');">v</a></tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">            <tt id="link-91" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-91', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s\t%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-92" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-92', 'x', 'link-78');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">            <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-93', 'write', 'link-41');">write</a></tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-94', 's', 'link-8');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">ljust</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-95', 'close', 'link-47');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"> </tt>
<a name="BaseFlatDB"></a><div id="BaseFlatDB-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="BaseFlatDB-toggle" onclick="return toggle('BaseFlatDB');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.BaseFlatDB-class.html">BaseFlatDB</a><tt class="py-op">(</tt><tt class="py-base-class">BaseDB</tt><tt class="py-op">.</tt><tt class="py-base-class">OpenDB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BaseFlatDB-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BaseFlatDB-expanded"><a name="BaseFlatDB.__init__"></a><div id="BaseFlatDB.__init__-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="BaseFlatDB.__init__-toggle" onclick="return toggle('BaseFlatDB.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.BaseFlatDB-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">dbname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BaseFlatDB.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BaseFlatDB.__init__-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt id="link-96" class="py-name"><a title="Bio.Mindy.BaseDB" class="py-name" href="#" onclick="return doclink('link-96', 'BaseDB', 'link-0');">BaseDB</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name" targets="Class Bio.Mindy.BaseDB.OpenDB=Bio.Mindy.BaseDB.OpenDB-class.html"><a title="Bio.Mindy.BaseDB.OpenDB" class="py-name" href="#" onclick="return doclink('link-97', 'OpenDB', 'link-97');">OpenDB</a></tt><tt class="py-op">.</tt><tt id="link-98" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-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.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-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.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-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.CDD.Iterator.__init__()=Bio.CDD.Iterator-class.html#__init__,Method Bio.CDD.Record.Record.__init__()=Bio.CDD.Record.Record-class.html#__init__,Method Bio.CDD.RecordParser.__init__()=Bio.CDD.RecordParser-class.html#__init__,Method Bio.CDD._RecordConsumer.__init__()=Bio.CDD._RecordConsumer-class.html#__init__,Method Bio.CDD._Scanner.__init__()=Bio.CDD._Scanner-class.html#__init__,Method Bio.Clustalw.ClustalAlignment.__init__()=Bio.Clustalw.ClustalAlignment-class.html#__init__,Method Bio.Clustalw.MultipleAlignCL.__init__()=Bio.Clustalw.MultipleAlignCL-class.html#__init__,Method Bio.Cluster.DataFile.__init__()=Bio.Cluster.DataFile-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.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.CrystalError.__init__()=Bio.Crystal.CrystalError-class.html#__init__,Method Bio.Crystal.Error.__init__()=Bio.Crystal.Error-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.DBXRef.DBXRef.__init__()=Bio.DBXRef.DBXRef-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.Decode.DecodeParser.__init__()=Bio.Decode.DecodeParser-class.html#__init__,Method Bio.Decode.DecodeScanner.__init__()=Bio.Decode.DecodeScanner-class.html#__init__,Method Bio.Decode.Float.__init__()=Bio.Decode.Float-class.html#__init__,Method Bio.Decode.Function.__init__()=Bio.Decode.Function-class.html#__init__,Method Bio.Decode.FunctionCall.__init__()=Bio.Decode.FunctionCall-class.html#__init__,Method Bio.Decode.FunctionCallChain.__init__()=Bio.Decode.FunctionCallChain-class.html#__init__,Method Bio.Decode.FunctionName.__init__()=Bio.Decode.FunctionName-class.html#__init__,Method Bio.Decode.Integer.__init__()=Bio.Decode.Integer-class.html#__init__,Method Bio.Decode.String.__init__()=Bio.Decode.String-class.html#__init__,Method Bio.Decode.Token.__init__()=Bio.Decode.Token-class.html#__init__,Method Bio.Decode.ValueToken.__init__()=Bio.Decode.ValueToken-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.ECell.ECellError.__init__()=Bio.ECell.ECellError-class.html#__init__,Method Bio.ECell.Error.__init__()=Bio.ECell.Error-class.html#__init__,Method Bio.ECell.Iterator.__init__()=Bio.ECell.Iterator-class.html#__init__,Method Bio.ECell.Record.Record.__init__()=Bio.ECell.Record.Record-class.html#__init__,Method Bio.ECell.RecordParser.__init__()=Bio.ECell.RecordParser-class.html#__init__,Method Bio.ECell._RecordConsumer.__init__()=Bio.ECell._RecordConsumer-class.html#__init__,Method Bio.ECell._Scanner.__init__()=Bio.ECell._Scanner-class.html#__init__,Method Bio.EUtils.Config.DatabaseInfo.__init__()=Bio.EUtils.Config.DatabaseInfo-class.html#__init__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsClient.__init__()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsLookup.__init__()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#__init__,Method Bio.EUtils.Datatypes.BinaryOp.__init__()=Bio.EUtils.Datatypes.BinaryOp-class.html#__init__,Method Bio.EUtils.Datatypes.CheckLinkSet.__init__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.DBIds.__init__()=Bio.EUtils.Datatypes.DBIds-class.html#__init__,Method Bio.EUtils.Datatypes.Date.__init__()=Bio.EUtils.Datatypes.Date-class.html#__init__,Method Bio.EUtils.Datatypes.DateRange.__init__()=Bio.EUtils.Datatypes.DateRange-class.html#__init__,Method Bio.EUtils.Datatypes.EUtilsSearchError.__init__()=Bio.EUtils.Datatypes.EUtilsSearchError-class.html#__init__,Method Bio.EUtils.Datatypes.IdCheck.__init__()=Bio.EUtils.Datatypes.IdCheck-class.html#__init__,Method Bio.EUtils.Datatypes.IdUrlSet.__init__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__init__,Method Bio.EUtils.Datatypes.Link.__init__()=Bio.EUtils.Datatypes.Link-class.html#__init__,Method Bio.EUtils.Datatypes.LinkSetDb.__init__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__init__,Method Bio.EUtils.Datatypes.LinksLinkSet.__init__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__init__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.ObjUrl.__init__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__init__,Method Bio.EUtils.Datatypes.PostResult.__init__()=Bio.EUtils.Datatypes.PostResult-class.html#__init__,Method Bio.EUtils.Datatypes.Problem.__init__()=Bio.EUtils.Datatypes.Problem-class.html#__init__,Method Bio.EUtils.Datatypes.Provider.__init__()=Bio.EUtils.Datatypes.Provider-class.html#__init__,Method Bio.EUtils.Datatypes.Range.__init__()=Bio.EUtils.Datatypes.Range-class.html#__init__,Method Bio.EUtils.Datatypes.SearchResult.__init__()=Bio.EUtils.Datatypes.SearchResult-class.html#__init__,Method Bio.EUtils.Datatypes.Summary.__init__()=Bio.EUtils.Datatypes.Summary-class.html#__init__,Method Bio.EUtils.Datatypes.Term.__init__()=Bio.EUtils.Datatypes.Term-class.html#__init__,Method Bio.EUtils.Datatypes.WithinNDays.__init__()=Bio.EUtils.Datatypes.WithinNDays-class.html#__init__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryClient.__init__()=Bio.EUtils.HistoryClient.HistoryClient-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryCookie.__init__()=Bio.EUtils.HistoryClient.HistoryCookie-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryLookup.__init__()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryRecord.__init__()=Bio.EUtils.HistoryClient.HistoryRecord-class.html#__init__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__init__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__init__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__init__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__init__,Method Bio.EUtils.POM.Comment.__init__()=Bio.EUtils.POM.Comment-class.html#__init__,Method Bio.EUtils.POM.ContentModel.__init__()=Bio.EUtils.POM.ContentModel-class.html#__init__,Method Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__()=Bio.EUtils.POM.DTDConsumerForSourceGeneration-class.html#__init__,Method Bio.EUtils.POM.ElementNode.__init__()=Bio.EUtils.POM.ElementNode-class.html#__init__,Method Bio.EUtils.POM.IndentedText.__init__()=Bio.EUtils.POM.IndentedText-class.html#__init__,Method Bio.EUtils.POM.ObjectParserHandler.__init__()=Bio.EUtils.POM.ObjectParserHandler-class.html#__init__,Method Bio.EUtils.POM.POMDocument.__init__()=Bio.EUtils.POM.POMDocument-class.html#__init__,Method Bio.EUtils.POM.XMLAttribute.__init__()=Bio.EUtils.POM.XMLAttribute-class.html#__init__,Method Bio.EUtils.POM._ContentModelGenerator.__init__()=Bio.EUtils.POM._ContentModelGenerator-class.html#__init__,Method Bio.EUtils.ReseekFile.ReseekFile.__init__()=Bio.EUtils.ReseekFile.ReseekFile-class.html#__init__,Method Bio.EUtils.ThinClient.ThinClient.__init__()=Bio.EUtils.ThinClient.ThinClient-class.html#__init__,Method Bio.EUtils.parse.UsePOMParser.__init__()=Bio.EUtils.parse.UsePOMParser-class.html#__init__,Method Bio.EUtils.sourcegen.ClassHolder.__init__()=Bio.EUtils.sourcegen.ClassHolder-class.html#__init__,Method Bio.EUtils.sourcegen.FunctionHolder.__init__()=Bio.EUtils.sourcegen.FunctionHolder-class.html#__init__,Method Bio.EUtils.sourcegen.MethodHolder.__init__()=Bio.EUtils.sourcegen.MethodHolder-class.html#__init__,Method Bio.EUtils.sourcegen.SourceFile.__init__()=Bio.EUtils.sourcegen.SourceFile-class.html#__init__,Method Bio.EUtils.sourcegen.SourceGen.__init__()=Bio.EUtils.sourcegen.SourceGen-class.html#__init__,Method Bio.Emboss.Applications.EConsenseCommandline.__init__()=Bio.Emboss.Applications.EConsenseCommandline-class.html#__init__,Method Bio.Emboss.Applications.EInvertedCommandline.__init__()=Bio.Emboss.Applications.EInvertedCommandline-class.html#__init__,Method Bio.Emboss.Applications.ENeighborCommandline.__init__()=Bio.Emboss.Applications.ENeighborCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtDistCommandline.__init__()=Bio.Emboss.Applications.EProtDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtParsCommandline.__init__()=Bio.Emboss.Applications.EProtParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.ESeqBootCommandline.__init__()=Bio.Emboss.Applications.ESeqBootCommandline-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.FuzznucCommandline.__init__()=Bio.Emboss.Applications.FuzznucCommandline-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.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.Primer.Primer3Parser.__init__()=Bio.Emboss.Primer.Primer3Parser-class.html#__init__,Method Bio.Emboss.Primer.Primer3Primers.__init__()=Bio.Emboss.Primer.Primer3Primers-class.html#__init__,Method Bio.Emboss.Primer.Primer3Record.__init__()=Bio.Emboss.Primer.Primer3Record-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchAmplifier.__init__()=Bio.Emboss.Primer.PrimerSearchAmplifier-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchInputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchInputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchParser.__init__()=Bio.Emboss.Primer.PrimerSearchParser-class.html#__init__,Method Bio.Emboss.Primer._Primer3RecordConsumer.__init__()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#__init__,Method Bio.Emboss.Primer._Primer3Scanner.__init__()=Bio.Emboss.Primer._Primer3Scanner-class.html#__init__,Method Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#__init__,Method Bio.Emboss.Primer._PrimerSearchScanner.__init__()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#__init__,Method Bio.Entrez.Parser.DataHandler.__init__()=Bio.Entrez.Parser.DataHandler-class.html#__init__,Method Bio.Entrez.Parser.StructureElement.__init__()=Bio.Entrez.Parser.StructureElement-class.html#__init__,Method Bio.Enzyme.DataRecord.__init__()=Bio.Enzyme.DataRecord-class.html#__init__,Method Bio.Enzyme.EnzymeRecord.__init__()=Bio.Enzyme.EnzymeRecord-class.html#__init__,Method Bio.Enzyme.Iterator.__init__()=Bio.Enzyme.Iterator-class.html#__init__,Method Bio.Enzyme.RecordParser.__init__()=Bio.Enzyme.RecordParser-class.html#__init__,Method Bio.Enzyme._RecordConsumer.__init__()=Bio.Enzyme._RecordConsumer-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.Fasta.FastaAlign.FastaAlignment.__init__()=Bio.Fasta.FastaAlign.FastaAlignment-class.html#__init__,Method Bio.Fasta.Iterator.__init__()=Bio.Fasta.Iterator-class.html#__init__,Method Bio.Fasta.Record.__init__()=Bio.Fasta.Record-class.html#__init__,Method Bio.Fasta.RecordParser.__init__()=Bio.Fasta.RecordParser-class.html#__init__,Method Bio.Fasta.SequenceParser.__init__()=Bio.Fasta.SequenceParser-class.html#__init__,Method Bio.File.SGMLHandle.__init__()=Bio.File.SGMLHandle-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.FilteredReader.FilteredReader.__init__()=Bio.FilteredReader.FilteredReader-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.GFF.Connection.__init__()=Bio.GFF.Connection-class.html#__init__,Method Bio.GFF.Feature.__init__()=Bio.GFF.Feature-class.html#__init__,Method Bio.GFF.FeatureAggregate.__init__()=Bio.GFF.FeatureAggregate-class.html#__init__,Method Bio.GFF.FeatureQuery.__init__()=Bio.GFF.FeatureQuery-class.html#__init__,Method Bio.GFF.FeatureQueryRow.__init__()=Bio.GFF.FeatureQueryRow-class.html#__init__,Method Bio.GFF.GenericTools.ArgsParser.__init__()=Bio.GFF.GenericTools.ArgsParser-class.html#__init__,Method Bio.GFF.GenericTools.Surrogate.__init__()=Bio.GFF.GenericTools.Surrogate-class.html#__init__,Method Bio.GFF.GenericTools.TempFile.__init__()=Bio.GFF.GenericTools.TempFile-class.html#__init__,Method Bio.GFF.RetrieveSeqname.__init__()=Bio.GFF.RetrieveSeqname-class.html#__init__,Method Bio.GFF.Segment.__init__()=Bio.GFF.Segment-class.html#__init__,Method Bio.GFF.easy.FeatureDict.__init__()=Bio.GFF.easy.FeatureDict-class.html#__init__,Method Bio.GFF.easy.Location.__init__()=Bio.GFF.easy.Location-class.html#__init__,Method Bio.GFF.easy.LocationFromCoords.__init__()=Bio.GFF.easy.LocationFromCoords-class.html#__init__,Method Bio.GFF.easy.LocationFromString.__init__()=Bio.GFF.easy.LocationFromString-class.html#__init__,Method Bio.GFF.easy.LocationJoin.__init__()=Bio.GFF.easy.LocationJoin-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.NCBIDictionary.__init__()=Bio.GenBank.NCBIDictionary-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.Gobase.Dictionary.__init__()=Bio.Gobase.Dictionary-class.html#__init__,Method Bio.Gobase.GeneRecord.__init__()=Bio.Gobase.GeneRecord-class.html#__init__,Method Bio.Gobase.Iterator.__init__()=Bio.Gobase.Iterator-class.html#__init__,Method Bio.Gobase.ProteinRecord.__init__()=Bio.Gobase.ProteinRecord-class.html#__init__,Method Bio.Gobase.Record.__init__()=Bio.Gobase.Record-class.html#__init__,Method Bio.Gobase.RecordParser.__init__()=Bio.Gobase.RecordParser-class.html#__init__,Method Bio.Gobase.SequenceRecord.__init__()=Bio.Gobase.SequenceRecord-class.html#__init__,Method Bio.Gobase._RecordConsumer.__init__()=Bio.Gobase._RecordConsumer-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.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.IntelliGenetics.IntelliGeneticsReader.__init__()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#__init__,Method Bio.IntelliGenetics.Iterator.__init__()=Bio.IntelliGenetics.Iterator-class.html#__init__,Method Bio.IntelliGenetics.Record.Record.__init__()=Bio.IntelliGenetics.Record.Record-class.html#__init__,Method Bio.IntelliGenetics.RecordParser.__init__()=Bio.IntelliGenetics.RecordParser-class.html#__init__,Method Bio.IntelliGenetics._RecordConsumer.__init__()=Bio.IntelliGenetics._RecordConsumer-class.html#__init__,Method Bio.IntelliGenetics._Scanner.__init__()=Bio.IntelliGenetics._Scanner-class.html#__init__,Method Bio.KDTree.CKDTree.KDTree.__init__()=Bio.KDTree.CKDTree.KDTree-class.html#__init__,Method Bio.KDTree.CKDTree.KDTreePtr.__init__()=Bio.KDTree.CKDTree.KDTreePtr-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.LocusLink.Iterator.__init__()=Bio.LocusLink.Iterator-class.html#__init__,Method Bio.LocusLink.Record.__init__()=Bio.LocusLink.Record-class.html#__init__,Method Bio.LocusLink.RecordParser.__init__()=Bio.LocusLink.RecordParser-class.html#__init__,Method Bio.LocusLink._RecordConsumer.__init__()=Bio.LocusLink._RecordConsumer-class.html#__init__,Method Bio.LocusLink._Scanner.__init__()=Bio.LocusLink._Scanner-class.html#__init__,Method Bio.LocusLink.web_parse.Record.__init__()=Bio.LocusLink.web_parse.Record-class.html#__init__,Method Bio.LocusLink.web_parse.Token.__init__()=Bio.LocusLink.web_parse.Token-class.html#__init__,Method Bio.LocusLink.web_parse.Url.__init__()=Bio.LocusLink.web_parse.Url-class.html#__init__,Method Bio.LogisticRegression.LogisticRegression.__init__()=Bio.LogisticRegression.LogisticRegression-class.html#__init__,Method Bio.MEME.Motif.Instance.__init__()=Bio.MEME.Motif.Instance-class.html#__init__,Method Bio.MEME.Motif.MEMEMotif.__init__()=Bio.MEME.Motif.MEMEMotif-class.html#__init__,Method Bio.MEME.Motif.Motif.__init__()=Bio.MEME.Motif.Motif-class.html#__init__,Method Bio.MEME.Parser.MASTParser.__init__()=Bio.MEME.Parser.MASTParser-class.html#__init__,Method Bio.MEME.Parser.MASTRecord.__init__()=Bio.MEME.Parser.MASTRecord-class.html#__init__,Method Bio.MEME.Parser.MEMEParser.__init__()=Bio.MEME.Parser.MEMEParser-class.html#__init__,Method Bio.MEME.Parser.MEMERecord.__init__()=Bio.MEME.Parser.MEMERecord-class.html#__init__,Method Bio.MEME.Parser._MASTConsumer.__init__()=Bio.MEME.Parser._MASTConsumer-class.html#__init__,Method Bio.MEME.Parser._MEMEConsumer.__init__()=Bio.MEME.Parser._MEMEConsumer-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.Medline.Iterator.__init__()=Bio.Medline.Iterator-class.html#__init__,Method Bio.Medline.Record.__init__()=Bio.Medline.Record-class.html#__init__,Method Bio.Medline.RecordParser.__init__()=Bio.Medline.RecordParser-class.html#__init__,Method Bio.Medline._RecordConsumer.__init__()=Bio.Medline._RecordConsumer-class.html#__init__,Method Bio.MetaTool.Iterator.__init__()=Bio.MetaTool.Iterator-class.html#__init__,Method Bio.MetaTool.Record.Metabolite.__init__()=Bio.MetaTool.Record.Metabolite-class.html#__init__,Method Bio.MetaTool.Record.MetaboliteRole.__init__()=Bio.MetaTool.Record.MetaboliteRole-class.html#__init__,Method Bio.MetaTool.Record.PathwayTransform.__init__()=Bio.MetaTool.Record.PathwayTransform-class.html#__init__,Method Bio.MetaTool.Record.Record.__init__()=Bio.MetaTool.Record.Record-class.html#__init__,Method Bio.MetaTool.RecordParser.__init__()=Bio.MetaTool.RecordParser-class.html#__init__,Method Bio.MetaTool._RecordConsumer.__init__()=Bio.MetaTool._RecordConsumer-class.html#__init__,Method Bio.MetaTool._Scanner.__init__()=Bio.MetaTool._Scanner-class.html#__init__,Method Bio.Mindy.BaseDB.OpenDB.__init__()=Bio.Mindy.BaseDB.OpenDB-class.html#__init__,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#__init__,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#__init__,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.BaseFlatDB.__init__()=Bio.Mindy.FlatDB.BaseFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.BisectFile.__init__()=Bio.Mindy.FlatDB.BisectFile-class.html#__init__,Method Bio.Mindy.FlatDB.DiskFlatDB.__init__()=Bio.Mindy.FlatDB.DiskFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.MemoryFlatDB.__init__()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.PrimaryNamespace.__init__()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.PrimaryTable.__init__()=Bio.Mindy.FlatDB.PrimaryTable-class.html#__init__,Method Bio.Mindy.FlatDB.SecondaryNamespace.__init__()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.SecondaryTable.__init__()=Bio.Mindy.FlatDB.SecondaryTable-class.html#__init__,Method Bio.Mindy.Location.Location.__init__()=Bio.Mindy.Location.Location-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__()=Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.FunctionIndexer-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.SimpleIndexer-class.html#__init__,Method Bio.Mindy.XPath.GrabXPathNodes.__init__()=Bio.Mindy.XPath.GrabXPathNodes-class.html#__init__,Method Bio.NBRF.Iterator.__init__()=Bio.NBRF.Iterator-class.html#__init__,Method Bio.NBRF.Record.Record.__init__()=Bio.NBRF.Record.Record-class.html#__init__,Method Bio.NBRF.RecordParser.__init__()=Bio.NBRF.RecordParser-class.html#__init__,Method Bio.NBRF._RecordConsumer.__init__()=Bio.NBRF._RecordConsumer-class.html#__init__,Method Bio.NBRF._Scanner.__init__()=Bio.NBRF._Scanner-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.Ndb.Record.__init__()=Bio.Ndb.Record-class.html#__init__,Method Bio.NetCatch.ExtractUrls.__init__()=Bio.NetCatch.ExtractUrls-class.html#__init__,Method Bio.NetCatch.NetCatch.__init__()=Bio.NetCatch.NetCatch-class.html#__init__,Method Bio.NetCatch.Url.__init__()=Bio.NetCatch.Url-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.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.FDist.RecordParser.__init__()=Bio.PopGen.FDist.RecordParser-class.html#__init__,Method Bio.PopGen.FDist._RecordConsumer.__init__()=Bio.PopGen.FDist._RecordConsumer-class.html#__init__,Method Bio.PopGen.GenePop.Record.__init__()=Bio.PopGen.GenePop.Record-class.html#__init__,Method Bio.PopGen.GenePop.RecordParser.__init__()=Bio.PopGen.GenePop.RecordParser-class.html#__init__,Method Bio.PopGen.GenePop._RecordConsumer.__init__()=Bio.PopGen.GenePop._RecordConsumer-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.PropertyManager.PropertyManager.__init__()=Bio.PropertyManager.PropertyManager-class.html#__init__,Method Bio.Prosite.Dictionary.__init__()=Bio.Prosite.Dictionary-class.html#__init__,Method Bio.Prosite.ExPASyDictionary.__init__()=Bio.Prosite.ExPASyDictionary-class.html#__init__,Method Bio.Prosite.Iterator.__init__()=Bio.Prosite.Iterator-class.html#__init__,Method Bio.Prosite.Pattern.Prosite.__init__()=Bio.Prosite.Pattern.Prosite-class.html#__init__,Method Bio.Prosite.Pattern.PrositeMatch.__init__()=Bio.Prosite.Pattern.PrositeMatch-class.html#__init__,Method Bio.Prosite.Pattern.PrositeTerm.__init__()=Bio.Prosite.Pattern.PrositeTerm-class.html#__init__,Method Bio.Prosite.PatternHit.__init__()=Bio.Prosite.PatternHit-class.html#__init__,Method Bio.Prosite.Prodoc.Dictionary.__init__()=Bio.Prosite.Prodoc.Dictionary-class.html#__init__,Method Bio.Prosite.Prodoc.ExPASyDictionary.__init__()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__init__,Method Bio.Prosite.Prodoc.Iterator.__init__()=Bio.Prosite.Prodoc.Iterator-class.html#__init__,Method Bio.Prosite.Prodoc.Record.__init__()=Bio.Prosite.Prodoc.Record-class.html#__init__,Method Bio.Prosite.Prodoc.RecordParser.__init__()=Bio.Prosite.Prodoc.RecordParser-class.html#__init__,Method Bio.Prosite.Prodoc.Reference.__init__()=Bio.Prosite.Prodoc.Reference-class.html#__init__,Method Bio.Prosite.Prodoc._RecordConsumer.__init__()=Bio.Prosite.Prodoc._RecordConsumer-class.html#__init__,Method Bio.Prosite.Record.__init__()=Bio.Prosite.Record-class.html#__init__,Method Bio.Prosite.RecordParser.__init__()=Bio.Prosite.RecordParser-class.html#__init__,Method Bio.Prosite._RecordConsumer.__init__()=Bio.Prosite._RecordConsumer-class.html#__init__,Method Bio.PubMed.Dictionary.__init__()=Bio.PubMed.Dictionary-class.html#__init__,Method Bio.Rebase.Dictionary.__init__()=Bio.Rebase.Dictionary-class.html#__init__,Method Bio.Rebase.Iterator.__init__()=Bio.Rebase.Iterator-class.html#__init__,Method Bio.Rebase.Record.__init__()=Bio.Rebase.Record-class.html#__init__,Method Bio.Rebase.RecordParser.__init__()=Bio.Rebase.RecordParser-class.html#__init__,Method Bio.Rebase._RecordConsumer.__init__()=Bio.Rebase._RecordConsumer-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.Iterator.__init__()=Bio.SCOP.Cla.Iterator-class.html#__init__,Method Bio.SCOP.Cla.Parser.__init__()=Bio.SCOP.Cla.Parser-class.html#__init__,Method Bio.SCOP.Cla.Record.__init__()=Bio.SCOP.Cla.Record-class.html#__init__,Method Bio.SCOP.Des.Iterator.__init__()=Bio.SCOP.Des.Iterator-class.html#__init__,Method Bio.SCOP.Des.Parser.__init__()=Bio.SCOP.Des.Parser-class.html#__init__,Method Bio.SCOP.Des.Record.__init__()=Bio.SCOP.Des.Record-class.html#__init__,Method Bio.SCOP.Dom.Iterator.__init__()=Bio.SCOP.Dom.Iterator-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.FileIndex.FileIndex.__init__()=Bio.SCOP.FileIndex.FileIndex-class.html#__init__,Method Bio.SCOP.FileIndex.defaultdict.__init__()=Bio.SCOP.FileIndex.defaultdict-class.html#__init__,Method Bio.SCOP.Hie.Iterator.__init__()=Bio.SCOP.Hie.Iterator-class.html#__init__,Method Bio.SCOP.Hie.Parser.__init__()=Bio.SCOP.Hie.Parser-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.Iterator.__init__()=Bio.SCOP.Raf.Iterator-class.html#__init__,Method Bio.SCOP.Raf.Parser.__init__()=Bio.SCOP.Raf.Parser-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.SGMLExtractor.SGMLExtractor.LocalParser.__init__()=Bio.SGMLExtractor.SGMLExtractor.LocalParser-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractor.__init__()=Bio.SGMLExtractor.SGMLExtractor-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractorHandle.__init__()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#__init__,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#__init__,Method Bio.Saf.Iterator.__init__()=Bio.Saf.Iterator-class.html#__init__,Method Bio.Saf.Record.Record.__init__()=Bio.Saf.Record.Record-class.html#__init__,Method Bio.Saf.RecordParser.__init__()=Bio.Saf.RecordParser-class.html#__init__,Method Bio.Saf._RecordConsumer.__init__()=Bio.Saf._RecordConsumer-class.html#__init__,Method Bio.Saf._Scanner.__init__()=Bio.Saf._Scanner-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.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.WithinPosition.__init__()=Bio.SeqFeature.WithinPosition-class.html#__init__,Method Bio.SeqIO.ClustalIO.ClustalWriter.__init__()=Bio.SeqIO.ClustalIO.ClustalWriter-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.PhylipIO.PhylipWriter.__init__()=Bio.SeqIO.PhylipIO.PhylipWriter-class.html#__init__,Method Bio.SeqIO.StockholmIO.StockholmIterator.__init__()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__init__,Method Bio.SeqIO.StockholmIO.StockholmWriter.__init__()=Bio.SeqIO.StockholmIO.StockholmWriter-class.html#__init__,Method Bio.SeqRecord.SeqRecord.__init__()=Bio.SeqRecord.SeqRecord-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.MissingTable.__init__()=Bio.SeqUtils.MissingTable-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.ACEParser.__init__()=Bio.Sequencing.Ace.ACEParser-class.html#__init__,Method Bio.Sequencing.Ace.Contig.__init__()=Bio.Sequencing.Ace.Contig-class.html#__init__,Method Bio.Sequencing.Ace.Iterator.__init__()=Bio.Sequencing.Ace.Iterator-class.html#__init__,Method Bio.Sequencing.Ace.Reads.__init__()=Bio.Sequencing.Ace.Reads-class.html#__init__,Method Bio.Sequencing.Ace.RecordParser.__init__()=Bio.Sequencing.Ace.RecordParser-class.html#__init__,Method Bio.Sequencing.Ace._RecordConsumer.__init__()=Bio.Sequencing.Ace._RecordConsumer-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.Phd.Iterator.__init__()=Bio.Sequencing.Phd.Iterator-class.html#__init__,Method Bio.Sequencing.Phd.Record.__init__()=Bio.Sequencing.Phd.Record-class.html#__init__,Method Bio.Sequencing.Phd.RecordParser.__init__()=Bio.Sequencing.Phd.RecordParser-class.html#__init__,Method Bio.Sequencing.Phd._RecordConsumer.__init__()=Bio.Sequencing.Phd._RecordConsumer-class.html#__init__,Method Bio.Std.StdTerm.__init__()=Bio.Std.StdTerm-class.html#__init__,Method Bio.StdHandler.ConvertDispatchHandler.__init__()=Bio.StdHandler.ConvertDispatchHandler-class.html#__init__,Method Bio.StdHandler.ConvertHandler.__init__()=Bio.StdHandler.ConvertHandler-class.html#__init__,Method Bio.StdHandler.Feature.__init__()=Bio.StdHandler.Feature-class.html#__init__,Method Bio.StdHandler.Handle_dbxref.__init__()=Bio.StdHandler.Handle_dbxref-class.html#__init__,Method Bio.StdHandler.Handle_feature_location.__init__()=Bio.StdHandler.Handle_feature_location-class.html#__init__,Method Bio.StdHandler.Handle_feature_qualifier.__init__()=Bio.StdHandler.Handle_feature_qualifier-class.html#__init__,Method Bio.StdHandler.Handle_features.__init__()=Bio.StdHandler.Handle_features-class.html#__init__,Method Bio.StdHandler.Handle_hsp.__init__()=Bio.StdHandler.Handle_hsp-class.html#__init__,Method Bio.StdHandler.RecognizeHandler.__init__()=Bio.StdHandler.RecognizeHandler-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.ListParser.__init__()=Bio.SwissProt.KeyWList.ListParser-class.html#__init__,Method Bio.SwissProt.KeyWList.Record.__init__()=Bio.SwissProt.KeyWList.Record-class.html#__init__,Method Bio.SwissProt.KeyWList._ListConsumer.__init__()=Bio.SwissProt.KeyWList._ListConsumer-class.html#__init__,Method Bio.SwissProt.KeyWList._Scanner.__init__()=Bio.SwissProt.KeyWList._Scanner-class.html#__init__,Method Bio.SwissProt.SProt.Dictionary.__init__()=Bio.SwissProt.SProt.Dictionary-class.html#__init__,Method Bio.SwissProt.SProt.ExPASyDictionary.__init__()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#__init__,Method Bio.SwissProt.SProt.Iterator.__init__()=Bio.SwissProt.SProt.Iterator-class.html#__init__,Method Bio.SwissProt.SProt.Record.__init__()=Bio.SwissProt.SProt.Record-class.html#__init__,Method Bio.SwissProt.SProt.RecordParser.__init__()=Bio.SwissProt.SProt.RecordParser-class.html#__init__,Method Bio.SwissProt.SProt.Reference.__init__()=Bio.SwissProt.SProt.Reference-class.html#__init__,Method Bio.SwissProt.SProt.SequenceParser.__init__()=Bio.SwissProt.SProt.SequenceParser-class.html#__init__,Method Bio.SwissProt.SProt._RecordConsumer.__init__()=Bio.SwissProt.SProt._RecordConsumer-class.html#__init__,Method Bio.SwissProt.SProt._SequenceConsumer.__init__()=Bio.SwissProt.SProt._SequenceConsumer-class.html#__init__,Method Bio.Transcribe.Transcribe.__init__()=Bio.Transcribe.Transcribe-class.html#__init__,Method Bio.Translate.Translator.__init__()=Bio.Translate.Translator-class.html#__init__,Method Bio.UniGene.Iterator.__init__()=Bio.UniGene.Iterator-class.html#__init__,Method Bio.UniGene.RecordParser.__init__()=Bio.UniGene.RecordParser-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.WWW.RequestLimiter.__init__()=Bio.WWW.RequestLimiter-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.Writer.Writer.__init__()=Bio.Writer.Writer-class.html#__init__,Method Bio.biblio.Biblio.__init__()=Bio.biblio.Biblio-class.html#__init__,Method Bio.biblio.BiblioCollection.__init__()=Bio.biblio.BiblioCollection-class.html#__init__,Method Bio.builders.Search.search.BuildSearch.__init__()=Bio.builders.Search.search.BuildSearch-class.html#__init__,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#__init__,Method Bio.config.DBRegistry.BioCorbaDB.__init__()=Bio.config.DBRegistry.BioCorbaDB-class.html#__init__,Method Bio.config.DBRegistry.BioSQLDB.__init__()=Bio.config.DBRegistry.BioSQLDB-class.html#__init__,Method Bio.config.DBRegistry.CGIDB.__init__()=Bio.config.DBRegistry.CGIDB-class.html#__init__,Method Bio.config.DBRegistry.DBGroup.__init__()=Bio.config.DBRegistry.DBGroup-class.html#__init__,Method Bio.config.DBRegistry.DBObject.__init__()=Bio.config.DBRegistry.DBObject-class.html#__init__,Method Bio.config.DBRegistry.DBRegistry.__init__()=Bio.config.DBRegistry.DBRegistry-class.html#__init__,Method Bio.config.DBRegistry.EUtilsDB.__init__()=Bio.config.DBRegistry.EUtilsDB-class.html#__init__,Method Bio.config.DBRegistry.IndexedFileDB.__init__()=Bio.config.DBRegistry.IndexedFileDB-class.html#__init__,Method Bio.config.FormatRegistry.FormatGroup.__init__()=Bio.config.FormatRegistry.FormatGroup-class.html#__init__,Method Bio.config.FormatRegistry.FormatObject.__init__()=Bio.config.FormatRegistry.FormatObject-class.html#__init__,Method Bio.config.FormatRegistry.FormatRegistry.__init__()=Bio.config.FormatRegistry.FormatRegistry-class.html#__init__,Method Bio.config.Registry.RegisterableGroup.__init__()=Bio.config.Registry.RegisterableGroup-class.html#__init__,Method Bio.config.Registry.RegisterableObject.__init__()=Bio.config.Registry.RegisterableObject-class.html#__init__,Method Bio.config.Registry.Registry.__init__()=Bio.config.Registry.Registry-class.html#__init__,Method Bio.config.SeqDBRegistry.SeqDBRegistry.__init__()=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#__init__,Method Bio.config._stanzaformat.Stanza.__init__()=Bio.config._stanzaformat.Stanza-class.html#__init__,Method Bio.config._stanzaformat.StanzaFormat.__init__()=Bio.config._stanzaformat.StanzaFormat-class.html#__init__,Method Bio.config._support.make_cached_expression.__init__()=Bio.config._support.make_cached_expression-class.html#__init__,Method Bio.config._support.make_rate_limited_function.__init__()=Bio.config._support.make_rate_limited_function-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 Bio.writers.SeqRecord.embl.WriteEmbl.__init__()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#__init__,Method Bio.writers.SeqRecord.fasta.WriteFasta.__init__()=Bio.writers.SeqRecord.fasta.WriteFasta-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__,Method Martel.Dispatch.Callback.__init__()=Martel.Dispatch.Callback-class.html#__init__,Method Martel.Dispatch.DispatchHandler.__init__()=Martel.Dispatch.DispatchHandler-class.html#__init__,Method Martel.Dispatch.Dispatcher.__init__()=Martel.Dispatch.Dispatcher-class.html#__init__,Method Martel.Dispatch.Multicall.__init__()=Martel.Dispatch.Multicall-class.html#__init__,Method Martel.Dispatch.RemapEnd.__init__()=Martel.Dispatch.RemapEnd-class.html#__init__,Method Martel.Dispatch.RemapStart.__init__()=Martel.Dispatch.RemapStart-class.html#__init__,Method Martel.Expression.Alt.__init__()=Martel.Expression.Alt-class.html#__init__,Method Martel.Expression.Any.__init__()=Martel.Expression.Any-class.html#__init__,Method Martel.Expression.Assert.__init__()=Martel.Expression.Assert-class.html#__init__,Method Martel.Expression.Debug.__init__()=Martel.Expression.Debug-class.html#__init__,Method Martel.Expression.FastFeature.__init__()=Martel.Expression.FastFeature-class.html#__init__,Method Martel.Expression.Group.__init__()=Martel.Expression.Group-class.html#__init__,Method Martel.Expression.GroupRef.__init__()=Martel.Expression.GroupRef-class.html#__init__,Method Martel.Expression.HeaderFooter.__init__()=Martel.Expression.HeaderFooter-class.html#__init__,Method Martel.Expression.Literal.__init__()=Martel.Expression.Literal-class.html#__init__,Method Martel.Expression.MaxRepeat.__init__()=Martel.Expression.MaxRepeat-class.html#__init__,Method Martel.Expression.NullOp.__init__()=Martel.Expression.NullOp-class.html#__init__,Method Martel.Expression.ParseRecords.__init__()=Martel.Expression.ParseRecords-class.html#__init__,Method Martel.Expression.PassThrough.__init__()=Martel.Expression.PassThrough-class.html#__init__,Method Martel.Expression.Seq.__init__()=Martel.Expression.Seq-class.html#__init__,Method Martel.Expression.Str.__init__()=Martel.Expression.Str-class.html#__init__,Method Martel.Generate.CheckAssert.__init__()=Martel.Generate.CheckAssert-class.html#__init__,Method Martel.Generate.CheckAssertNot.__init__()=Martel.Generate.CheckAssertNot-class.html#__init__,Method Martel.Generate.CheckGroupRef.__init__()=Martel.Generate.CheckGroupRef-class.html#__init__,Method Martel.Generate.GeneratorState.__init__()=Martel.Generate.GeneratorState-class.html#__init__,Method Martel.Generate.HandleRepeatCount.__init__()=Martel.Generate.HandleRepeatCount-class.html#__init__,Method Martel.Generate.SetGroupValue.__init__()=Martel.Generate.SetGroupValue-class.html#__init__,Method Martel.Generate._call_call.__init__()=Martel.Generate._call_call-class.html#__init__,Method Martel.Generate._call_calltag.__init__()=Martel.Generate._call_calltag-class.html#__init__,Method Martel.Generate.print_debug.__init__()=Martel.Generate.print_debug-class.html#__init__,Method Martel.Generate.print_info.__init__()=Martel.Generate.print_info-class.html#__init__,Method Martel.IterParser.IterHeaderFooter.__init__()=Martel.IterParser.IterHeaderFooter-class.html#__init__,Method Martel.IterParser.IterRecords.__init__()=Martel.IterParser.IterRecords-class.html#__init__,Method Martel.Iterator.EventStream.__init__()=Martel.Iterator.EventStream-class.html#__init__,Method Martel.Iterator.HeaderFooterEventStream.__init__()=Martel.Iterator.HeaderFooterEventStream-class.html#__init__,Method Martel.Iterator.Iterate.__init__()=Martel.Iterator.Iterate-class.html#__init__,Method Martel.Iterator.Iterator.__init__()=Martel.Iterator.Iterator-class.html#__init__,Method Martel.Iterator.IteratorHeaderFooter.__init__()=Martel.Iterator.IteratorHeaderFooter-class.html#__init__,Method Martel.Iterator.IteratorRecords.__init__()=Martel.Iterator.IteratorRecords-class.html#__init__,Method Martel.Iterator.RecordEventStream.__init__()=Martel.Iterator.RecordEventStream-class.html#__init__,Method Martel.Iterator.StoreEvents.__init__()=Martel.Iterator.StoreEvents-class.html#__init__,Method Martel.LAX.ElementInfo.__init__()=Martel.LAX.ElementInfo-class.html#__init__,Method Martel.LAX.LAX.__init__()=Martel.LAX.LAX-class.html#__init__,Method Martel.Parser.HeaderFooterParser.__init__()=Martel.Parser.HeaderFooterParser-class.html#__init__,Method Martel.Parser.Parser.__init__()=Martel.Parser.Parser-class.html#__init__,Method Martel.Parser.ParserIncompleteException.__init__()=Martel.Parser.ParserIncompleteException-class.html#__init__,Method Martel.Parser.ParserPositionException.__init__()=Martel.Parser.ParserPositionException-class.html#__init__,Method Martel.Parser.RecordParser.__init__()=Martel.Parser.RecordParser-class.html#__init__,Method Martel.RecordReader.CountLines.__init__()=Martel.RecordReader.CountLines-class.html#__init__,Method Martel.RecordReader.EndsWith.__init__()=Martel.RecordReader.EndsWith-class.html#__init__,Method Martel.RecordReader.Everything.__init__()=Martel.RecordReader.Everything-class.html#__init__,Method Martel.RecordReader.Nothing.__init__()=Martel.RecordReader.Nothing-class.html#__init__,Method Martel.RecordReader.RecordReader.__init__()=Martel.RecordReader.RecordReader-class.html#__init__,Method Martel.RecordReader.StartsWith.__init__()=Martel.RecordReader.StartsWith-class.html#__init__,Method Martel.RecordReader.Until.__init__()=Martel.RecordReader.Until-class.html#__init__,Method Martel.convert_re.GroupNames.__init__()=Martel.convert_re.GroupNames-class.html#__init__,Method Martel.msre_parse.Pattern.__init__()=Martel.msre_parse.Pattern-class.html#__init__,Method Martel.msre_parse.SubPattern.__init__()=Martel.msre_parse.SubPattern-class.html#__init__,Method Martel.msre_parse.Tokenizer.__init__()=Martel.msre_parse.Tokenizer-class.html#__init__,Method Martel.test.support.CheckGood.__init__()=Martel.test.support.CheckGood-class.html#__init__,Method Martel.test.support.Dump.__init__()=Martel.test.support.Dump-class.html#__init__,Method Martel.test.support.Storage.__init__()=Martel.test.support.Storage-class.html#__init__,Method Martel.test.test_Parser.CountErrors.__init__()=Martel.test.test_Parser.CountErrors-class.html#__init__,Method Martel.test.test_Parser.CountRecords.__init__()=Martel.test.test_Parser.CountRecords-class.html#__init__,Method Martel.test.test_delimiter.CatchFields.__init__()=Martel.test.test_delimiter.CatchFields-class.html#__init__,Method Martel.test.test_optimize.GetErrorPos.__init__()=Martel.test.test_optimize.GetErrorPos-class.html#__init__"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__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.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__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.NCBIWWW.BlastParser.__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.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__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.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__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.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__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.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__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.NCBIDictionary.__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.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__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.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.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__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.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.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__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.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__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.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__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.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.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__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.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__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.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-98', '__init__', 'link-98');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-99" class="py-name"><a title="Bio.Mindy.BerkeleyDB.INDEX_TYPE
Bio.Mindy.FlatDB.INDEX_TYPE" class="py-name" href="#" onclick="return doclink('link-99', 'INDEX_TYPE', 'link-5');">INDEX_TYPE</a></tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">key_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">                                         <tt class="py-string">"key_%s.key"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">         </tt>
<a name="PrimaryTable"></a><div id="PrimaryTable-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="PrimaryTable-toggle" onclick="return toggle('PrimaryTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryTable-class.html">PrimaryTable</a><tt class="py-op">(</tt><tt class="py-base-class">BaseDB</tt><tt class="py-op">.</tt><tt class="py-base-class">DictLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimaryTable-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrimaryTable-expanded"><a name="PrimaryTable.__init__"></a><div id="PrimaryTable.__init__-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="PrimaryTable.__init__-toggle" onclick="return toggle('PrimaryTable.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryTable-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">db</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimaryTable.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimaryTable.__init__-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name" targets="Variable Bio.LocusLink.locus_format.db=Bio.LocusLink.locus_format-module.html#db,Variable Bio.config.DBRegistry.db=Bio.config.DBRegistry-module.html#db"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-100', 'db', 'link-100');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-101" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-101', 'db', 'link-100');">db</a></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Variable Bio.Std.namespace=Bio.Std-module.html#namespace,Variable Bio.biblio.namespace=Bio.biblio-module.html#namespace"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-102', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-op">=</tt> <tt id="link-103" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-103', 'namespace', 'link-102');">namespace</a></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-104', 'table', 'link-15');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-105" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-105', 'table', 'link-15');">table</a></tt> </tt>
</div><a name="PrimaryTable.__getitem__"></a><div id="PrimaryTable.__getitem__-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="PrimaryTable.__getitem__-toggle" onclick="return toggle('PrimaryTable.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryTable-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimaryTable.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimaryTable.__getitem__-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-name">fileid</tt><tt class="py-op">,</tt> <tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt id="link-106" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-106', 'length', 'link-7');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-107', 'table', 'link-15');">table</a></tt><tt class="py-op">[</tt><tt id="link-108" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-108', 'name', 'link-6');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-109" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-109', 'Location', 'link-1');">Location</a></tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-110', 'Location', 'link-1');">Location</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-111', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">                                  <tt id="link-112" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-112', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">                                  <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-113', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt><tt class="py-op">[</tt><tt class="py-name">fileid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">                                  <tt class="py-name">startpos</tt><tt class="py-op">,</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">                                  <tt id="link-114" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-114', 'length', 'link-7');">length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">                <tt class="py-op">]</tt> </tt>
</div><a name="PrimaryTable.keys"></a><div id="PrimaryTable.keys-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="PrimaryTable.keys-toggle" onclick="return toggle('PrimaryTable.keys');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryTable-class.html#keys">keys</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="PrimaryTable.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimaryTable.keys-expanded"><a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-115', 'table', 'link-15');">table</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-116', 'keys', 'link-116');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"> </tt>
<a name="SecondaryTable"></a><div id="SecondaryTable-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="SecondaryTable-toggle" onclick="return toggle('SecondaryTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryTable-class.html">SecondaryTable</a><tt class="py-op">(</tt><tt class="py-base-class">BaseDB</tt><tt class="py-op">.</tt><tt class="py-base-class">DictLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SecondaryTable-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SecondaryTable-expanded"><a name="SecondaryTable.__init__"></a><div id="SecondaryTable.__init__-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="SecondaryTable.__init__-toggle" onclick="return toggle('SecondaryTable.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryTable-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">db</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SecondaryTable.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SecondaryTable.__init__-expanded"><a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-117', 'db', 'link-100');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-118', 'db', 'link-100');">db</a></tt> </tt>
<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 id="link-119" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-119', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-op">=</tt> <tt id="link-120" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-120', 'namespace', 'link-102');">namespace</a></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-121', 'table', 'link-15');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-122" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-122', 'table', 'link-15');">table</a></tt> </tt>
</div><a name="SecondaryTable.__getitem__"></a><div id="SecondaryTable.__getitem__-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="SecondaryTable.__getitem__-toggle" onclick="return toggle('SecondaryTable.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryTable-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SecondaryTable.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SecondaryTable.__getitem__-expanded"><a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">        <tt id="link-123" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-123', 'data', 'link-123');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-124', 'table', 'link-15');">table</a></tt><tt class="py-op">[</tt><tt id="link-125" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-125', 'name', 'link-6');">name</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">            <tt class="py-name">fileid</tt><tt class="py-op">,</tt> <tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt id="link-126" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-126', 'length', 'link-7');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-127', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">primary_table</tt><tt class="py-op">[</tt><tt class="py-name">entry</tt><tt class="py-op">]</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">            <tt id="link-128" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-128', 'data', 'link-123');">data</a></tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-129', 'append', 'link-67');">append</a></tt><tt class="py-op">(</tt> <tt id="link-130" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-130', 'Location', 'link-1');">Location</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-131', 'Location', 'link-1');">Location</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-132', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">                                           <tt id="link-133" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-133', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">                                           <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-134', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt><tt class="py-op">[</tt><tt class="py-name">fileid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">                                           <tt class="py-name">startpos</tt><tt class="py-op">,</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">                                           <tt id="link-135" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-135', 'length', 'link-7');">length</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-136" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-136', 'data', 'link-123');">data</a></tt> </tt>
</div><a name="SecondaryTable.keys"></a><div id="SecondaryTable.keys-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="SecondaryTable.keys-toggle" onclick="return toggle('SecondaryTable.keys');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryTable-class.html#keys">keys</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="SecondaryTable.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SecondaryTable.keys-expanded"><a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-137', 'table', 'link-15');">table</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-138', 'keys', 'link-116');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"> </tt>
<a name="MemoryFlatDB"></a><div id="MemoryFlatDB-def"><a name="L126"></a><tt class="py-lineno">126</tt> <a class="py-toggle" href="#" id="MemoryFlatDB-toggle" onclick="return toggle('MemoryFlatDB');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.MemoryFlatDB-class.html">MemoryFlatDB</a><tt class="py-op">(</tt><tt class="py-base-class">BaseDB</tt><tt class="py-op">.</tt><tt class="py-base-class">WriteDB</tt><tt class="py-op">,</tt> <tt class="py-base-class">BaseFlatDB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MemoryFlatDB-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MemoryFlatDB-expanded"><a name="MemoryFlatDB.__init__"></a><div id="MemoryFlatDB.__init__-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="MemoryFlatDB.__init__-toggle" onclick="return toggle('MemoryFlatDB.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.MemoryFlatDB-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">dbname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MemoryFlatDB.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MemoryFlatDB.__init__-expanded"><a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__in_constructor</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_need_flush</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">        <tt id="link-139" class="py-name" targets="Class Bio.Mindy.FlatDB.BaseFlatDB=Bio.Mindy.FlatDB.BaseFlatDB-class.html"><a title="Bio.Mindy.FlatDB.BaseFlatDB" class="py-name" href="#" onclick="return doclink('link-139', 'BaseFlatDB', 'link-139');">BaseFlatDB</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__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.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__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.NCBIWWW.BlastParser.__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.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__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.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__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.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__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.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__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.NCBIDictionary.__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.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__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.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.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__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.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.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__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.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__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.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__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.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.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__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.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__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.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-140', '__init__', 'link-98');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">        <tt class="py-name">primary_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">                             <tt class="py-string">"key_%s.key"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_table</tt> <tt class="py-op">=</tt> <tt id="link-141" class="py-name" targets="Function Bio.Mindy.FlatDB._read_primary_table()=Bio.Mindy.FlatDB-module.html#_read_primary_table"><a title="Bio.Mindy.FlatDB._read_primary_table" class="py-name" href="#" onclick="return doclink('link-141', '_read_primary_table', 'link-141');">_read_primary_table</a></tt><tt class="py-op">(</tt><tt class="py-name">primary_filename</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_tables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-142" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-142', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_namespaces</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">filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"id_%s.index"</tt> <tt class="py-op">%</tt> <tt id="link-143" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-143', 'namespace', 'link-102');">namespace</a></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">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_tables</tt><tt class="py-op">[</tt><tt id="link-144" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-144', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-145" class="py-name" targets="Function Bio.Mindy.FlatDB._read_secondary_table()=Bio.Mindy.FlatDB-module.html#_read_secondary_table"><a title="Bio.Mindy.FlatDB._read_secondary_table" class="py-name" href="#" onclick="return doclink('link-145', '_read_secondary_table', 'link-145');">_read_secondary_table</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__in_constructor</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"> </tt>
<a name="MemoryFlatDB.add_record"></a><div id="MemoryFlatDB.add_record-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="MemoryFlatDB.add_record-toggle" onclick="return toggle('MemoryFlatDB.add_record');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.MemoryFlatDB-class.html#add_record">add_record</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filetag</tt><tt class="py-op">,</tt> <tt class="py-param">startpos</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MemoryFlatDB.add_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MemoryFlatDB.add_record-expanded"><a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-name">key_list</tt> <tt class="py-op">=</tt> <tt id="link-146" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-146', 'table', 'link-15');">table</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">]</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">key_list</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">                <tt class="py-string">"Field %s has %d entries but must have only one "</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">                <tt class="py-string">"(must be unique)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">unique</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">key_list</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">        <tt id="link-147" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-147', 'key', 'link-147');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">key_list</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</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">primary_table</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-148', 'has_key', 'link-148');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-149', 'key', 'link-147');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Field %r = %r already exists; must be unique"</tt> <tt class="py-op">%</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">                            <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt> <tt id="link-150" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-150', 'key', 'link-147');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_table</tt><tt class="py-op">[</tt><tt id="link-151" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-151', 'key', 'link-147');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s\t%s\t%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">filetag</tt><tt class="py-op">,</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">                                                  <tt id="link-152" class="py-name"><a title="Bio.Mindy.BaseDB" class="py-name" href="#" onclick="return doclink('link-152', 'BaseDB', 'link-0');">BaseDB</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Function Bio.Mindy.BaseDB._int_str()=Bio.Mindy.BaseDB-module.html#_int_str"><a title="Bio.Mindy.BaseDB._int_str" class="py-name" href="#" onclick="return doclink('link-153', '_int_str', 'link-153');">_int_str</a></tt><tt class="py-op">(</tt><tt class="py-name">startpos</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">                                                  <tt id="link-154" class="py-name"><a title="Bio.Mindy.BaseDB" class="py-name" href="#" onclick="return doclink('link-154', 'BaseDB', 'link-0');">BaseDB</a></tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.Mindy.BaseDB._int_str" class="py-name" href="#" onclick="return doclink('link-155', '_int_str', 'link-153');">_int_str</a></tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-156', 'length', 'link-7');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line"> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-157" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-157', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_namespaces</tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">            <tt id="link-158" class="py-name" targets="Method Bio.Mindy.BaseDB.OpenDB.lookup()=Bio.Mindy.BaseDB.OpenDB-class.html#lookup,Method BioSQL.BioSeqDatabase.BioSeqDatabase.lookup()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#lookup"><a title="Bio.Mindy.BaseDB.OpenDB.lookup
BioSQL.BioSeqDatabase.BioSeqDatabase.lookup" class="py-name" href="#" onclick="return doclink('link-158', 'lookup', 'link-158');">lookup</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_tables</tt><tt class="py-op">[</tt><tt id="link-159" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-159', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">]</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">            <tt class="py-comment"># Get the list of secondary identifiers for this identifier</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-160" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-160', 'table', 'link-15');">table</a></tt><tt class="py-op">.</tt><tt id="link-161" 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.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-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.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-161', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt id="link-162" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-162', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">                <tt class="py-comment"># Go from secondary identifier to list of primary identifiers</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt id="link-163" class="py-name"><a title="Bio.Mindy.BaseDB.OpenDB.lookup
BioSQL.BioSeqDatabase.BioSeqDatabase.lookup" class="py-name" href="#" onclick="return doclink('link-163', 'lookup', 'link-158');">lookup</a></tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-164', 'setdefault', 'link-66');">setdefault</a></tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-165', 'append', 'link-67');">append</a></tt><tt class="py-op">(</tt><tt id="link-166" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-166', 'key', 'link-147');">key</a></tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_need_flush</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"> </tt>
<a name="MemoryFlatDB.flush"></a><div id="MemoryFlatDB.flush-def"><a name="L165"></a><tt class="py-lineno">165</tt> <a class="py-toggle" href="#" id="MemoryFlatDB.flush-toggle" onclick="return toggle('MemoryFlatDB.flush');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.MemoryFlatDB-class.html#flush">flush</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="MemoryFlatDB.flush-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MemoryFlatDB.flush-expanded"><a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_need_flush</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">        <tt class="py-name">config_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"config.dat"</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">        <tt id="link-167" class="py-name"><a title="Bio.Mindy.BaseDB" class="py-name" href="#" onclick="return doclink('link-167', 'BaseDB', 'link-0');">BaseDB</a></tt><tt class="py-op">.</tt><tt id="link-168" class="py-name" targets="Function Bio.Mindy.BaseDB.write_config()=Bio.Mindy.BaseDB-module.html#write_config"><a title="Bio.Mindy.BaseDB.write_config" class="py-name" href="#" onclick="return doclink('link-168', 'write_config', 'link-168');">write_config</a></tt><tt class="py-op">(</tt><tt class="py-name">config_filename</tt> <tt class="py-op">=</tt> <tt class="py-name">config_filename</tt><tt class="py-op">,</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">                            <tt class="py-name">index_type</tt> <tt class="py-op">=</tt> <tt id="link-169" class="py-name"><a title="Bio.Mindy.BerkeleyDB.INDEX_TYPE
Bio.Mindy.FlatDB.INDEX_TYPE" class="py-name" href="#" onclick="return doclink('link-169', 'INDEX_TYPE', 'link-5');">INDEX_TYPE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">                            <tt class="py-name">primary_namespace</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">                            <tt class="py-name">secondary_namespaces</tt> <tt class="py-op">=</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">                                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_tables</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-170', 'keys', 'link-116');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">                            <tt class="py-name">fileid_info</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt><tt class="py-op">,</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">                            <tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">formatname</tt><tt class="py-op">,</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">                      <tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt class="py-name">primary_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">                           <tt class="py-string">"key_%s.key"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">        <tt id="link-171" class="py-name" targets="Function Bio.Mindy.FlatDB._write_primary_table()=Bio.Mindy.FlatDB-module.html#_write_primary_table"><a title="Bio.Mindy.FlatDB._write_primary_table" class="py-name" href="#" onclick="return doclink('link-171', '_write_primary_table', 'link-171');">_write_primary_table</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">primary_filename</tt><tt class="py-op">,</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">                             <tt class="py-name">primary_table</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_table</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line"> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">        <tt class="py-comment"># Write the secondary identifier information</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt id="link-172" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-172', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> <tt id="link-173" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-173', 'table', 'link-15');">table</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_tables</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-174', 'items', 'link-32');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">            <tt class="py-name">filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"id_%s.index"</tt> <tt class="py-op">%</tt> <tt id="link-175" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-175', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">            <tt id="link-176" class="py-name" targets="Function Bio.Mindy.FlatDB._write_secondary_table()=Bio.Mindy.FlatDB-module.html#_write_secondary_table"><a title="Bio.Mindy.FlatDB._write_secondary_table" class="py-name" href="#" onclick="return doclink('link-176', '_write_secondary_table', 'link-176');">_write_secondary_table</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">filename</tt><tt class="py-op">,</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">                                   <tt id="link-177" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-177', 'table', 'link-15');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-178" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-178', 'table', 'link-15');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line"> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_need_flush</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"> </tt>
<a name="MemoryFlatDB.close"></a><div id="MemoryFlatDB.close-def"><a name="L193"></a><tt class="py-lineno">193</tt> <a class="py-toggle" href="#" id="MemoryFlatDB.close-toggle" onclick="return toggle('MemoryFlatDB.close');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close">close</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="MemoryFlatDB.close-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MemoryFlatDB.close-expanded"><a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name" targets="Method Bio.Mindy.BerkeleyDB.BerkeleyDB.flush()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#flush,Method Bio.Mindy.FlatDB.MemoryFlatDB.flush()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#flush"><a title="Bio.Mindy.BerkeleyDB.BerkeleyDB.flush
Bio.Mindy.FlatDB.MemoryFlatDB.flush" class="py-name" href="#" onclick="return doclink('link-179', 'flush', 'link-179');">flush</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_table</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename_map</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">                             <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_tables</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"> </tt>
<a name="MemoryFlatDB.__del__"></a><div id="MemoryFlatDB.__del__-def"><a name="L198"></a><tt class="py-lineno">198</tt> <a class="py-toggle" href="#" id="MemoryFlatDB.__del__-toggle" onclick="return toggle('MemoryFlatDB.__del__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.MemoryFlatDB-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="MemoryFlatDB.__del__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MemoryFlatDB.__del__-expanded"><a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__in_constructor</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-180', 'close', 'link-47');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"> </tt>
<a name="MemoryFlatDB.__getitem__"></a><div id="MemoryFlatDB.__getitem__-def"><a name="L203"></a><tt class="py-lineno">203</tt> <a class="py-toggle" href="#" id="MemoryFlatDB.__getitem__-toggle" onclick="return toggle('MemoryFlatDB.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.MemoryFlatDB-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MemoryFlatDB.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MemoryFlatDB.__getitem__-expanded"><a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">        <tt class="py-docstring">"""return the database table lookup for the given namespace"""</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-181" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-181', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-182" class="py-name" targets="Class Bio.Mindy.FlatDB.PrimaryTable=Bio.Mindy.FlatDB.PrimaryTable-class.html"><a title="Bio.Mindy.FlatDB.PrimaryTable" class="py-name" href="#" onclick="return doclink('link-182', 'PrimaryTable', 'link-182');">PrimaryTable</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-183" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-183', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_table</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-184" class="py-name" targets="Class Bio.Mindy.FlatDB.SecondaryTable=Bio.Mindy.FlatDB.SecondaryTable-class.html"><a title="Bio.Mindy.FlatDB.SecondaryTable" class="py-name" href="#" onclick="return doclink('link-184', 'SecondaryTable', 'link-184');">SecondaryTable</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-185" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-185', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_tables</tt><tt class="py-op">[</tt><tt id="link-186" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-186', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line"> </tt>
<a name="BisectFile"></a><div id="BisectFile-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="BisectFile-toggle" onclick="return toggle('BisectFile');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.BisectFile-class.html">BisectFile</a><tt class="py-op">:</tt> </tt>
</div><div id="BisectFile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BisectFile-expanded"><a name="BisectFile.__init__"></a><div id="BisectFile.__init__-def"><a name="L211"></a><tt class="py-lineno">211</tt> <a class="py-toggle" href="#" id="BisectFile.__init__-toggle" onclick="return toggle('BisectFile.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.BisectFile-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">infile</tt><tt class="py-op">,</tt> <tt class="py-param">size</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BisectFile.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BisectFile.__init__-expanded"><a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-187', 'size', 'link-13');">size</a></tt> <tt class="py-op">=</tt> <tt id="link-188" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-188', 'size', 'link-13');">size</a></tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-189', 'seek', 'link-189');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_size</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-190', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-op">(</tt><tt id="link-191" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-191', 'size', 'link-13');">size</a></tt> <tt class="py-op">-</tt> <tt class="py-number">4</tt><tt class="py-op">)</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_size</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"record size is wrong"</tt> </tt>
</div><a name="BisectFile.__len__"></a><div id="BisectFile.__len__-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="BisectFile.__len__-toggle" onclick="return toggle('BisectFile.__len__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.BisectFile-class.html#__len__">__len__</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="BisectFile.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BisectFile.__len__-expanded"><a name="L218"></a><tt class="py-lineno">218</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">record_size</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">int</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-192" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-192', 'size', 'link-13');">size</a></tt> <tt class="py-op">-</tt> <tt class="py-number">4</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_size</tt><tt class="py-op">)</tt> </tt>
</div><a name="BisectFile.__getitem__"></a><div id="BisectFile.__getitem__-def"><a name="L221"></a><tt class="py-lineno">221</tt> <a class="py-toggle" href="#" id="BisectFile.__getitem__-toggle" onclick="return toggle('BisectFile.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.BisectFile-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BisectFile.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BisectFile.__getitem__-expanded"><a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-193', 'seek', 'link-189');">seek</a></tt><tt class="py-op">(</tt><tt id="link-194" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-194', 'i', 'link-194');">i</a></tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_size</tt> <tt class="py-op">+</tt> <tt class="py-number">4</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-195', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_size</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-196', 'split', 'link-9');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="BisectFile.get_entry"></a><div id="BisectFile.get_entry-def"><a name="L224"></a><tt class="py-lineno">224</tt> <a class="py-toggle" href="#" id="BisectFile.get_entry-toggle" onclick="return toggle('BisectFile.get_entry');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.BisectFile-class.html#get_entry">get_entry</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BisectFile.get_entry-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BisectFile.get_entry-expanded"><a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-197', 'seek', 'link-189');">seek</a></tt><tt class="py-op">(</tt><tt id="link-198" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-198', 'i', 'link-194');">i</a></tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_size</tt> <tt class="py-op">+</tt> <tt class="py-number">4</tt><tt class="py-op">)</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-199', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_size</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"> </tt>
<a name="_find_entry"></a><div id="_find_entry-def"><a name="L228"></a><tt class="py-lineno">228</tt> <a class="py-toggle" href="#" id="_find_entry-toggle" onclick="return toggle('_find_entry');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_find_entry">_find_entry</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">wantword</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_find_entry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_find_entry-expanded"><a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">    <tt id="link-200" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-200', 'size', 'link-13');">size</a></tt> <tt class="py-op">=</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">getsize</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">    <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-201" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-201', '_open', 'link-3');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">    <tt class="py-name">bf</tt> <tt class="py-op">=</tt> <tt id="link-202" class="py-name" targets="Class Bio.Mindy.FlatDB.BisectFile=Bio.Mindy.FlatDB.BisectFile-class.html"><a title="Bio.Mindy.FlatDB.BisectFile" class="py-name" href="#" onclick="return doclink('link-202', 'BisectFile', 'link-202');">BisectFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt id="link-203" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-203', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">    <tt class="py-name">left</tt> <tt class="py-op">=</tt> <tt class="py-name">bisect</tt><tt class="py-op">.</tt><tt class="py-name">bisect_left</tt><tt class="py-op">(</tt><tt class="py-name">bf</tt><tt class="py-op">,</tt> <tt class="py-name">wantword</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">    <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">bf</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name" targets="Function Bio.ECell.Record.get_entry()=Bio.ECell.Record-module.html#get_entry,Method Bio.Mindy.FlatDB.BisectFile.get_entry()=Bio.Mindy.FlatDB.BisectFile-class.html#get_entry"><a title="Bio.ECell.Record.get_entry
Bio.Mindy.FlatDB.BisectFile.get_entry" class="py-name" href="#" onclick="return doclink('link-204', 'get_entry', 'link-204');">get_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">left</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-name">wantword</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"> </tt>
<a name="_find_range"></a><div id="_find_range-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="_find_range-toggle" onclick="return toggle('_find_range');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_find_range">_find_range</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">wantword</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_find_range-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_find_range-expanded"><a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">    <tt id="link-205" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-205', 'size', 'link-13');">size</a></tt> <tt class="py-op">=</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">getsize</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">    <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-206" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-206', '_open', 'link-3');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">    <tt class="py-name">bf</tt> <tt class="py-op">=</tt> <tt id="link-207" class="py-name"><a title="Bio.Mindy.FlatDB.BisectFile" class="py-name" href="#" onclick="return doclink('link-207', 'BisectFile', 'link-202');">BisectFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt id="link-208" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-208', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt class="py-name">left</tt> <tt class="py-op">=</tt> <tt class="py-name">bisect</tt><tt class="py-op">.</tt><tt class="py-name">bisect_left</tt><tt class="py-op">(</tt><tt class="py-name">bf</tt><tt class="py-op">,</tt> <tt class="py-name">wantword</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">    <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">bf</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="Bio.ECell.Record.get_entry
Bio.Mindy.FlatDB.BisectFile.get_entry" class="py-name" href="#" onclick="return doclink('link-209', 'get_entry', 'link-204');">get_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">left</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-name">wantword</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">     </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">    <tt class="py-name">right</tt> <tt class="py-op">=</tt> <tt class="py-name">bisect</tt><tt class="py-op">.</tt><tt class="py-name">bisect_right</tt><tt class="py-op">(</tt><tt class="py-name">bf</tt><tt class="py-op">,</tt> <tt class="py-name">wantword</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">    <tt id="link-210" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-210', 'data', 'link-123');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-211" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-211', 'i', 'link-194');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">left</tt><tt class="py-op">,</tt> <tt class="py-name">right</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">        <tt id="link-212" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-212', 'x', 'link-78');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">bf</tt><tt class="py-op">.</tt><tt id="link-213" class="py-name"><a title="Bio.ECell.Record.get_entry
Bio.Mindy.FlatDB.BisectFile.get_entry" class="py-name" href="#" onclick="return doclink('link-213', 'get_entry', 'link-204');">get_entry</a></tt><tt class="py-op">(</tt><tt id="link-214" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-214', 'i', 'link-194');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">        <tt id="link-215" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-215', 'data', 'link-123');">data</a></tt><tt class="py-op">.</tt><tt id="link-216" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-216', 'append', 'link-67');">append</a></tt><tt class="py-op">(</tt><tt id="link-217" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-217', 'x', 'link-78');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-218" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-218', 'data', 'link-123');">data</a></tt> </tt>
</div><a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line"> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"> </tt>
<a name="_lookup_location"></a><div id="_lookup_location-def"><a name="L257"></a><tt class="py-lineno">257</tt> <a class="py-toggle" href="#" id="_lookup_location-toggle" onclick="return toggle('_lookup_location');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_lookup_location">_lookup_location</a><tt class="py-op">(</tt><tt class="py-param">key_filename</tt><tt class="py-op">,</tt> <tt class="py-param">word</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_lookup_location-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_lookup_location-expanded"><a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">    <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-219" class="py-name" targets="Function Bio.Mindy.FlatDB._find_entry()=Bio.Mindy.FlatDB-module.html#_find_entry"><a title="Bio.Mindy.FlatDB._find_entry" class="py-name" href="#" onclick="return doclink('link-219', '_find_entry', 'link-219');">_find_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">key_filename</tt><tt class="py-op">,</tt> <tt class="py-name">word</tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">line</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-220" class="py-name"><a title="Bio.Mindy.FlatDB._parse_primary_table_entry" class="py-name" href="#" onclick="return doclink('link-220', '_parse_primary_table_entry', 'link-26');">_parse_primary_table_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
</div><a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"> </tt>
<a name="_lookup_alias"></a><div id="_lookup_alias-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="_lookup_alias-toggle" onclick="return toggle('_lookup_alias');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_lookup_alias">_lookup_alias</a><tt class="py-op">(</tt><tt class="py-param">id_filename</tt><tt class="py-op">,</tt> <tt class="py-param">word</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_lookup_alias-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_lookup_alias-expanded"><a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">    <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt id="link-221" class="py-name" targets="Function Bio.Mindy.FlatDB._find_range()=Bio.Mindy.FlatDB-module.html#_find_range"><a title="Bio.Mindy.FlatDB._find_range" class="py-name" href="#" onclick="return doclink('link-221', '_find_range', 'link-221');">_find_range</a></tt><tt class="py-op">(</tt><tt class="py-name">id_filename</tt><tt class="py-op">,</tt> <tt class="py-name">word</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">    <tt class="py-name">primary_keys</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt class="py-name">alias</tt><tt class="py-op">,</tt> <tt class="py-name">primary_key</tt> <tt class="py-op">=</tt> <tt id="link-222" class="py-name"><a title="Bio.Mindy.FlatDB._parse_secondary_table_entry" class="py-name" href="#" onclick="return doclink('link-222', '_parse_secondary_table_entry', 'link-63');">_parse_secondary_table_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">alias</tt> <tt class="py-op">==</tt> <tt class="py-name">word</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">alias</tt><tt class="py-op">,</tt> <tt class="py-name">word</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt class="py-name">primary_keys</tt><tt class="py-op">.</tt><tt id="link-223" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-223', 'append', 'link-67');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">primary_key</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">primary_keys</tt> </tt>
</div><a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line"> </tt>
<a name="create"></a><div id="create-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="create-toggle" onclick="return toggle('create');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#create">create</a><tt class="py-op">(</tt><tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">primary_namespace</tt><tt class="py-op">,</tt> <tt class="py-param">secondary_namespaces</tt><tt class="py-op">,</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">           <tt class="py-param">formatname</tt> <tt class="py-op">=</tt> <tt class="py-string">"unknown"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="create-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="create-expanded"><a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">    <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">mkdir</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">    <tt class="py-name">config_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"config.dat"</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">    <tt id="link-224" class="py-name"><a title="Bio.Mindy.BaseDB" class="py-name" href="#" onclick="return doclink('link-224', 'BaseDB', 'link-0');">BaseDB</a></tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.Mindy.BaseDB.write_config" class="py-name" href="#" onclick="return doclink('link-225', 'write_config', 'link-168');">write_config</a></tt><tt class="py-op">(</tt><tt class="py-name">config_filename</tt> <tt class="py-op">=</tt> <tt class="py-name">config_filename</tt><tt class="py-op">,</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">                        <tt class="py-name">index_type</tt> <tt class="py-op">=</tt> <tt id="link-226" class="py-name"><a title="Bio.Mindy.BerkeleyDB.INDEX_TYPE
Bio.Mindy.FlatDB.INDEX_TYPE" class="py-name" href="#" onclick="return doclink('link-226', 'INDEX_TYPE', 'link-5');">INDEX_TYPE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">                        <tt class="py-name">primary_namespace</tt> <tt class="py-op">=</tt> <tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">                        <tt class="py-name">secondary_namespaces</tt> <tt class="py-op">=</tt> <tt class="py-name">secondary_namespaces</tt><tt class="py-op">,</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">                        <tt class="py-name">fileid_info</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">                        <tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt class="py-name">formatname</tt><tt class="py-op">,</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">                        <tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">    <tt class="py-name">primary_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">                       <tt class="py-string">"key_%s.key"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">    <tt id="link-227" class="py-name"><a title="Bio.Mindy.FlatDB._write_primary_table" class="py-name" href="#" onclick="return doclink('link-227', '_write_primary_table', 'link-171');">_write_primary_table</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">primary_filename</tt><tt class="py-op">,</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line">                         <tt class="py-name">primary_table</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line"> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">    <tt class="py-comment"># Write the secondary identifier information</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">for</tt> <tt id="link-228" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-228', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">secondary_namespaces</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">        <tt class="py-name">filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"id_%s.index"</tt> <tt class="py-op">%</tt> <tt id="link-229" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-229', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">        <tt id="link-230" class="py-name"><a title="Bio.Mindy.FlatDB._write_secondary_table" class="py-name" href="#" onclick="return doclink('link-230', '_write_secondary_table', 'link-176');">_write_secondary_table</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">filename</tt><tt class="py-op">,</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">                               <tt id="link-231" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-231', 'table', 'link-15');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-232" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-232', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"rw"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">     </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line"> </tt>
<a name="open"></a><div id="open-def"><a name="L300"></a><tt class="py-lineno">300</tt> <a class="py-toggle" href="#" id="open-toggle" onclick="return toggle('open');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#open">open</a><tt class="py-op">(</tt><tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">mode</tt> <tt class="py-op">=</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="open-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="open-expanded"><a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">mode</tt> <tt class="py-op">==</tt> <tt class="py-string">"r"</tt><tt class="py-op">:</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-233" class="py-name" targets="Class Bio.Mindy.FlatDB.DiskFlatDB=Bio.Mindy.FlatDB.DiskFlatDB-class.html"><a title="Bio.Mindy.FlatDB.DiskFlatDB" class="py-name" href="#" onclick="return doclink('link-233', 'DiskFlatDB', 'link-233');">DiskFlatDB</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">mode</tt> <tt class="py-op">==</tt> <tt class="py-string">"rw"</tt><tt class="py-op">:</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-234" class="py-name" targets="Class Bio.Mindy.FlatDB.MemoryFlatDB=Bio.Mindy.FlatDB.MemoryFlatDB-class.html"><a title="Bio.Mindy.FlatDB.MemoryFlatDB" class="py-name" href="#" onclick="return doclink('link-234', 'MemoryFlatDB', 'link-234');">MemoryFlatDB</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">mode</tt> <tt class="py-op">==</tt> <tt class="py-string">"a"</tt><tt class="py-op">:</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Must call FlatDB.create to create the database"</tt><tt class="py-op">)</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown mode: %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">mode</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"> </tt>
<a name="_get_first_words"></a><div id="_get_first_words-def"><a name="L310"></a><tt class="py-lineno">310</tt> <a class="py-toggle" href="#" id="_get_first_words-toggle" onclick="return toggle('_get_first_words');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB-module.html#_get_first_words">_get_first_words</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_first_words-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_first_words-expanded"><a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">    <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt id="link-235" class="py-name"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-235', '_open', 'link-3');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">    <tt id="link-236" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-236', 'size', 'link-13');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-237', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">    <tt id="link-238" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-238', 'data', 'link-123');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">        <tt id="link-239" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-239', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-240', 'read', 'link-14');">read</a></tt><tt class="py-op">(</tt><tt id="link-241" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-241', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-242" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-242', 's', 'link-8');">s</a></tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">            <tt class="py-keyword">break</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-243" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-243', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-244" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-244', 'size', 'link-13');">size</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-245" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-245', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-246" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-246', 'size', 'link-13');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt id="link-247" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-247', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-248" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-248', 's', 'link-8');">s</a></tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-249', 'split', 'link-9');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-250" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-250', 'data', 'link-123');">data</a></tt> <tt class="py-keyword">or</tt> <tt id="link-251" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-251', 'data', 'link-123');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-252" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-252', 's', 'link-8');">s</a></tt><tt class="py-op">:</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">            <tt id="link-253" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-253', 'data', 'link-123');">data</a></tt><tt class="py-op">.</tt><tt id="link-254" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-254', 'append', 'link-67');">append</a></tt><tt class="py-op">(</tt><tt id="link-255" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-255', 's', 'link-8');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-256" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-256', 'data', 'link-123');">data</a></tt> </tt>
</div><a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"> </tt>
<a name="PrimaryNamespace"></a><div id="PrimaryNamespace-def"><a name="L324"></a><tt class="py-lineno">324</tt> <a class="py-toggle" href="#" id="PrimaryNamespace-toggle" onclick="return toggle('PrimaryNamespace');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryNamespace-class.html">PrimaryNamespace</a><tt class="py-op">(</tt><tt class="py-base-class">BaseDB</tt><tt class="py-op">.</tt><tt class="py-base-class">DictLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimaryNamespace-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PrimaryNamespace-expanded"><a name="PrimaryNamespace.__init__"></a><div id="PrimaryNamespace.__init__-def"><a name="L325"></a><tt class="py-lineno">325</tt> <a class="py-toggle" href="#" id="PrimaryNamespace.__init__-toggle" onclick="return toggle('PrimaryNamespace.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryNamespace-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">db</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimaryNamespace.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimaryNamespace.__init__-expanded"><a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-257', 'db', 'link-100');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-258" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-258', 'db', 'link-100');">db</a></tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-259', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-op">=</tt> <tt id="link-260" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-260', 'namespace', 'link-102');">namespace</a></tt> </tt>
</div><a name="PrimaryNamespace.__getitem__"></a><div id="PrimaryNamespace.__getitem__-def"><a name="L328"></a><tt class="py-lineno">328</tt> <a class="py-toggle" href="#" id="PrimaryNamespace.__getitem__-toggle" onclick="return toggle('PrimaryNamespace.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryNamespace-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PrimaryNamespace.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimaryNamespace.__getitem__-expanded"><a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">        <tt class="py-name">loc</tt> <tt class="py-op">=</tt> <tt id="link-261" class="py-name" targets="Function Bio.Mindy.FlatDB._lookup_location()=Bio.Mindy.FlatDB-module.html#_lookup_location"><a title="Bio.Mindy.FlatDB._lookup_location" class="py-name" href="#" onclick="return doclink('link-261', '_lookup_location', 'link-261');">_lookup_location</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-262', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">key_filename</tt><tt class="py-op">,</tt> <tt id="link-263" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-263', 'name', 'link-6');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">loc</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find primary key %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-264" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-264', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">        <tt id="link-265" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-265', 'data', 'link-123');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">            <tt id="link-266" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-266', 'Location', 'link-1');">Location</a></tt><tt class="py-op">.</tt><tt id="link-267" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-267', 'Location', 'link-1');">Location</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-268" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-268', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">                              <tt id="link-269" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-269', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">                              <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-270', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt><tt class="py-op">[</tt><tt class="py-name">loc</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">                              <tt class="py-name">loc</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">                              <tt class="py-name">loc</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">        <tt class="py-op">]</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-271" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-271', 'data', 'link-123');">data</a></tt> </tt>
</div><a name="PrimaryNamespace.keys"></a><div id="PrimaryNamespace.keys-def"><a name="L340"></a><tt class="py-lineno">340</tt> <a class="py-toggle" href="#" id="PrimaryNamespace.keys-toggle" onclick="return toggle('PrimaryNamespace.keys');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys">keys</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="PrimaryNamespace.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PrimaryNamespace.keys-expanded"><a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-272" class="py-name" targets="Function Bio.Mindy.FlatDB._get_first_words()=Bio.Mindy.FlatDB-module.html#_get_first_words"><a title="Bio.Mindy.FlatDB._get_first_words" class="py-name" href="#" onclick="return doclink('link-272', '_get_first_words', 'link-272');">_get_first_words</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-273', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">key_filename</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">     </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">         </tt>
<a name="SecondaryNamespace"></a><div id="SecondaryNamespace-def"><a name="L344"></a><tt class="py-lineno">344</tt> <a class="py-toggle" href="#" id="SecondaryNamespace-toggle" onclick="return toggle('SecondaryNamespace');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryNamespace-class.html">SecondaryNamespace</a><tt class="py-op">(</tt><tt class="py-base-class">BaseDB</tt><tt class="py-op">.</tt><tt class="py-base-class">DictLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SecondaryNamespace-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SecondaryNamespace-expanded"><a name="SecondaryNamespace.__init__"></a><div id="SecondaryNamespace.__init__-def"><a name="L345"></a><tt class="py-lineno">345</tt> <a class="py-toggle" href="#" id="SecondaryNamespace.__init__-toggle" onclick="return toggle('SecondaryNamespace.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryNamespace-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">db</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SecondaryNamespace.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SecondaryNamespace.__init__-expanded"><a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-274" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-274', 'db', 'link-100');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-275" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-275', 'db', 'link-100');">db</a></tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-276" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-276', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-op">=</tt> <tt id="link-277" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-277', 'namespace', 'link-102');">namespace</a></tt> </tt>
</div><a name="SecondaryNamespace.__getitem__"></a><div id="SecondaryNamespace.__getitem__-def"><a name="L348"></a><tt class="py-lineno">348</tt> <a class="py-toggle" href="#" id="SecondaryNamespace.__getitem__-toggle" onclick="return toggle('SecondaryNamespace.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryNamespace-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SecondaryNamespace.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SecondaryNamespace.__getitem__-expanded"><a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">        <tt class="py-name">id_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-278" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-278', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">                                   <tt class="py-string">"id_%s.index"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-279" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-279', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">        <tt class="py-name">primary_keys</tt> <tt class="py-op">=</tt> <tt id="link-280" class="py-name" targets="Function Bio.Mindy.FlatDB._lookup_alias()=Bio.Mindy.FlatDB-module.html#_lookup_alias"><a title="Bio.Mindy.FlatDB._lookup_alias" class="py-name" href="#" onclick="return doclink('link-280', '_lookup_alias', 'link-280');">_lookup_alias</a></tt><tt class="py-op">(</tt><tt class="py-name">id_filename</tt><tt class="py-op">,</tt> <tt id="link-281" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-281', 'name', 'link-6');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">primary_keys</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find %r key %r"</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-282" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-282', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> <tt id="link-283" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-283', 'name', 'link-6');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line"> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">        <tt id="link-284" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-284', 'data', 'link-123');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-285" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-285', 'key', 'link-147');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">primary_keys</tt><tt class="py-op">:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">            <tt class="py-name">loc</tt> <tt class="py-op">=</tt> <tt id="link-286" class="py-name"><a title="Bio.Mindy.FlatDB._lookup_location" class="py-name" href="#" onclick="return doclink('link-286', '_lookup_location', 'link-261');">_lookup_location</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-287', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">key_filename</tt><tt class="py-op">,</tt> <tt id="link-288" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-288', 'key', 'link-147');">key</a></tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">loc</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find primary key %r -- "</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">                                     <tt class="py-string">"lost database integrety"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-289" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-289', 'key', 'link-147');">key</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">            <tt id="link-290" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-290', 'data', 'link-123');">data</a></tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-291', 'append', 'link-67');">append</a></tt><tt class="py-op">(</tt><tt id="link-292" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-292', 'Location', 'link-1');">Location</a></tt><tt class="py-op">.</tt><tt id="link-293" class="py-name"><a title="Bio.GFF.easy.Location
Bio.Mindy.Location
Bio.Mindy.Location.Location" class="py-name" href="#" onclick="return doclink('link-293', 'Location', 'link-1');">Location</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-294', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">,</tt> <tt id="link-295" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-295', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">                                          <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-296', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt><tt class="py-op">[</tt><tt class="py-name">loc</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">                                          <tt class="py-name">loc</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">                                          <tt class="py-name">loc</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-297" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-297', 'data', 'link-123');">data</a></tt> </tt>
</div><a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line"> </tt>
<a name="SecondaryNamespace.keys"></a><div id="SecondaryNamespace.keys-def"><a name="L367"></a><tt class="py-lineno">367</tt> <a class="py-toggle" href="#" id="SecondaryNamespace.keys-toggle" onclick="return toggle('SecondaryNamespace.keys');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys">keys</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="SecondaryNamespace.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SecondaryNamespace.keys-expanded"><a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">        <tt class="py-name">id_filename</tt> <tt class="py-op">=</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">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-298', 'db', 'link-100');">db</a></tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">                                   <tt class="py-string">"id_%s.index"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-299" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-299', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-300" class="py-name"><a title="Bio.Mindy.FlatDB._get_first_words" class="py-name" href="#" onclick="return doclink('link-300', '_get_first_words', 'link-272');">_get_first_words</a></tt><tt class="py-op">(</tt><tt class="py-name">id_filename</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line"> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line"> </tt>
<a name="DiskFlatDB"></a><div id="DiskFlatDB-def"><a name="L373"></a><tt class="py-lineno">373</tt> <a class="py-toggle" href="#" id="DiskFlatDB-toggle" onclick="return toggle('DiskFlatDB');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.DiskFlatDB-class.html">DiskFlatDB</a><tt class="py-op">(</tt><tt class="py-base-class">BaseFlatDB</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DiskFlatDB-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DiskFlatDB-expanded"><a name="DiskFlatDB.__init__"></a><div id="DiskFlatDB.__init__-def"><a name="L374"></a><tt class="py-lineno">374</tt> <a class="py-toggle" href="#" id="DiskFlatDB.__init__-toggle" onclick="return toggle('DiskFlatDB.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.DiskFlatDB-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">dbname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DiskFlatDB.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DiskFlatDB.__init__-expanded"><a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">        <tt id="link-301" class="py-name"><a title="Bio.Mindy.FlatDB.BaseFlatDB" class="py-name" href="#" onclick="return doclink('link-301', 'BaseFlatDB', 'link-139');">BaseFlatDB</a></tt><tt class="py-op">.</tt><tt id="link-302" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__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.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__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.NCBIWWW.BlastParser.__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.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__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.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__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.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__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.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__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.NCBIDictionary.__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.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__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.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.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__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.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.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__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.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__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.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__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.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.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__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.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__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.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-302', '__init__', 'link-98');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
</div><a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">         </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line"> </tt>
<a name="DiskFlatDB.__getitem__"></a><div id="DiskFlatDB.__getitem__-def"><a name="L378"></a><tt class="py-lineno">378</tt> <a class="py-toggle" href="#" id="DiskFlatDB.__getitem__-toggle" onclick="return toggle('DiskFlatDB.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.FlatDB.DiskFlatDB-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DiskFlatDB.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DiskFlatDB.__getitem__-expanded"><a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">        <tt class="py-docstring">"""return the database table lookup for the given namespace"""</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-303" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-303', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">:</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-304" class="py-name" targets="Class Bio.Mindy.BerkeleyDB.PrimaryNamespace=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html,Class Bio.Mindy.FlatDB.PrimaryNamespace=Bio.Mindy.FlatDB.PrimaryNamespace-class.html"><a title="Bio.Mindy.BerkeleyDB.PrimaryNamespace
Bio.Mindy.FlatDB.PrimaryNamespace" class="py-name" href="#" onclick="return doclink('link-304', 'PrimaryNamespace', 'link-304');">PrimaryNamespace</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-305" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-305', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-306" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-306', 'namespace', 'link-102');">namespace</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_namespaces</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-307" class="py-name" targets="Class Bio.Mindy.BerkeleyDB.SecondaryNamespace=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html,Class Bio.Mindy.FlatDB.SecondaryNamespace=Bio.Mindy.FlatDB.SecondaryNamespace-class.html"><a title="Bio.Mindy.BerkeleyDB.SecondaryNamespace
Bio.Mindy.FlatDB.SecondaryNamespace" class="py-name" href="#" onclick="return doclink('link-307', 'SecondaryNamespace', 'link-307');">SecondaryNamespace</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-308" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-308', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt id="link-309" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-309', 'namespace', 'link-102');">namespace</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L385"></a><tt class="py-lineno">385</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>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

      <th class="navbar" width="100%"></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Mon Sep 15 09:27:16 2008
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>