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Package MetaTool
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<h1 class="epydoc">Source Code for <a href="Bio.MetaTool-module.html">Package Bio.MetaTool</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""Parser for output from MetaTool, a program which defines metabolic routes</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">within networks.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">list_uids=10222413&dopt=Abstract</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">Matrix</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"># XML from python 2.0</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> <tt class="py-keyword">import</tt> <tt class="py-name">handler</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"># Martel</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-3');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-4', 'ParserSupport', 'link-4');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.ParserSupport.EventGenerator=Bio.ParserSupport.EventGenerator-class.html"><a title="Bio.ParserSupport.EventGenerator" class="py-name" href="#" onclick="return doclink('link-5', 'EventGenerator', 'link-5');">EventGenerator</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-3');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-7', 'File', 'link-7');">File</a></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Module Bio.MetaTool.metatool_format=Bio.MetaTool.metatool_format-module.html"><a title="Bio.MetaTool.metatool_format" class="py-name" href="#" onclick="return doclink('link-8', 'metatool_format', 'link-8');">metatool_format</a></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-9', 'Record', 'link-9');">Record</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="Iterator"></a><div id="Iterator-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="Iterator-toggle" onclick="return toggle('Iterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MetaTool.Iterator-class.html">Iterator</a><tt class="py-op">:</tt> </tt>
</div><div id="Iterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterator-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterator interface to move over a file of MetaTool entries one at a time.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="Iterator.__init__-toggle" onclick="return toggle('Iterator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool.Iterator-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">handle</tt><tt class="py-op">,</tt> <tt class="py-param">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__init__-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the iterator.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> o handle - A handle with Kabat entries to iterate through.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> o parser - An optional parser to pass the entries through before</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> returning them. If None, then the raw entry will be returned.</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-10', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Class Martel.RecordReader.StartsWith=Martel.RecordReader.StartsWith-class.html"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-11', 'StartsWith', 'link-11');">StartsWith</a></tt><tt class="py-op">(</tt><tt id="link-12" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-12', 'handle', 'link-12');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-string">"METATOOL"</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"># self._reader = RecordReader.EndsWith(handle, "RECEND|\n")</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt> </tt>
</div><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <a class="py-toggle" href="#" id="Iterator.next-toggle" onclick="return toggle('Iterator.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool.Iterator-class.html#next">next</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="Iterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.next-expanded"><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the next MetaTool record from the handle.</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> Will return None if we ran out of records.</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt id="link-13" 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-13', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-14', 'next', 'link-14');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</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">_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-15" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-15', 'data', 'link-13');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">dumpfile</tt> <tt class="py-op">=</tt> <tt id="link-16" 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-16', 'open', 'link-16');">open</a></tt><tt class="py-op">(</tt> <tt class="py-string">'dump'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt> <tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">dumpfile</tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'write', 'link-17');">write</a></tt><tt class="py-op">(</tt> <tt id="link-18" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-18', 'data', 'link-13');">data</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">dumpfile</tt><tt class="py-op">.</tt><tt id="link-19" 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-19', 'close', 'link-19');">close</a></tt><tt class="py-op">(</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">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-20', 'parse', 'link-20');">parse</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-21', 'File', 'link-7');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-22', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-23" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-23', 'data', 'link-13');">data</a></tt> </tt>
</div><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="Iterator.__iter__-toggle" onclick="return toggle('Iterator.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool.Iterator-class.html#__iter__">__iter__</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="Iterator.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__iter__-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-24', 'next', 'link-14');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer"></a><div id="_RecordConsumer-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="_RecordConsumer-toggle" onclick="return toggle('_RecordConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html">_RecordConsumer</a><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_RecordConsumer-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a MetaTool Record object from scanner generated information.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_RecordConsumer.__init__"></a><div id="_RecordConsumer.__init__-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="_RecordConsumer.__init__-toggle" onclick="return toggle('_RecordConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#__init__">__init__</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="_RecordConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.__init__-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-25', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-26', 'Record', 'link-9');">Record</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-27', 'Record', 'link-9');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-28', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">internal_metabolites</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-29', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">external_metabolites</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.input_file_name"></a><div id="_RecordConsumer.input_file_name-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="_RecordConsumer.input_file_name-toggle" onclick="return toggle('_RecordConsumer.input_file_name');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#input_file_name">input_file_name</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.input_file_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.input_file_name-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-30', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.input_file_name()=Bio.MetaTool._RecordConsumer-class.html#input_file_name"><a title="Bio.MetaTool._RecordConsumer.input_file_name" class="py-name" href="#" onclick="return doclink('link-31', 'input_file_name', 'link-31');">input_file_name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">content</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.input_file_tag"></a><div id="_RecordConsumer.input_file_tag-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="_RecordConsumer.input_file_tag-toggle" onclick="return toggle('_RecordConsumer.input_file_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#input_file_tag">input_file_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.input_file_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.input_file_tag-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"input_file_state"</tt> </tt>
</div><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.metabolite_count_tag"></a><div id="_RecordConsumer.metabolite_count_tag-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="_RecordConsumer.metabolite_count_tag-toggle" onclick="return toggle('_RecordConsumer.metabolite_count_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#metabolite_count_tag">metabolite_count_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.metabolite_count_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.metabolite_count_tag-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"metabolite_count_state"</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.reaction_count_tag"></a><div id="_RecordConsumer.reaction_count_tag-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="_RecordConsumer.reaction_count_tag-toggle" onclick="return toggle('_RecordConsumer.reaction_count_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#reaction_count_tag">reaction_count_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.reaction_count_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.reaction_count_tag-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"reaction_count_state"</tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.matrix_row"></a><div id="_RecordConsumer.matrix_row-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="_RecordConsumer.matrix_row-toggle" onclick="return toggle('_RecordConsumer.matrix_row');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#matrix_row">matrix_row</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">matrix_rows</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.matrix_row-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.matrix_row-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-32" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.matrix_row()=Bio.MetaTool._RecordConsumer-class.html#matrix_row,Variable Bio.MetaTool.metatool_format.matrix_row=Bio.MetaTool.metatool_format-module.html#matrix_row"><a title="Bio.MetaTool._RecordConsumer.matrix_row
Bio.MetaTool.metatool_format.matrix_row" class="py-name" href="#" onclick="return doclink('link-32', 'matrix_row', 'link-32');">matrix_row</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">matrix_rows</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt id="link-33" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.elements()=Bio.Restriction.Restriction.RestrictionBatch-class.html#elements"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-33', 'elements', 'link-33');">elements</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.MetaTool._RecordConsumer.matrix_row
Bio.MetaTool.metatool_format.matrix_row" class="py-name" href="#" onclick="return doclink('link-34', 'matrix_row', 'link-32');">matrix_row</a></tt><tt class="py-op">.</tt><tt id="link-35" 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-35', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">vector</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-36" class="py-name" targets="Method Martel.LAX.LAX.element()=Martel.LAX.LAX-class.html#element,Method Martel.LAX.LAXAttrs.element()=Martel.LAX.LAXAttrs-class.html#element,Method Martel.LAX.LAXPositions.element()=Martel.LAX.LAXPositions-class.html#element"><a title="Martel.LAX.LAX.element
Martel.LAX.LAXAttrs.element
Martel.LAX.LAXPositions.element" class="py-name" href="#" onclick="return doclink('link-36', 'element', 'link-36');">element</a></tt> <tt class="py-keyword">in</tt> <tt id="link-37" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-37', 'elements', 'link-33');">elements</a></tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">vector</tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-39" class="py-name"><a title="Martel.LAX.LAX.element
Martel.LAX.LAXAttrs.element
Martel.LAX.LAXPositions.element" class="py-name" href="#" onclick="return doclink('link-39', 'element', 'link-36');">element</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">vector</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.unbalanced_metabolite"></a><div id="_RecordConsumer.unbalanced_metabolite-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="_RecordConsumer.unbalanced_metabolite-toggle" onclick="return toggle('_RecordConsumer.unbalanced_metabolite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#unbalanced_metabolite">unbalanced_metabolite</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.unbalanced_metabolite-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.unbalanced_metabolite-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">metabolite</tt> <tt class="py-keyword">in</tt> <tt class="py-name">content</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-41', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">unbalanced_metabolites</tt><tt class="py-op">.</tt><tt id="link-42" 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-42', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">metabolite</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.branch_metabolite"></a><div id="_RecordConsumer.branch_metabolite-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="_RecordConsumer.branch_metabolite-toggle" onclick="return toggle('_RecordConsumer.branch_metabolite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#branch_metabolite">branch_metabolite</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.branch_metabolite-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.branch_metabolite-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">metabolite</tt> <tt class="py-keyword">in</tt> <tt class="py-name">content</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt id="link-43" 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-43', 'items', 'link-43');">items</a></tt> <tt class="py-op">=</tt> <tt class="py-name">metabolite</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-44', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt id="link-45" 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-45', 'name', 'link-45');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-46" 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-46', 'items', 'link-43');">items</a></tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">consumed</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-47" 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-47', 'items', 'link-43');">items</a></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="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">built</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-48" 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-48', 'items', 'link-43');">items</a></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="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">vector</tt> <tt class="py-op">=</tt> <tt id="link-49" 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-49', 'items', 'link-43');">items</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">replace</tt><tt class="py-op">(</tt> <tt class="py-string">'r'</tt><tt class="py-op">,</tt> <tt class="py-string">'0'</tt> <tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">vector</tt> <tt class="py-op">=</tt> <tt class="py-name">vector</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> <tt class="py-string">'i'</tt><tt class="py-op">,</tt> <tt class="py-string">'1'</tt> <tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">vector</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-50', 'list', 'link-50');">list</a></tt><tt class="py-op">(</tt> <tt class="py-name">vector</tt> <tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt id="link-51" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-51', 'map', 'link-51');">map</a></tt><tt class="py-op">(</tt> <tt class="py-name">int</tt><tt class="py-op">,</tt> <tt class="py-name">vector</tt> <tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">entry</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-52', 'Record', 'link-9');">Record</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Class Bio.MetaTool.Record.MetaboliteRole=Bio.MetaTool.Record.MetaboliteRole-class.html"><a title="Bio.MetaTool.Record.MetaboliteRole" class="py-name" href="#" onclick="return doclink('link-53', 'MetaboliteRole', 'link-53');">MetaboliteRole</a></tt><tt class="py-op">(</tt> <tt id="link-54" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-54', 'name', 'link-45');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">consumed</tt><tt class="py-op">,</tt> <tt class="py-name">built</tt><tt class="py-op">,</tt> <tt class="py-name">vector</tt> <tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-55', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branch_metabolites</tt><tt class="py-op">.</tt><tt id="link-56" 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-56', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">entry</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.non_branch_metabolite"></a><div id="_RecordConsumer.non_branch_metabolite-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="_RecordConsumer.non_branch_metabolite-toggle" onclick="return toggle('_RecordConsumer.non_branch_metabolite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#non_branch_metabolite">non_branch_metabolite</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.non_branch_metabolite-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.non_branch_metabolite-expanded"><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">metabolite</tt> <tt class="py-keyword">in</tt> <tt class="py-name">content</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt id="link-57" 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-57', 'items', 'link-43');">items</a></tt> <tt class="py-op">=</tt> <tt class="py-name">metabolite</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-58', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt id="link-59" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-59', 'name', 'link-45');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-60" 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-60', 'items', 'link-43');">items</a></tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">consumed</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-61" 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-61', 'items', 'link-43');">items</a></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="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">built</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-62" 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-62', 'items', 'link-43');">items</a></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="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">vector</tt> <tt class="py-op">=</tt> <tt id="link-63" 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-63', 'items', 'link-43');">items</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">replace</tt><tt class="py-op">(</tt> <tt class="py-string">'r'</tt><tt class="py-op">,</tt> <tt class="py-string">'0'</tt> <tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">vector</tt> <tt class="py-op">=</tt> <tt class="py-name">vector</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt> <tt class="py-string">'i'</tt><tt class="py-op">,</tt> <tt class="py-string">'1'</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">vector</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-64', 'list', 'link-50');">list</a></tt><tt class="py-op">(</tt> <tt class="py-name">vector</tt> <tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">entry</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-65', 'Record', 'link-9');">Record</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.MetaTool.Record.MetaboliteRole" class="py-name" href="#" onclick="return doclink('link-66', 'MetaboliteRole', 'link-53');">MetaboliteRole</a></tt><tt class="py-op">(</tt> <tt id="link-67" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-67', 'name', 'link-45');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">consumed</tt><tt class="py-op">,</tt> <tt class="py-name">built</tt><tt class="py-op">,</tt> <tt class="py-name">vector</tt> <tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-68', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">non_branch_metabolites</tt><tt class="py-op">.</tt><tt id="link-69" 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-69', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">entry</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.stoichiometric_tag"></a><div id="_RecordConsumer.stoichiometric_tag-def"><a name="L120"></a><tt class="py-lineno">120</tt> <a class="py-toggle" href="#" id="_RecordConsumer.stoichiometric_tag-toggle" onclick="return toggle('_RecordConsumer.stoichiometric_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#stoichiometric_tag">stoichiometric_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.stoichiometric_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.stoichiometric_tag-expanded"><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"stoichiometry_state"</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.kernel_tag"></a><div id="_RecordConsumer.kernel_tag-def"><a name="L126"></a><tt class="py-lineno">126</tt> <a class="py-toggle" href="#" id="_RecordConsumer.kernel_tag-toggle" onclick="return toggle('_RecordConsumer.kernel_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#kernel_tag">kernel_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">kernel_tag</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.kernel_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.kernel_tag-expanded"><a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"kernel_state"</tt> </tt>
<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">_vectors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</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">_enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.subsets_tag"></a><div id="_RecordConsumer.subsets_tag-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="_RecordConsumer.subsets_tag-toggle" onclick="return toggle('_RecordConsumer.subsets_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#subsets_tag">subsets_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.subsets_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.subsets_tag-expanded"><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"subsets_state"</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">_vectors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </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">_reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.reduced_system_tag"></a><div id="_RecordConsumer.reduced_system_tag-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="_RecordConsumer.reduced_system_tag-toggle" onclick="return toggle('_RecordConsumer.reduced_system_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#reduced_system_tag">reduced_system_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.reduced_system_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.reduced_system_tag-expanded"><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">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"reduced_system_state"</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </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">_enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.convex_basis_tag"></a><div id="_RecordConsumer.convex_basis_tag-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="_RecordConsumer.convex_basis_tag-toggle" onclick="return toggle('_RecordConsumer.convex_basis_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#convex_basis_tag">convex_basis_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.convex_basis_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.convex_basis_tag-expanded"><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"convex_basis_state"</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.conservation_relations_tag"></a><div id="_RecordConsumer.conservation_relations_tag-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="_RecordConsumer.conservation_relations_tag-toggle" onclick="return toggle('_RecordConsumer.conservation_relations_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#conservation_relations_tag">conservation_relations_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.conservation_relations_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.conservation_relations_tag-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"conservation_relations_state"</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">=</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">_enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.elementary_modes_tag"></a><div id="_RecordConsumer.elementary_modes_tag-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="_RecordConsumer.elementary_modes_tag-toggle" onclick="return toggle('_RecordConsumer.elementary_modes_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#elementary_modes_tag">elementary_modes_tag</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.elementary_modes_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.elementary_modes_tag-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">"elementary_modes_state"</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.metabolite_line"></a><div id="_RecordConsumer.metabolite_line-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="_RecordConsumer.metabolite_line-toggle" onclick="return toggle('_RecordConsumer.metabolite_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#metabolite_line">metabolite_line</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.metabolite_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.metabolite_line-expanded"><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 id="link-70" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-70', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">external_metabolites</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-71', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">internal_metabolites</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">metabolite</tt> <tt class="py-keyword">in</tt> <tt class="py-name">content</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt id="link-72" 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-72', 'items', 'link-43');">items</a></tt> <tt class="py-op">=</tt> <tt class="py-name">metabolite</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-73', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">entry</tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-74', 'Record', 'link-9');">Record</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Class Bio.MetaTool.Record.Metabolite=Bio.MetaTool.Record.Metabolite-class.html"><a title="Bio.MetaTool.Record.Metabolite" class="py-name" href="#" onclick="return doclink('link-75', 'Metabolite', 'link-75');">Metabolite</a></tt><tt class="py-op">(</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-76" 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-76', 'items', 'link-43');">items</a></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 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-43');">items</a></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="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-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-78" 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-78', 'items', 'link-43');">items</a></tt><tt class="py-op">[</tt> <tt class="py-number">1</tt> <tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"external"</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-79', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">external_metabolites</tt><tt class="py-op">.</tt><tt id="link-80" 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-80', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">entry</tt> <tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">else</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">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-81', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">internal_metabolites</tt><tt class="py-op">.</tt><tt id="link-82" 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-82', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">entry</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.num_int_metabolites"></a><div id="_RecordConsumer.num_int_metabolites-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="_RecordConsumer.num_int_metabolites-toggle" onclick="return toggle('_RecordConsumer.num_int_metabolites');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#num_int_metabolites">num_int_metabolites</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.num_int_metabolites-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.num_int_metabolites-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-83" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.num_int_metabolites()=Bio.MetaTool._RecordConsumer-class.html#num_int_metabolites"><a title="Bio.MetaTool._RecordConsumer.num_int_metabolites" class="py-name" href="#" onclick="return doclink('link-83', 'num_int_metabolites', 'link-83');">num_int_metabolites</a></tt> <tt class="py-op">=</tt> <tt class="py-name">content</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-84', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.MetaTool._RecordConsumer.num_int_metabolites" class="py-name" href="#" onclick="return doclink('link-85', 'num_int_metabolites', 'link-83');">num_int_metabolites</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-86" class="py-name"><a title="Bio.MetaTool._RecordConsumer.num_int_metabolites" class="py-name" href="#" onclick="return doclink('link-86', 'num_int_metabolites', 'link-83');">num_int_metabolites</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.num_reactions"></a><div id="_RecordConsumer.num_reactions-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="_RecordConsumer.num_reactions-toggle" onclick="return toggle('_RecordConsumer.num_reactions');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#num_reactions">num_reactions</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.num_reactions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.num_reactions-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt id="link-87" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.num_reactions()=Bio.MetaTool._RecordConsumer-class.html#num_reactions"><a title="Bio.MetaTool._RecordConsumer.num_reactions" class="py-name" href="#" onclick="return doclink('link-87', 'num_reactions', 'link-87');">num_reactions</a></tt> <tt class="py-op">=</tt> <tt class="py-name">content</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-88', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.MetaTool._RecordConsumer.num_reactions" class="py-name" href="#" onclick="return doclink('link-89', 'num_reactions', 'link-87');">num_reactions</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt> <tt id="link-90" class="py-name"><a title="Bio.MetaTool._RecordConsumer.num_reactions" class="py-name" href="#" onclick="return doclink('link-90', 'num_reactions', 'link-87');">num_reactions</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.irreversible_vector"></a><div id="_RecordConsumer.irreversible_vector-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="_RecordConsumer.irreversible_vector-toggle" onclick="return toggle('_RecordConsumer.irreversible_vector');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#irreversible_vector">irreversible_vector</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.irreversible_vector-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.irreversible_vector-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_irreversible_vector</tt> <tt class="py-op">=</tt> <tt class="py-name">content</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-91', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.reaction"></a><div id="_RecordConsumer.reaction-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="_RecordConsumer.reaction-toggle" onclick="return toggle('_RecordConsumer.reaction');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#reaction">reaction</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">reactions</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.reaction-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.reaction-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-92" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.reaction()=Bio.MetaTool._RecordConsumer-class.html#reaction,Variable Bio.MetaTool.metatool_format.reaction=Bio.MetaTool.metatool_format-module.html#reaction"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-92', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt id="link-93" class="py-name" targets="Method Bio.Pathway.System.reactions()=Bio.Pathway.System-class.html#reactions"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-93', 'reactions', 'link-93');">reactions</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-94" 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-94', 'items', 'link-43');">items</a></tt> <tt class="py-op">=</tt> <tt id="link-95" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-95', 'reaction', 'link-92');">reaction</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-96', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt id="link-97" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-97', 'item', 'link-97');">item</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt id="link-98" 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-98', 'items', 'link-43');">items</a></tt><tt class="py-op">[</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt><tt class="py-op">.</tt><tt id="link-99" 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-99', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt><tt id="link-100" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-100', 'item', 'link-97');">item</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.enzyme"></a><div id="_RecordConsumer.enzyme-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="_RecordConsumer.enzyme-toggle" onclick="return toggle('_RecordConsumer.enzyme');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#enzyme">enzyme</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">enzymes</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.enzyme-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.enzyme-expanded"><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-101" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.enzyme()=Bio.MetaTool._RecordConsumer-class.html#enzyme,Variable Bio.MetaTool.metatool_format.enzyme=Bio.MetaTool.metatool_format-module.html#enzyme"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-101', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">enzymes</tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt id="link-102" 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-102', 'items', 'link-43');">items</a></tt> <tt class="py-op">=</tt> <tt id="link-103" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-103', 'enzyme', 'link-101');">enzyme</a></tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-104', 'split', 'link-35');">split</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 id="link-105" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-105', 'item', 'link-97');">item</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt id="link-106" 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-106', 'items', 'link-43');">items</a></tt><tt class="py-op">[</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-op">]</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">_enzymes</tt><tt class="py-op">.</tt><tt id="link-107" 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-107', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt><tt id="link-108" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-108', 'item', 'link-97');">item</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.sum_is_constant_line"></a><div id="_RecordConsumer.sum_is_constant_line-def"><a name="L198"></a><tt class="py-lineno">198</tt> <a class="py-toggle" href="#" id="_RecordConsumer.sum_is_constant_line-toggle" onclick="return toggle('_RecordConsumer.sum_is_constant_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#sum_is_constant_line">sum_is_constant_line</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">lines</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.sum_is_constant_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.sum_is_constant_line-expanded"><a name="L199"></a><tt class="py-lineno">199</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="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt id="link-109" 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-109', 'items', 'link-43');">items</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-110', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt> <tt class="py-string">':'</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt id="link-111" 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-111', 'items', 'link-43');">items</a></tt> <tt class="py-op">=</tt> <tt id="link-112" 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-112', 'items', 'link-43');">items</a></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-113" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-113', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt> <tt class="py-string">'='</tt> <tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-114', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">sum_is_constant_lines</tt><tt class="py-op">.</tt><tt id="link-115" 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-115', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-116" 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-116', 'items', 'link-43');">items</a></tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.num_rows"></a><div id="_RecordConsumer.num_rows-def"><a name="L204"></a><tt class="py-lineno">204</tt> <a class="py-toggle" href="#" id="_RecordConsumer.num_rows-toggle" onclick="return toggle('_RecordConsumer.num_rows');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#num_rows">num_rows</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">num_rows</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.num_rows-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.num_rows-expanded"><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.num_cols"></a><div id="_RecordConsumer.num_cols-def"><a name="L207"></a><tt class="py-lineno">207</tt> <a class="py-toggle" href="#" id="_RecordConsumer.num_cols-toggle" onclick="return toggle('_RecordConsumer.num_cols');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#num_cols">num_cols</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">num_cols</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.num_cols-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.num_cols-expanded"><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.metabolite_roles"></a><div id="_RecordConsumer.metabolite_roles-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="_RecordConsumer.metabolite_roles-toggle" onclick="return toggle('_RecordConsumer.metabolite_roles');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#metabolite_roles">metabolite_roles</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.metabolite_roles-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.metabolite_roles-expanded"><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">metabolite_role</tt> <tt class="py-keyword">in</tt> <tt class="py-name">content</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">cols</tt> <tt class="py-op">=</tt> <tt class="py-name">metabolite_role</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-117', 'split', 'link-35');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_stochiometric"></a><div id="_RecordConsumer.end_stochiometric-def"><a name="L214"></a><tt class="py-lineno">214</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_stochiometric-toggle" onclick="return toggle('_RecordConsumer.end_stochiometric');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#end_stochiometric">end_stochiometric</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.end_stochiometric-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_stochiometric-expanded"><a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-118', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">stochiometric</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.matrix()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#matrix,Variable Bio.MetaTool.metatool_format.matrix=Bio.MetaTool.metatool_format-module.html#matrix,Method Bio.Prosite._RecordConsumer.matrix()=Bio.Prosite._RecordConsumer-class.html#matrix"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-119', 'matrix', 'link-119');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Matrix</tt><tt class="py-op">.</tt><tt class="py-name">Matrix</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-120', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">stochiometric</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-121" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-121', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-122', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">stochiometric</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">.</tt><tt id="link-123" 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-123', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-124" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-124', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-125', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">stochiometric</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-126" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-126', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt><tt class="py-op">:</tt> </tt>
<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 id="link-127" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-127', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">stochiometric</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-128', 'reactions', 'link-93');">reactions</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-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-130" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-130', 'reaction', 'link-92');">reaction</a></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">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_irreversible_vector</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-131', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">stochiometric</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.irreversible_vector()=Bio.MetaTool._RecordConsumer-class.html#irreversible_vector,Variable Bio.MetaTool.metatool_format.irreversible_vector=Bio.MetaTool.metatool_format-module.html#irreversible_vector"><a title="Bio.MetaTool._RecordConsumer.irreversible_vector
Bio.MetaTool.metatool_format.irreversible_vector" class="py-name" href="#" onclick="return doclink('link-132', 'irreversible_vector', 'link-132');">irreversible_vector</a></tt><tt class="py-op">.</tt><tt id="link-133" 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-133', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">col</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_kernel"></a><div id="_RecordConsumer.end_kernel-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_kernel-toggle" onclick="return toggle('_RecordConsumer.end_kernel');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#end_kernel">end_kernel</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.end_kernel-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_kernel-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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="L228"></a><tt class="py-lineno">228</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="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-134', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">kernel</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-135', 'matrix', 'link-119');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Matrix</tt><tt class="py-op">.</tt><tt class="py-name">Matrix</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</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-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">kernel</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-137" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-137', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt><tt class="py-op">:</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-138', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">kernel</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">.</tt><tt id="link-139" 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-139', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-140" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-140', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-141" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-141', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</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">self</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-142', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">kernel</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-143', 'reactions', 'link-93');">reactions</a></tt><tt class="py-op">.</tt><tt id="link-144" 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-144', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-145" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-145', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_subsets"></a><div id="_RecordConsumer.end_subsets-def"><a name="L235"></a><tt class="py-lineno">235</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_subsets-toggle" onclick="return toggle('_RecordConsumer.end_subsets');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#end_subsets">end_subsets</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.end_subsets-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_subsets-expanded"><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-146', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">subsets</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-147', 'matrix', 'link-119');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Matrix</tt><tt class="py-op">.</tt><tt class="py-name">Matrix</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-148', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">subsets</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-149" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-149', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-150', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">subsets</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">.</tt><tt id="link-151" 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-151', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-152" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-152', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-153" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-153', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-154', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">subsets</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-155', 'reactions', 'link-93');">reactions</a></tt><tt class="py-op">.</tt><tt id="link-156" 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-156', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-157" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-157', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_reduced_system"></a><div id="_RecordConsumer.end_reduced_system-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_reduced_system-toggle" onclick="return toggle('_RecordConsumer.end_reduced_system');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#end_reduced_system">end_reduced_system</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.end_reduced_system-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_reduced_system-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-158', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">reduced_system</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-159', 'matrix', 'link-119');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Matrix</tt><tt class="py-op">.</tt><tt class="py-name">Matrix</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">14</tt><tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-160', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">reduced_system</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-161" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-161', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-162', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">reduced_system</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">.</tt><tt id="link-163" 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-163', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-164" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-164', 'enzyme', 'link-101');">enzyme</a></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-165" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-165', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt><tt class="py-op">:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-166', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">reduced_system</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-167', 'reactions', 'link-93');">reactions</a></tt><tt class="py-op">.</tt><tt id="link-168" 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-168', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-169" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-169', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">col</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_irreversible_vector</tt><tt class="py-op">:</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-170', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">reduced_system</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.MetaTool._RecordConsumer.irreversible_vector
Bio.MetaTool.metatool_format.irreversible_vector" class="py-name" href="#" onclick="return doclink('link-171', 'irreversible_vector', 'link-132');">irreversible_vector</a></tt><tt class="py-op">.</tt><tt id="link-172" 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-172', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">col</tt> <tt class="py-op">)</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="_RecordConsumer.end_convex_basis"></a><div id="_RecordConsumer.end_convex_basis-def"><a name="L257"></a><tt class="py-lineno">257</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_convex_basis-toggle" onclick="return toggle('_RecordConsumer.end_convex_basis');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#end_convex_basis">end_convex_basis</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.end_convex_basis-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_convex_basis-expanded"><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-173', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">convex_basis</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-174', 'matrix', 'link-119');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Matrix</tt><tt class="py-op">.</tt><tt class="py-name">Matrix</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</tt> <tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-175', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">convex_basis</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-176" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-176', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-177', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">convex_basis</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">.</tt><tt id="link-178" 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-178', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-179" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-179', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-180" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-180', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt><tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-181', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">convex_basis</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-182', 'reactions', 'link-93');">reactions</a></tt><tt class="py-op">.</tt><tt id="link-183" 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-183', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-184" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-184', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_conservation_relations"></a><div id="_RecordConsumer.end_conservation_relations-def"><a name="L266"></a><tt class="py-lineno">266</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_conservation_relations-toggle" onclick="return toggle('_RecordConsumer.end_conservation_relations');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#end_conservation_relations">end_conservation_relations</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.end_conservation_relations-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_conservation_relations-expanded"><a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-185" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-185', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">conservation_relations</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-186', 'matrix', 'link-119');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Matrix</tt><tt class="py-op">.</tt><tt class="py-name">Matrix</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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">self</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-187', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">conservation_relations</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</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">for</tt> <tt id="link-188" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-188', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</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">self</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-189', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">conservation_relations</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">.</tt><tt id="link-190" 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-190', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-191" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-191', 'enzyme', 'link-101');">enzyme</a></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">for</tt> <tt id="link-192" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-192', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</tt><tt class="py-op">:</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-193', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">conservation_relations</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-194', 'reactions', 'link-93');">reactions</a></tt><tt class="py-op">.</tt><tt id="link-195" 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-195', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-196" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-196', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_elementary_modes"></a><div id="_RecordConsumer.end_elementary_modes-def"><a name="L276"></a><tt class="py-lineno">276</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_elementary_modes-toggle" onclick="return toggle('_RecordConsumer.end_elementary_modes');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._RecordConsumer-class.html#end_elementary_modes">end_elementary_modes</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.end_elementary_modes-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_elementary_modes-expanded"><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-197', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">elementary_modes</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix
Bio.MetaTool.metatool_format.matrix
Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-198', 'matrix', 'link-119');">matrix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Matrix</tt><tt class="py-op">.</tt><tt class="py-name">Matrix</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_vectors</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">self</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-199', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">elementary_modes</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-200" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-200', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_enzymes</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">self</tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-201', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">elementary_modes</tt><tt class="py-op">.</tt><tt class="py-name">enzymes</tt><tt class="py-op">.</tt><tt id="link-202" 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-202', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-203" class="py-name"><a title="Bio.MetaTool._RecordConsumer.enzyme
Bio.MetaTool.metatool_format.enzyme" class="py-name" href="#" onclick="return doclink('link-203', 'enzyme', 'link-101');">enzyme</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-204" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-204', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reactions</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">self</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-205', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">elementary_modes</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-206', 'reactions', 'link-93');">reactions</a></tt><tt class="py-op">.</tt><tt id="link-207" 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-207', 'append', 'link-38');">append</a></tt><tt class="py-op">(</tt> <tt id="link-208" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-208', 'reaction', 'link-92');">reaction</a></tt> <tt class="py-op">)</tt> </tt>
</div></div><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
<a name="_Scanner"></a><div id="_Scanner-def"><a name="L285"></a><tt class="py-lineno">285</tt> <a class="py-toggle" href="#" id="_Scanner-toggle" onclick="return toggle('_Scanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MetaTool._Scanner-class.html">_Scanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Scanner-expanded"><a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-docstring">"""Start up Martel to do the scanning of the file.</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-docstring"> This initialzes the Martel based parser and connects it to a handler</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-docstring"> that will generate events for a Feature Consumer.</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_Scanner.__init__"></a><div id="_Scanner.__init__-def"><a name="L291"></a><tt class="py-lineno">291</tt> <a class="py-toggle" href="#" id="_Scanner.__init__-toggle" onclick="return toggle('_Scanner.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._Scanner-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">debug</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.__init__-expanded"><a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the scanner by setting up our caches.</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"> Creating the parser takes a long time, so we want to cache it</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> to reduce parsing time.</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> o debug - The level of debugging that the parser should</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> display. Level 0 is no debugging, Level 2 displays the most</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> debugging info (but is much slower). See Martel documentation</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> for more info on this.</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-comment"># a listing of all tags we are interested in scanning for</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in the MartelParser</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">"input_file_name"</tt><tt class="py-op">,</tt> <tt class="py-string">"num_int_metabolites"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-string">"num_reactions"</tt><tt class="py-op">,</tt> <tt class="py-string">"metabolite_line"</tt><tt class="py-op">,</tt> <tt class="py-string">"unbalanced_metabolite"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-string">"num_rows"</tt><tt class="py-op">,</tt> <tt class="py-string">"num_cols"</tt><tt class="py-op">,</tt> <tt class="py-string">"irreversible_vector"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-string">"branch_metabolite"</tt><tt class="py-op">,</tt> <tt class="py-string">"non_branch_metabolite"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-string">"stoichiometric_tag"</tt><tt class="py-op">,</tt> <tt class="py-string">"kernel_tag"</tt><tt class="py-op">,</tt> <tt class="py-string">"subsets_tag"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-string">"reduced_system_tag"</tt><tt class="py-op">,</tt> <tt class="py-string">"convex_basis_tag"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-string">"conservation_relations_tag"</tt><tt class="py-op">,</tt> <tt class="py-string">"elementary_modes_tag"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-string">"reaction"</tt><tt class="py-op">,</tt> <tt class="py-string">"enzyme"</tt><tt class="py-op">,</tt> <tt class="py-string">"matrix_row"</tt><tt class="py-op">,</tt> <tt class="py-string">"sum_is_constant_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-string">"end_stochiometric"</tt><tt class="py-op">,</tt> <tt class="py-string">"end_kernel"</tt><tt class="py-op">,</tt> <tt class="py-string">"end_subsets"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-string">"end_reduced_system"</tt><tt class="py-op">,</tt> <tt class="py-string">"end_convex_basis"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-string">"end_conservation_relations"</tt><tt class="py-op">,</tt> <tt class="py-string">"end_elementary_modes"</tt> <tt class="py-op">]</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-comment"># make a parser that returns only the tags we are interested in</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt id="link-209" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-209', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-210" class="py-name" targets="Function Martel.select_names()=Martel-module.html#select_names"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-210', 'select_names', 'link-210');">select_names</a></tt><tt class="py-op">(</tt> <tt id="link-211" class="py-name"><a title="Bio.MetaTool.metatool_format" class="py-name" href="#" onclick="return doclink('link-211', 'metatool_format', 'link-8');">metatool_format</a></tt><tt class="py-op">.</tt><tt id="link-212" class="py-name" targets="Variable Bio.MetaTool.metatool_format.metatool_record=Bio.MetaTool.metatool_format-module.html#metatool_record"><a title="Bio.MetaTool.metatool_format.metatool_record" class="py-name" href="#" onclick="return doclink('link-212', 'metatool_record', 'link-212');">metatool_record</a></tt><tt class="py-op">,</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">expression</tt><tt class="py-op">.</tt><tt id="link-213" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_parser()=Bio.config.FormatRegistry.FormatObject-class.html#make_parser,Method Bio.config._support.make_cached_expression.make_parser()=Bio.config._support.make_cached_expression-class.html#make_parser,Method Martel.Expression.Expression.make_parser()=Martel.Expression.Expression-class.html#make_parser,Method Martel.Expression.HeaderFooter.make_parser()=Martel.Expression.HeaderFooter-class.html#make_parser,Method Martel.Expression.ParseRecords.make_parser()=Martel.Expression.ParseRecords-class.html#make_parser"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-213', 'make_parser', 'link-213');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug</tt><tt class="py-op">)</tt> </tt>
</div><a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> </tt>
<a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L322"></a><tt class="py-lineno">322</tt> <a class="py-toggle" href="#" id="_Scanner.feed-toggle" onclick="return toggle('_Scanner.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool._Scanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.feed-expanded"><a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-docstring">"""Feeed a set of data into the scanner.</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-docstring"> o handle - A handle with the information to parse.</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-docstring"> o consumer - The consumer that should be informed of events.</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt id="link-214" class="py-name"><a title="Bio.ParserSupport.EventGenerator" class="py-name" href="#" onclick="return doclink('link-214', 'EventGenerator', 'link-5');">EventGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">consumer</tt><tt class="py-op">,</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-comment"># _strip_and_combine ))</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</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>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.parseFile()=Bio.EUtils.POM.POMDocument-class.html#parseFile,Method Martel.Parser.HeaderFooterParser.parseFile()=Martel.Parser.HeaderFooterParser-class.html#parseFile,Method Martel.Parser.Parser.parseFile()=Martel.Parser.Parser-class.html#parseFile,Method Martel.Parser.RecordParser.parseFile()=Martel.Parser.RecordParser-class.html#parseFile"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-215', 'parseFile', 'link-215');">parseFile</a></tt><tt class="py-op">(</tt><tt id="link-216" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-216', 'handle', 'link-12');">handle</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> </tt>
<a name="RecordParser"></a><div id="RecordParser-def"><a name="L336"></a><tt class="py-lineno">336</tt> <a class="py-toggle" href="#" id="RecordParser-toggle" onclick="return toggle('RecordParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MetaTool.RecordParser-class.html">RecordParser</a><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordParser-expanded"><a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse MetaTool files into Record objects</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="RecordParser.__init__"></a><div id="RecordParser.__init__-def"><a name="L339"></a><tt class="py-lineno">339</tt> <a class="py-toggle" href="#" id="RecordParser.__init__-toggle" onclick="return toggle('RecordParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool.RecordParser-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">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.__init__-expanded"><a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the parser.</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt class="py-docstring"> o debug_level - An optional argument that species the amount of</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-docstring"> debugging information Martel should spit out. By default we have</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-docstring"> no debugging info (the fastest way to do things), but if you want</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-docstring"> you can set this as high as two and see exactly where a parse fails.</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-217" class="py-name" targets="Class Bio.Blast.NCBIStandalone._Scanner=Bio.Blast.NCBIStandalone._Scanner-class.html,Class Bio.Blast.NCBIWWW._Scanner=Bio.Blast.NCBIWWW._Scanner-class.html,Class Bio.CDD._Scanner=Bio.CDD._Scanner-class.html,Class Bio.Compass._Scanner=Bio.Compass._Scanner-class.html,Class Bio.ECell._Scanner=Bio.ECell._Scanner-class.html,Class Bio.Enzyme._Scanner=Bio.Enzyme._Scanner-class.html,Class Bio.Gobase._Scanner=Bio.Gobase._Scanner-class.html,Class Bio.IntelliGenetics._Scanner=Bio.IntelliGenetics._Scanner-class.html,Class Bio.LocusLink._Scanner=Bio.LocusLink._Scanner-class.html,Class Bio.Medline._Scanner=Bio.Medline._Scanner-class.html,Class Bio.MetaTool._Scanner=Bio.MetaTool._Scanner-class.html,Class Bio.NBRF._Scanner=Bio.NBRF._Scanner-class.html,Class Bio.PopGen.FDist._Scanner=Bio.PopGen.FDist._Scanner-class.html,Class Bio.PopGen.GenePop._Scanner=Bio.PopGen.GenePop._Scanner-class.html,Class Bio.Prosite.Prodoc._Scanner=Bio.Prosite.Prodoc._Scanner-class.html,Class Bio.Prosite._Scanner=Bio.Prosite._Scanner-class.html,Class Bio.Rebase._Scanner=Bio.Rebase._Scanner-class.html,Class Bio.Saf._Scanner=Bio.Saf._Scanner-class.html,Class Bio.Sequencing.Ace._Scanner=Bio.Sequencing.Ace._Scanner-class.html,Class Bio.Sequencing.Phd._Scanner=Bio.Sequencing.Phd._Scanner-class.html,Class Bio.SwissProt.KeyWList._Scanner=Bio.SwissProt.KeyWList._Scanner-class.html,Class Bio.SwissProt.SProt._Scanner=Bio.SwissProt.SProt._Scanner-class.html,Class Bio.UniGene._Scanner=Bio.UniGene._Scanner-class.html"><a title="Bio.Blast.NCBIStandalone._Scanner
Bio.Blast.NCBIWWW._Scanner
Bio.CDD._Scanner
Bio.Compass._Scanner
Bio.ECell._Scanner
Bio.Enzyme._Scanner
Bio.Gobase._Scanner
Bio.IntelliGenetics._Scanner
Bio.LocusLink._Scanner
Bio.Medline._Scanner
Bio.MetaTool._Scanner
Bio.NBRF._Scanner
Bio.PopGen.FDist._Scanner
Bio.PopGen.GenePop._Scanner
Bio.Prosite.Prodoc._Scanner
Bio.Prosite._Scanner
Bio.Rebase._Scanner
Bio.Saf._Scanner
Bio.Sequencing.Ace._Scanner
Bio.Sequencing.Phd._Scanner
Bio.SwissProt.KeyWList._Scanner
Bio.SwissProt.SProt._Scanner
Bio.UniGene._Scanner" class="py-name" href="#" onclick="return doclink('link-217', '_Scanner', 'link-217');">_Scanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> </tt>
<a name="RecordParser.parse"></a><div id="RecordParser.parse-def"><a name="L350"></a><tt class="py-lineno">350</tt> <a class="py-toggle" href="#" id="RecordParser.parse-toggle" onclick="return toggle('RecordParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool.RecordParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.parse-expanded"><a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse the specified handle into a MetaTool record.</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-218" class="py-name" targets="Class Bio.CDD._RecordConsumer=Bio.CDD._RecordConsumer-class.html,Class Bio.ECell._RecordConsumer=Bio.ECell._RecordConsumer-class.html,Class Bio.Enzyme._RecordConsumer=Bio.Enzyme._RecordConsumer-class.html,Class Bio.GenBank._RecordConsumer=Bio.GenBank._RecordConsumer-class.html,Class Bio.Gobase._RecordConsumer=Bio.Gobase._RecordConsumer-class.html,Class Bio.IntelliGenetics._RecordConsumer=Bio.IntelliGenetics._RecordConsumer-class.html,Class Bio.LocusLink._RecordConsumer=Bio.LocusLink._RecordConsumer-class.html,Class Bio.Medline._RecordConsumer=Bio.Medline._RecordConsumer-class.html,Class Bio.MetaTool._RecordConsumer=Bio.MetaTool._RecordConsumer-class.html,Class Bio.NBRF._RecordConsumer=Bio.NBRF._RecordConsumer-class.html,Class Bio.PopGen.FDist._RecordConsumer=Bio.PopGen.FDist._RecordConsumer-class.html,Class Bio.PopGen.GenePop._RecordConsumer=Bio.PopGen.GenePop._RecordConsumer-class.html,Class Bio.Prosite.Prodoc._RecordConsumer=Bio.Prosite.Prodoc._RecordConsumer-class.html,Class Bio.Prosite._RecordConsumer=Bio.Prosite._RecordConsumer-class.html,Class Bio.Rebase._RecordConsumer=Bio.Rebase._RecordConsumer-class.html,Class Bio.Saf._RecordConsumer=Bio.Saf._RecordConsumer-class.html,Class Bio.Sequencing.Ace._RecordConsumer=Bio.Sequencing.Ace._RecordConsumer-class.html,Class Bio.Sequencing.Phd._RecordConsumer=Bio.Sequencing.Phd._RecordConsumer-class.html,Class Bio.SwissProt.SProt._RecordConsumer=Bio.SwissProt.SProt._RecordConsumer-class.html,Class Bio.UniGene._RecordConsumer=Bio.UniGene._RecordConsumer-class.html"><a title="Bio.CDD._RecordConsumer
Bio.ECell._RecordConsumer
Bio.Enzyme._RecordConsumer
Bio.GenBank._RecordConsumer
Bio.Gobase._RecordConsumer
Bio.IntelliGenetics._RecordConsumer
Bio.LocusLink._RecordConsumer
Bio.Medline._RecordConsumer
Bio.MetaTool._RecordConsumer
Bio.NBRF._RecordConsumer
Bio.PopGen.FDist._RecordConsumer
Bio.PopGen.GenePop._RecordConsumer
Bio.Prosite.Prodoc._RecordConsumer
Bio.Prosite._RecordConsumer
Bio.Rebase._RecordConsumer
Bio.Saf._RecordConsumer
Bio.Sequencing.Ace._RecordConsumer
Bio.Sequencing.Phd._RecordConsumer
Bio.SwissProt.SProt._RecordConsumer
Bio.UniGene._RecordConsumer" class="py-name" href="#" onclick="return doclink('link-218', '_RecordConsumer', 'link-218');">_RecordConsumer</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 class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-219', 'feed', 'link-219');">feed</a></tt><tt class="py-op">(</tt><tt id="link-220" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-220', 'handle', 'link-12');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</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">_consumer</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-221', 'data', 'link-13');">data</a></tt> </tt>
</div></div><a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> </tt>
<a name="_strip_and_combine"></a><div id="_strip_and_combine-def"><a name="L357"></a><tt class="py-lineno">357</tt> <a class="py-toggle" href="#" id="_strip_and_combine-toggle" onclick="return toggle('_strip_and_combine');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MetaTool-module.html#_strip_and_combine">_strip_and_combine</a><tt class="py-op">(</tt><tt class="py-param">line_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_strip_and_combine-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_strip_and_combine-expanded"><a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-docstring">"""Combine multiple lines of content separated by spaces.</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-docstring"> This function is used by the EventGenerator callback function to</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-docstring"> combine multiple lines of information. The lines are first</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-docstring"> stripped to remove whitepsace, and then combined so they are separated</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-docstring"> by a space. This is a simple minded way to combine lines, but should</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-docstring"> work for most cases.</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-comment"># first strip out extra whitespace</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">stripped_line_list</tt> <tt class="py-op">=</tt> <tt id="link-222" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-222', 'map', 'link-51');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-223" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-223', 'strip', 'link-223');">strip</a></tt><tt class="py-op">,</tt> <tt class="py-name">line_list</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-comment"># now combine everything with spaces</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">stripped_line_list</tt><tt class="py-op">)</tt> </tt>
</div><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt><script type="text/javascript">
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