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

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

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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.Parsers-module.html">Package&nbsp;Parsers</a> ::
        Module&nbsp;spark
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<h1 class="epydoc">Source Code for <a href="Bio.Parsers.spark-module.html">Module Bio.Parsers.spark</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 (c) 1998-2000 John Aycock</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">#  </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">#  Permission is hereby granted, free of charge, to any person obtaining</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">#  a copy of this software and associated documentation files (the</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  "Software"), to deal in the Software without restriction, including</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  without limitation the rights to use, copy, modify, merge, publish,</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  distribute, sublicense, and/or sell copies of the Software, and to</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  permit persons to whom the Software is furnished to do so, subject to</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  the following conditions:</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  The above copyright notice and this permission notice shall be</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  included in all copies or substantial portions of the Software.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  </tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-docstring">'SPARK-0.6.1'</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"> </tt>
<a name="_namelist"></a><div id="_namelist-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="_namelist-toggle" onclick="return toggle('_namelist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark-module.html#_namelist">_namelist</a><tt class="py-op">(</tt><tt class="py-param">instance</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_namelist-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_namelist-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-name">namelist</tt><tt class="py-op">,</tt> <tt class="py-name">namedict</tt><tt class="py-op">,</tt> <tt class="py-name">classlist</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 class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt id="link-0" class="py-name" targets="Variable Bio.PopGen.SimCoal.instance=Bio.PopGen.SimCoal-module.html#instance"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-0', 'instance', 'link-0');">instance</a></tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">]</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">classlist</tt><tt class="py-op">:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">__bases__</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">            <tt class="py-name">classlist</tt><tt class="py-op">.</tt><tt id="link-1" 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-1', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-2" 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-2', 'name', 'link-2');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">dir</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">namedict</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-3', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-4" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-4', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">                <tt class="py-name">namelist</tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-6', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">                <tt class="py-name">namedict</tt><tt class="py-op">[</tt><tt id="link-7" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-2');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">namelist</tt> </tt>
</div><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"> </tt>
<a name="GenericScanner"></a><div id="GenericScanner-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="GenericScanner-toggle" onclick="return toggle('GenericScanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericScanner-class.html">GenericScanner</a><tt class="py-op">:</tt> </tt>
</div><div id="GenericScanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenericScanner-expanded"><a name="GenericScanner.__init__"></a><div id="GenericScanner.__init__-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="GenericScanner.__init__-toggle" onclick="return toggle('GenericScanner.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericScanner-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="GenericScanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericScanner.__init__-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">        <tt id="link-8" class="py-name" targets="Method Bio.Prosite._RecordConsumer.pattern()=Bio.Prosite._RecordConsumer-class.html#pattern"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-8', 'pattern', 'link-8');">pattern</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Parsers.spark.GenericScanner.reflect()=Bio.Parsers.spark.GenericScanner-class.html#reflect"><a title="Bio.Parsers.spark.GenericScanner.reflect" class="py-name" href="#" onclick="return doclink('link-9', 'reflect', 'link-9');">reflect</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-10', 'compile', 'link-10');">compile</a></tt><tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-11', 'pattern', 'link-8');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">VERBOSE</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index2func</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-12" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-12', 'name', 'link-2');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">number</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">groupindex</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'items', 'link-13');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index2func</tt><tt class="py-op">[</tt><tt class="py-name">number</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-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">'t_'</tt> <tt class="py-op">+</tt> <tt id="link-14" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-14', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"> </tt>
<a name="GenericScanner.makeRE"></a><div id="GenericScanner.makeRE-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="GenericScanner.makeRE-toggle" onclick="return toggle('GenericScanner.makeRE');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericScanner-class.html#makeRE">makeRE</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericScanner.makeRE-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericScanner.makeRE-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">        <tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-15', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-16', '__doc__', 'link-16');">__doc__</a></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-string">'(?P&lt;%s&gt;%s)'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-17', 'name', 'link-2');">name</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">doc</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">return</tt> <tt class="py-name">rv</tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"> </tt>
<a name="GenericScanner.reflect"></a><div id="GenericScanner.reflect-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="GenericScanner.reflect-toggle" onclick="return toggle('GenericScanner.reflect');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericScanner-class.html#reflect">reflect</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="GenericScanner.reflect-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericScanner.reflect-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">        <tt class="py-name">rv</tt> <tt class="py-op">=</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">for</tt> <tt id="link-18" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-18', 'name', 'link-2');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-19" class="py-name" targets="Function Bio.Parsers.spark._namelist()=Bio.Parsers.spark-module.html#_namelist"><a title="Bio.Parsers.spark._namelist" class="py-name" href="#" onclick="return doclink('link-19', '_namelist', 'link-19');">_namelist</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-20" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-2');">name</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'t_'</tt> <tt class="py-keyword">and</tt> <tt id="link-21" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-21', 'name', 'link-2');">name</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">'t_default'</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">                <tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-22" 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-22', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Parsers.spark.GenericScanner.makeRE()=Bio.Parsers.spark.GenericScanner-class.html#makeRE"><a title="Bio.Parsers.spark.GenericScanner.makeRE" class="py-name" href="#" onclick="return doclink('link-23', 'makeRE', 'link-23');">makeRE</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-24', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">        <tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Parsers.spark.GenericScanner.makeRE" class="py-name" href="#" onclick="return doclink('link-26', 'makeRE', 'link-23');">makeRE</a></tt><tt class="py-op">(</tt><tt class="py-string">'t_default'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-keyword">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">rv</tt><tt class="py-op">,</tt> <tt class="py-string">'|'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"> </tt>
<a name="GenericScanner.error"></a><div id="GenericScanner.error-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="GenericScanner.error-toggle" onclick="return toggle('GenericScanner.error');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericScanner-class.html#error">error</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">pos</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericScanner.error-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericScanner.error-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Lexical error at position %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">pos</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">SystemExit</tt> </tt>
</div><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"> </tt>
<a name="GenericScanner.tokenize"></a><div id="GenericScanner.tokenize-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="GenericScanner.tokenize-toggle" onclick="return toggle('GenericScanner.tokenize');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericScanner-class.html#tokenize">tokenize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericScanner.tokenize-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericScanner.tokenize-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">        <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-27', 's', 'link-27');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">pos</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">            <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-28', 'match', 'link-28');">match</a></tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-29', 's', 'link-27');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.error()=Bio.Parsers.spark.GenericParser-class.html#error,Method Bio.Parsers.spark.GenericScanner.error()=Bio.Parsers.spark.GenericScanner-class.html#error,Method Martel.Iterator.StoreEvents.error()=Martel.Iterator.StoreEvents-class.html#error,Class Martel.msre_constants.error=Martel.msre_constants.error-class.html,Method Martel.test.support.Dump.error()=Martel.test.support.Dump-class.html#error,Method Martel.test.test_Parser.CountErrors.error()=Martel.test.test_Parser.CountErrors-class.html#error,Method Martel.test.test_optimize.GetErrorPos.error()=Martel.test.test_optimize.GetErrorPos-class.html#error"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-30', 'error', 'link-30');">error</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-31', 's', 'link-27');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">            <tt id="link-32" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.groups()=Bio.Prosite.Pattern.PrositeMatch-class.html#groups"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-32', 'groups', 'link-32');">groups</a></tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-33', 'groups', 'link-32');">groups</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-34" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-34');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-35', 'groups', 'link-32');">groups</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-36" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-36', 'groups', 'link-32');">groups</a></tt><tt class="py-op">[</tt><tt id="link-37" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-37', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index2func</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-38', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index2func</tt><tt class="py-op">[</tt><tt id="link-40" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-40', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-41', 'groups', 'link-32');">groups</a></tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-42', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">            <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-43', 'end', 'link-43');">end</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"> </tt>
<a name="GenericScanner.t_default"></a><div id="GenericScanner.t_default-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="GenericScanner.t_default-toggle" onclick="return toggle('GenericScanner.t_default');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericScanner-class.html#t_default">t_default</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericScanner.t_default-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericScanner.t_default-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-docstring">r'( . | \n )+'</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"> </tt>
<a name="GenericParser"></a><div id="GenericParser-def"><a name="L84"></a><tt class="py-lineno"> 84</tt> <a class="py-toggle" href="#" id="GenericParser-toggle" onclick="return toggle('GenericParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html">GenericParser</a><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenericParser-expanded"><a name="GenericParser.__init__"></a><div id="GenericParser.__init__-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="GenericParser.__init__-toggle" onclick="return toggle('GenericParser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-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">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.__init__-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rule2func</tt> <tt class="py-op">=</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">rule2name</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.collectRules()=Bio.Parsers.spark.GenericParser-class.html#collectRules"><a title="Bio.Parsers.spark.GenericParser.collectRules" class="py-name" href="#" onclick="return doclink('link-44', 'collectRules', 'link-44');">collectRules</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startRule</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.augment()=Bio.Parsers.spark.GenericParser-class.html#augment"><a title="Bio.Parsers.spark.GenericParser.augment" class="py-name" href="#" onclick="return doclink('link-45', 'augment', 'link-45');">augment</a></tt><tt class="py-op">(</tt><tt id="link-46" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-46', 'start', 'link-46');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ruleschanged</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">    <tt id="link-47" class="py-name" targets="Variable Bio.Parsers.spark.GenericParser._START=Bio.Parsers.spark.GenericParser-class.html#_START"><a title="Bio.Parsers.spark.GenericParser._START" class="py-name" href="#" onclick="return doclink('link-47', '_START', 'link-47');">_START</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'START'</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt id="link-48" class="py-name" targets="Variable Bio.Parsers.spark.GenericParser._EOF=Bio.Parsers.spark.GenericParser-class.html#_EOF"><a title="Bio.Parsers.spark.GenericParser._EOF" class="py-name" href="#" onclick="return doclink('link-48', '_EOF', 'link-48');">_EOF</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'EOF'</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-comment">#</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#  A hook for GenericASTBuilder and GenericASTMatcher.</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#</tt> </tt>
<a name="GenericParser.preprocess"></a><div id="GenericParser.preprocess-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="GenericParser.preprocess-toggle" onclick="return toggle('GenericParser.preprocess');">-</a><tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#preprocess">preprocess</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">rule</tt><tt class="py-op">,</tt> <tt class="py-param">func</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>   <tt class="py-keyword">return</tt> <tt id="link-49" class="py-name" targets="Method Bio.Prosite._RecordConsumer.rule()=Bio.Prosite._RecordConsumer-class.html#rule"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-49', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">func</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.addRule"></a><div id="GenericParser.addRule-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="GenericParser.addRule-toggle" onclick="return toggle('GenericParser.addRule');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#addRule">addRule</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">,</tt> <tt class="py-param">func</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.addRule-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.addRule-expanded"><a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-name">rules</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-50" 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-50', 'split', 'link-50');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"> </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.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-51', 'index', 'link-51');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-52" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-52', 'i', 'link-34');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rules</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">rules</tt><tt class="py-op">[</tt><tt id="link-53" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-53', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'::='</tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">                <tt id="link-54" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-54', 'index', 'link-51');">index</a></tt><tt class="py-op">.</tt><tt id="link-55" 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-55', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-56', 'i', 'link-34');">i</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt id="link-57" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-57', 'index', 'link-51');">index</a></tt><tt class="py-op">.</tt><tt id="link-58" 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-58', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rules</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-59" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-59', 'i', 'link-34');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-60', 'index', 'link-51');">index</a></tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">            <tt class="py-name">lhs</tt> <tt class="py-op">=</tt> <tt class="py-name">rules</tt><tt class="py-op">[</tt><tt id="link-61" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-61', 'index', 'link-51');">index</a></tt><tt class="py-op">[</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-62', 'i', 'link-34');">i</a></tt><tt class="py-op">]</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">rhs</tt> <tt class="py-op">=</tt> <tt class="py-name">rules</tt><tt class="py-op">[</tt><tt id="link-63" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-63', 'index', 'link-51');">index</a></tt><tt class="py-op">[</tt><tt id="link-64" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-64', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt id="link-65" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-65', 'index', 'link-51');">index</a></tt><tt class="py-op">[</tt><tt id="link-66" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-66', 'i', 'link-34');">i</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 id="link-67" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-67', 'rule', 'link-49');">rule</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">rhs</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>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">            <tt id="link-68" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-68', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">fn</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.Parsers.spark.GenericASTBuilder.preprocess()=Bio.Parsers.spark.GenericASTBuilder-class.html#preprocess,Method Bio.Parsers.spark.GenericASTMatcher.preprocess()=Bio.Parsers.spark.GenericASTMatcher-class.html#preprocess,Method Bio.Parsers.spark.GenericParser.preprocess()=Bio.Parsers.spark.GenericParser-class.html#preprocess"><a title="Bio.Parsers.spark.GenericASTBuilder.preprocess
Bio.Parsers.spark.GenericASTMatcher.preprocess
Bio.Parsers.spark.GenericParser.preprocess" class="py-name" href="#" onclick="return doclink('link-69', 'preprocess', 'link-69');">preprocess</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-70', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">func</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</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">rules</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-71', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">[</tt><tt class="py-name">lhs</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-72" 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-72', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-73', 'rule', 'link-49');">rule</a></tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">[</tt><tt class="py-name">lhs</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt id="link-74" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-74', 'rule', 'link-49');">rule</a></tt> <tt class="py-op">]</tt> </tt>
<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">rule2func</tt><tt class="py-op">[</tt><tt id="link-75" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-75', 'rule', 'link-49');">rule</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">fn</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">rule2name</tt><tt class="py-op">[</tt><tt id="link-76" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-76', 'rule', 'link-49');">rule</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">func</tt><tt class="py-op">.</tt><tt class="py-name">__name__</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="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">ruleschanged</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.collectRules"></a><div id="GenericParser.collectRules-def"><a name="L125"></a><tt class="py-lineno">125</tt> <a class="py-toggle" href="#" id="GenericParser.collectRules-toggle" onclick="return toggle('GenericParser.collectRules');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#collectRules">collectRules</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="GenericParser.collectRules-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.collectRules-expanded"><a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-77" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-77', 'name', 'link-2');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-78" class="py-name"><a title="Bio.Parsers.spark._namelist" class="py-name" href="#" onclick="return doclink('link-78', '_namelist', 'link-19');">_namelist</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-79" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-79', 'name', 'link-2');">name</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'p_'</tt><tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">                <tt class="py-name">func</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-80" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-80', 'name', 'link-2');">name</a></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">doc</tt> <tt class="py-op">=</tt> <tt class="py-name">func</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-81', '__doc__', 'link-16');">__doc__</a></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 id="link-82" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.addRule()=Bio.Parsers.spark.GenericParser-class.html#addRule"><a title="Bio.Parsers.spark.GenericParser.addRule" class="py-name" href="#" onclick="return doclink('link-82', 'addRule', 'link-82');">addRule</a></tt><tt class="py-op">(</tt><tt class="py-name">doc</tt><tt class="py-op">,</tt> <tt class="py-name">func</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="GenericParser.augment"></a><div id="GenericParser.augment-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="GenericParser.augment-toggle" onclick="return toggle('GenericParser.augment');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#augment">augment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.augment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.augment-expanded"><a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">        <tt class="py-comment">#</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  Tempting though it is, this isn't made into a call</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  to self.addRule() because the start rule shouldn't</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  be subject to preprocessing.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">startRule</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Parsers.spark.GenericParser._START" class="py-name" href="#" onclick="return doclink('link-83', '_START', 'link-47');">_START</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt> <tt id="link-84" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-84', 'start', 'link-46');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Parsers.spark.GenericParser._EOF" class="py-name" href="#" onclick="return doclink('link-85', '_EOF', 'link-48');">_EOF</a></tt> <tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rule2func</tt><tt class="py-op">[</tt><tt class="py-name">startRule</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</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">rules</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Parsers.spark.GenericParser._START" class="py-name" href="#" onclick="return doclink('link-86', '_START', 'link-47');">_START</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-name">startRule</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">rule2name</tt><tt class="py-op">[</tt><tt class="py-name">startRule</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">startRule</tt> </tt>
</div><a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.makeFIRST"></a><div id="GenericParser.makeFIRST-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="GenericParser.makeFIRST-toggle" onclick="return toggle('GenericParser.makeFIRST');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#makeFIRST">makeFIRST</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="GenericParser.makeFIRST-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.makeFIRST-expanded"><a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt id="link-87" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.union()=Bio.Pathway.Rep.HashSet.HashSet-class.html#union"><a title="Bio.Pathway.Rep.HashSet.HashSet.union" class="py-name" href="#" onclick="return doclink('link-87', 'union', 'link-87');">union</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</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">first</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>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">rulelist</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-88', 'values', 'link-88');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">rhs</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rulelist</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-89', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">[</tt><tt class="py-name">lhs</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="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">first</tt><tt class="py-op">[</tt><tt class="py-name">lhs</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line"> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">                <tt class="py-name">sym</tt> <tt class="py-op">=</tt> <tt class="py-name">rhs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-90', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sym</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">first</tt><tt class="py-op">[</tt><tt class="py-name">lhs</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">sym</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">                    <tt id="link-91" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.union" class="py-name" href="#" onclick="return doclink('link-91', 'union', 'link-87');">union</a></tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">sym</tt><tt class="py-op">,</tt> <tt class="py-name">lhs</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-name">changes</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">changes</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">changes</tt> <tt class="py-op">=</tt> <tt class="py-number">0</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">src</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt> <tt class="py-keyword">in</tt> <tt id="link-92" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.union" class="py-name" href="#" onclick="return doclink('link-92', 'union', 'link-87');">union</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-93', 'keys', 'link-93');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">                <tt class="py-name">destlen</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">[</tt><tt class="py-name">dest</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">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">[</tt><tt class="py-name">dest</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-94', 'update', 'link-94');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">[</tt><tt class="py-name">src</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 class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">[</tt><tt class="py-name">dest</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">destlen</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">                    <tt class="py-name">changes</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">    <tt class="py-comment">#</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#  An Earley parser, as per J. Earley, "An Efficient Context-Free</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#  Parsing Algorithm", CACM 13(2), pp. 94-102.  Also J. C. Earley,</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#  "An Efficient Context-Free Parsing Algorithm", Ph.D. thesis,</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#  Carnegie-Mellon University, August 1968, p. 27.</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-comment"></tt>     </tt>
<a name="GenericParser.typestring"></a><div id="GenericParser.typestring-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="GenericParser.typestring-toggle" onclick="return toggle('GenericParser.typestring');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#typestring">typestring</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">token</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.typestring-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.typestring-expanded"><a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.error"></a><div id="GenericParser.error-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="GenericParser.error-toggle" onclick="return toggle('GenericParser.error');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#error">error</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">token</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.error-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.error-expanded"><a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">"Syntax error at or near `%s' token"</tt> <tt class="py-op">%</tt> <tt class="py-name">token</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">SystemExit</tt> </tt>
</div><a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.parse"></a><div id="GenericParser.parse-def"><a name="L185"></a><tt class="py-lineno">185</tt> <a class="py-toggle" href="#" id="GenericParser.parse-toggle" onclick="return toggle('GenericParser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-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">tokens</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.parse-expanded"><a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">        <tt class="py-name">tree</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">        <tt class="py-name">tokens</tt><tt class="py-op">.</tt><tt id="link-95" 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-95', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.Parsers.spark.GenericParser._EOF" class="py-name" href="#" onclick="return doclink('link-96', '_EOF', 'link-48');">_EOF</a></tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">        <tt class="py-name">states</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startRule</tt><tt class="py-op">,</tt> <tt class="py-number">0</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>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">         </tt>
<a name="L190"></a><tt class="py-lineno">190</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">ruleschanged</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.makeFIRST()=Bio.Parsers.spark.GenericParser-class.html#makeFIRST"><a title="Bio.Parsers.spark.GenericParser.makeFIRST" class="py-name" href="#" onclick="return doclink('link-97', 'makeFIRST', 'link-97');">makeFIRST</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-98" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-98', 'i', 'link-34');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-99" class="py-name" targets="Method Bio.GFF.Feature.xrange()=Bio.GFF.Feature-class.html#xrange"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-99', 'xrange', 'link-99');">xrange</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">            <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-100" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-100', 'i', 'link-34');">i</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 class="py-op">]</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-101" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-101', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt>                </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.buildState()=Bio.Parsers.spark.GenericParser-class.html#buildState"><a title="Bio.Parsers.spark.GenericParser.buildState" class="py-name" href="#" onclick="return doclink('link-102', 'buildState', 'link-102');">buildState</a></tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt id="link-103" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-103', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">states</tt><tt class="py-op">,</tt> <tt id="link-104" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-104', 'i', 'link-34');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">tree</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line"> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">        <tt class="py-comment">#_dump(tokens, states)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-105" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-105', 'i', 'link-34');">i</a></tt> <tt class="py-op">&lt;</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-106" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-106', 'i', 'link-34');">i</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 class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startRule</tt><tt class="py-op">,</tt> <tt class="py-number">2</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>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">            <tt class="py-keyword">del</tt> <tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-107', 'error', 'link-30');">error</a></tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt id="link-108" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-108', 'i', 'link-34');">i</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="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.buildTree()=Bio.Parsers.spark.GenericParser-class.html#buildTree"><a title="Bio.Parsers.spark.GenericParser.buildTree" class="py-name" href="#" onclick="return doclink('link-109', 'buildTree', 'link-109');">buildTree</a></tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">,</tt> <tt class="py-name">tree</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startRule</tt><tt class="py-op">,</tt> <tt class="py-number">2</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-110" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-110', 'i', 'link-34');">i</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="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">        <tt class="py-keyword">del</tt> <tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt> </tt>
</div><a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.buildState"></a><div id="GenericParser.buildState-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="GenericParser.buildState-toggle" onclick="return toggle('GenericParser.buildState');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#buildState">buildState</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">token</tt><tt class="py-op">,</tt> <tt class="py-param">states</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">,</tt> <tt class="py-param">tree</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.buildState-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.buildState-expanded"><a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">        <tt class="py-name">needsCompletion</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-111" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-111', 'i', 'link-34');">i</a></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">predicted</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">         </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-112" 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-112', 'item', 'link-112');">item</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">state</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">            <tt id="link-113" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-113', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt id="link-114" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-114', 'item', 'link-112');">item</a></tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">            <tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">rhs</tt> <tt class="py-op">=</tt> <tt id="link-115" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-115', 'rule', 'link-49');">rule</a></tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">            <tt class="py-comment">#</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#  A -&gt; a . (completer)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-name">pos</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">                    <tt class="py-name">needsCompletion</tt><tt class="py-op">[</tt><tt class="py-name">lhs</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-116" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-116', 'item', 'link-112');">item</a></tt><tt class="py-op">,</tt> <tt id="link-117" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-117', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line"> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">pitem</tt> <tt class="py-keyword">in</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt class="py-name">parent</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">pitem</tt> <tt class="py-keyword">is</tt> <tt id="link-118" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-118', 'item', 'link-112');">item</a></tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">                        <tt class="py-keyword">break</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">                    <tt class="py-name">prule</tt><tt class="py-op">,</tt> <tt class="py-name">ppos</tt><tt class="py-op">,</tt> <tt class="py-name">pparent</tt> <tt class="py-op">=</tt> <tt class="py-name">pitem</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">                    <tt class="py-name">plhs</tt><tt class="py-op">,</tt> <tt class="py-name">prhs</tt> <tt class="py-op">=</tt> <tt class="py-name">prule</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">prhs</tt><tt class="py-op">[</tt><tt class="py-name">ppos</tt><tt class="py-op">:</tt><tt class="py-name">ppos</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 class="py-name">lhs</tt><tt class="py-op">,</tt><tt class="py-op">)</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">new</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">prule</tt><tt class="py-op">,</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">                               <tt class="py-name">ppos</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">                               <tt class="py-name">pparent</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-name">new</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state</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">state</tt><tt class="py-op">.</tt><tt id="link-119" 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-119', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new</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">tree</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">,</tt> <tt id="link-120" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-120', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-121', 'item', 'link-112');">item</a></tt><tt class="py-op">,</tt> <tt id="link-122" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-122', 'i', 'link-34');">i</a></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">else</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">tree</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">,</tt> <tt id="link-123" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-123', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-124" 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-124', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-125" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-125', 'item', 'link-112');">item</a></tt><tt class="py-op">,</tt> <tt id="link-126" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-126', 'i', 'link-34');">i</a></tt><tt class="py-op">)</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">continue</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">            <tt class="py-name">nextSym</tt> <tt class="py-op">=</tt> <tt class="py-name">rhs</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line"> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">            <tt class="py-comment">#</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#  A -&gt; a . B (predictor)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-127', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">nextSym</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-comment">#</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  Work on completer step some more; for rules</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  with empty RHS, the "parent state" is the</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  current state we're adding Earley items to,</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  so the Earley items the completer step needs</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  may not all be present when it runs.</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-keyword">if</tt> <tt class="py-name">needsCompletion</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-128', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">nextSym</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">                    <tt class="py-name">new</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-129" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-129', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">                    <tt class="py-name">olditem_i</tt> <tt class="py-op">=</tt> <tt class="py-name">needsCompletion</tt><tt class="py-op">[</tt><tt class="py-name">nextSym</tt><tt class="py-op">]</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">new</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state</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">state</tt><tt class="py-op">.</tt><tt id="link-130" 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-130', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">                        <tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">,</tt> <tt id="link-131" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-131', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">olditem_i</tt><tt class="py-op">]</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">                        <tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">,</tt> <tt id="link-132" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-132', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</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-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">olditem_i</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line"> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">                <tt class="py-comment">#</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  Has this been predicted already?</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-keyword">if</tt> <tt class="py-name">predicted</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-134', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">nextSym</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">                <tt class="py-name">predicted</tt><tt class="py-op">[</tt><tt class="py-name">nextSym</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line"> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">                <tt class="py-name">ttype</tt> <tt class="py-op">=</tt> <tt class="py-name">token</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.Parsers.spark.GenericParser._EOF" class="py-name" href="#" onclick="return doclink('link-135', '_EOF', 'link-48');">_EOF</a></tt> <tt class="py-keyword">and</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-136" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.typestring()=Bio.Parsers.spark.GenericASTTraversal-class.html#typestring,Method Bio.Parsers.spark.GenericParser.typestring()=Bio.Parsers.spark.GenericParser-class.html#typestring"><a title="Bio.Parsers.spark.GenericASTTraversal.typestring
Bio.Parsers.spark.GenericParser.typestring" class="py-name" href="#" onclick="return doclink('link-136', 'typestring', 'link-136');">typestring</a></tt><tt class="py-op">(</tt><tt class="py-name">token</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">                    <tt class="py-name">None</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">ttype</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="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">                    <tt class="py-comment">#</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  Even smarter predictor, when the</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  token's type is known.  The code is</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  grungy, but runs pretty fast.  Three</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  cases are looked for: rules with</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  empty RHS; first symbol on RHS is a</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  terminal; first symbol on RHS is a</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  nonterminal (and isn't nullable).</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-keyword">for</tt> <tt class="py-name">prule</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">[</tt><tt class="py-name">nextSym</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">                        <tt class="py-name">new</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">prule</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-137" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-137', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">                        <tt class="py-name">prhs</tt> <tt class="py-op">=</tt> <tt class="py-name">prule</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">prhs</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line">                            <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-138" 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-138', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">                            <tt class="py-keyword">continue</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">                        <tt class="py-name">prhs0</tt> <tt class="py-op">=</tt> <tt class="py-name">prhs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-139', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">prhs0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">                            <tt class="py-keyword">if</tt> <tt class="py-name">prhs0</tt> <tt class="py-op">!=</tt> <tt class="py-name">ttype</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">                                <tt class="py-keyword">continue</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">                            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">                                <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-140" 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-140', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">                                <tt class="py-keyword">continue</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">                        <tt class="py-name">first</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">[</tt><tt class="py-name">prhs0</tt><tt class="py-op">]</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">first</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-141', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">                           <tt class="py-keyword">not</tt> <tt class="py-name">first</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-142', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">ttype</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">                            <tt class="py-keyword">continue</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">                        <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-143" 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-143', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">                    <tt class="py-keyword">continue</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">prule</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">[</tt><tt class="py-name">nextSym</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">                    <tt class="py-comment">#</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  Smarter predictor, as per Grune &amp;</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  Jacobs' _Parsing Techniques_.  Not</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#  as good as FIRST sets though.</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-comment">#</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-name">prhs</tt> <tt class="py-op">=</tt> <tt class="py-name">prule</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">prhs</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">                       <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-144', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">prhs</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-keyword">and</tt> \ </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">                       <tt class="py-name">token</tt> <tt class="py-op">!=</tt> <tt class="py-name">prhs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">                        <tt class="py-keyword">continue</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">                    <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-145" 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-145', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">prule</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-146" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-146', 'i', 'link-34');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">            <tt class="py-comment">#</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#  A -&gt; a . c (scanner)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment">#</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">elif</tt> <tt class="py-name">token</tt> <tt class="py-op">==</tt> <tt class="py-name">nextSym</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">                <tt class="py-comment">#assert new not in states[i+1]</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-147" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-147', 'i', 'link-34');">i</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-148" 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-148', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-149', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.buildTree"></a><div id="GenericParser.buildTree-def"><a name="L325"></a><tt class="py-lineno">325</tt> <a class="py-toggle" href="#" id="GenericParser.buildTree-toggle" onclick="return toggle('GenericParser.buildTree');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#buildTree">buildTree</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tokens</tt><tt class="py-op">,</tt> <tt class="py-param">tree</tt><tt class="py-op">,</tt> <tt class="py-param">root</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.buildTree-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.buildTree-expanded"><a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">        <tt class="py-name">stack</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.buildTree_r()=Bio.Parsers.spark.GenericParser-class.html#buildTree_r"><a title="Bio.Parsers.spark.GenericParser.buildTree_r" class="py-name" href="#" onclick="return doclink('link-150', 'buildTree_r', 'link-150');">buildTree_r</a></tt><tt class="py-op">(</tt><tt class="py-name">stack</tt><tt class="py-op">,</tt> <tt class="py-name">tokens</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">tree</tt><tt class="py-op">,</tt> <tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">stack</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.buildTree_r"></a><div id="GenericParser.buildTree_r-def"><a name="L330"></a><tt class="py-lineno">330</tt> <a class="py-toggle" href="#" id="GenericParser.buildTree_r-toggle" onclick="return toggle('GenericParser.buildTree_r');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#buildTree_r">buildTree_r</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">stack</tt><tt class="py-op">,</tt> <tt class="py-param">tokens</tt><tt class="py-op">,</tt> <tt class="py-param">tokpos</tt><tt class="py-op">,</tt> <tt class="py-param">tree</tt><tt class="py-op">,</tt> <tt class="py-param">root</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.buildTree_r-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.buildTree_r-expanded"><a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-151', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-name">root</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">         </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">pos</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">            <tt class="py-name">want</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-152" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-152', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">state</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-153', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">want</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">                <tt class="py-comment">#</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  Since pos &gt; 0, it didn't come from closure,</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  and if it isn't in tree[], then there must</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  be a terminal symbol to the left of the dot.</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  (It must be from a "scanner" step.)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">pos</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">                <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-name">state</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">                <tt class="py-name">stack</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.EUtils.POM.Comment.insert()=Bio.EUtils.POM.Comment-class.html#insert,Method Bio.EUtils.POM.ElementNode.insert()=Bio.EUtils.POM.ElementNode-class.html#insert,Method Bio.EUtils.POM.IndentedText.insert()=Bio.EUtils.POM.IndentedText-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert,Method Martel.msre_parse.SubPattern.insert()=Martel.msre_parse.SubPattern-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-154', 'insert', 'link-154');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt class="py-name">tokpos</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">                <tt class="py-name">tokpos</tt> <tt class="py-op">=</tt> <tt class="py-name">tokpos</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">                <tt class="py-comment">#</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  There's a NT to the left of the dot.</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  Follow the tree pointer recursively (&gt;1</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  tree pointers from it indicates ambiguity).</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  Since the item must have come about from a</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  "completer" step, the state where the item</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  came from must be the parent state of the</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#  item the tree pointer points to.</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt id="link-155" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.children()=Bio.Pathway.Rep.Graph.Graph-class.html#children,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.children()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#children"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-155', 'children', 'link-155');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-name">want</tt><tt class="py-op">]</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-156', 'children', 'link-155');">children</a></tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">                    <tt class="py-name">child</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.ambiguity()=Bio.Parsers.spark.GenericParser-class.html#ambiguity"><a title="Bio.Parsers.spark.GenericParser.ambiguity" class="py-name" href="#" onclick="return doclink('link-157', 'ambiguity', 'link-157');">ambiguity</a></tt><tt class="py-op">(</tt><tt id="link-158" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-158', 'children', 'link-155');">children</a></tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">                    <tt class="py-name">child</tt> <tt class="py-op">=</tt> <tt id="link-159" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-159', 'children', 'link-155');">children</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">                 </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">                <tt class="py-name">tokpos</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Parsers.spark.GenericParser.buildTree_r" class="py-name" href="#" onclick="return doclink('link-160', 'buildTree_r', 'link-150');">buildTree_r</a></tt><tt class="py-op">(</tt><tt class="py-name">stack</tt><tt class="py-op">,</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">                              <tt class="py-name">tokens</tt><tt class="py-op">,</tt> <tt class="py-name">tokpos</tt><tt class="py-op">,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">                              <tt class="py-name">tree</tt><tt class="py-op">,</tt> <tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">                <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">pos</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">                <tt class="py-op">(</tt><tt class="py-name">crule</tt><tt class="py-op">,</tt> <tt class="py-name">cpos</tt><tt class="py-op">,</tt> <tt class="py-name">cparent</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">cstate</tt> <tt class="py-op">=</tt> <tt class="py-name">child</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">                <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-name">cparent</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-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">rhs</tt> <tt class="py-op">=</tt> <tt id="link-161" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-161', 'rule', 'link-49');">rule</a></tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">        <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rule2func</tt><tt class="py-op">[</tt><tt id="link-162" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-162', 'rule', 'link-49');">rule</a></tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-name">stack</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">        <tt class="py-name">stack</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">result</tt><tt class="py-op">]</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">tokpos</tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.ambiguity"></a><div id="GenericParser.ambiguity-def"><a name="L374"></a><tt class="py-lineno">374</tt> <a class="py-toggle" href="#" id="GenericParser.ambiguity-toggle" onclick="return toggle('GenericParser.ambiguity');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#ambiguity">ambiguity</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">children</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.ambiguity-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.ambiguity-expanded"><a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">        <tt class="py-comment">#</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  XXX - problem here and in collectRules() if the same</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#    rule appears in &gt;1 method.  But in that case the</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#    user probably gets what they deserve :-)  Also</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#    undefined results if rules causing the ambiguity</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#    appear in the same method.</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">sortlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">        <tt class="py-name">name2index</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-163" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-163', 'i', 'link-34');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-164" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-164', 'children', 'link-155');">children</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-165" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-165', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-166" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-166', 'index', 'link-51');">index</a></tt><tt class="py-op">)</tt> <tt class="py-op">=</tt> <tt id="link-167" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-167', 'children', 'link-155');">children</a></tt><tt class="py-op">[</tt><tt id="link-168" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-168', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">            <tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">rhs</tt> <tt class="py-op">=</tt> <tt id="link-169" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-169', 'rule', 'link-49');">rule</a></tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line">            <tt id="link-170" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-170', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rule2name</tt><tt class="py-op">[</tt><tt id="link-171" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-171', 'rule', 'link-49');">rule</a></tt><tt class="py-op">]</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">            <tt class="py-name">sortlist</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-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-173" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-173', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">            <tt class="py-name">name2index</tt><tt class="py-op">[</tt><tt id="link-174" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-174', 'name', 'link-2');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-175" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-175', 'i', 'link-34');">i</a></tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">        <tt class="py-name">sortlist</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-176', 'sort', 'link-176');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">        <tt id="link-177" 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-177', 'list', 'link-177');">list</a></tt> <tt class="py-op">=</tt> <tt id="link-178" 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-178', 'map', 'link-178');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-name">b</tt><tt class="py-op">,</tt> <tt class="py-name">sortlist</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-179" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-179', 'children', 'link-155');">children</a></tt><tt class="py-op">[</tt><tt class="py-name">name2index</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.resolve()=Bio.Parsers.spark.GenericASTMatcher-class.html#resolve,Method Bio.Parsers.spark.GenericParser.resolve()=Bio.Parsers.spark.GenericParser-class.html#resolve,Method Bio.PropertyManager.PropertyManager.resolve()=Bio.PropertyManager.PropertyManager-class.html#resolve"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve
Bio.PropertyManager.PropertyManager.resolve" class="py-name" href="#" onclick="return doclink('link-180', 'resolve', 'link-180');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-181" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-181', 'list', 'link-177');">list</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
</div><a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line"> </tt>
<a name="GenericParser.resolve"></a><div id="GenericParser.resolve-def"><a name="L394"></a><tt class="py-lineno">394</tt> <a class="py-toggle" href="#" id="GenericParser.resolve-toggle" onclick="return toggle('GenericParser.resolve');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericParser-class.html#resolve">resolve</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericParser.resolve-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericParser.resolve-expanded"><a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line">        <tt class="py-comment">#</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  Resolve ambiguity in favor of the shortest RHS.</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  Since we walk the tree from the top down, this</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  should effectively resolve in favor of a "shift".</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">return</tt> <tt id="link-182" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-182', 'list', 'link-177');">list</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line"> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  GenericASTBuilder automagically constructs a concrete/abstract syntax tree</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  for a given input.  The extra argument is a class (not an instance!)</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  which supports the "__setslice__" and "__len__" methods.</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  XXX - silently overrides any user code in methods.</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="GenericASTBuilder"></a><div id="GenericASTBuilder-def"><a name="L410"></a><tt class="py-lineno">410</tt> <a class="py-toggle" href="#" id="GenericASTBuilder-toggle" onclick="return toggle('GenericASTBuilder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTBuilder-class.html">GenericASTBuilder</a><tt class="py-op">(</tt><tt class="py-base-class">GenericParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTBuilder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenericASTBuilder-expanded"><a name="GenericASTBuilder.__init__"></a><div id="GenericASTBuilder.__init__-def"><a name="L411"></a><tt class="py-lineno">411</tt> <a class="py-toggle" href="#" id="GenericASTBuilder.__init__-toggle" onclick="return toggle('GenericASTBuilder.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTBuilder-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">AST</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTBuilder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTBuilder.__init__-expanded"><a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">        <tt id="link-183" class="py-name" targets="Class Bio.Parsers.spark.GenericParser=Bio.Parsers.spark.GenericParser-class.html"><a title="Bio.Parsers.spark.GenericParser" class="py-name" href="#" onclick="return doclink('link-183', 'GenericParser', 'link-183');">GenericParser</a></tt><tt class="py-op">.</tt><tt id="link-184" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.CDD.Iterator.__init__()=Bio.CDD.Iterator-class.html#__init__,Method Bio.CDD.Record.Record.__init__()=Bio.CDD.Record.Record-class.html#__init__,Method Bio.CDD.RecordParser.__init__()=Bio.CDD.RecordParser-class.html#__init__,Method Bio.CDD._RecordConsumer.__init__()=Bio.CDD._RecordConsumer-class.html#__init__,Method Bio.CDD._Scanner.__init__()=Bio.CDD._Scanner-class.html#__init__,Method Bio.Clustalw.ClustalAlignment.__init__()=Bio.Clustalw.ClustalAlignment-class.html#__init__,Method Bio.Clustalw.MultipleAlignCL.__init__()=Bio.Clustalw.MultipleAlignCL-class.html#__init__,Method Bio.Cluster.DataFile.__init__()=Bio.Cluster.DataFile-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method Bio.Compass.Iterator.__init__()=Bio.Compass.Iterator-class.html#__init__,Method Bio.Compass.Record.__init__()=Bio.Compass.Record-class.html#__init__,Method Bio.Compass.RecordParser.__init__()=Bio.Compass.RecordParser-class.html#__init__,Method Bio.Compass._Consumer.__init__()=Bio.Compass._Consumer-class.html#__init__,Method Bio.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.CrystalError.__init__()=Bio.Crystal.CrystalError-class.html#__init__,Method Bio.Crystal.Error.__init__()=Bio.Crystal.Error-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.DBXRef.DBXRef.__init__()=Bio.DBXRef.DBXRef-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousCodonTable.__init__()=Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__init__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__init__,Method Bio.Data.CodonTable.CodonTable.__init__()=Bio.Data.CodonTable.CodonTable-class.html#__init__,Method Bio.Data.CodonTable.NCBICodonTable.__init__()=Bio.Data.CodonTable.NCBICodonTable-class.html#__init__,Method Bio.Decode.DecodeParser.__init__()=Bio.Decode.DecodeParser-class.html#__init__,Method Bio.Decode.DecodeScanner.__init__()=Bio.Decode.DecodeScanner-class.html#__init__,Method Bio.Decode.Float.__init__()=Bio.Decode.Float-class.html#__init__,Method Bio.Decode.Function.__init__()=Bio.Decode.Function-class.html#__init__,Method Bio.Decode.FunctionCall.__init__()=Bio.Decode.FunctionCall-class.html#__init__,Method Bio.Decode.FunctionCallChain.__init__()=Bio.Decode.FunctionCallChain-class.html#__init__,Method Bio.Decode.FunctionName.__init__()=Bio.Decode.FunctionName-class.html#__init__,Method Bio.Decode.Integer.__init__()=Bio.Decode.Integer-class.html#__init__,Method Bio.Decode.String.__init__()=Bio.Decode.String-class.html#__init__,Method Bio.Decode.Token.__init__()=Bio.Decode.Token-class.html#__init__,Method Bio.Decode.ValueToken.__init__()=Bio.Decode.ValueToken-class.html#__init__,Method Bio.DocSQL.Create.__init__()=Bio.DocSQL.Create-class.html#__init__,Method Bio.DocSQL.Insert.__init__()=Bio.DocSQL.Insert-class.html#__init__,Method Bio.DocSQL.IterationCursor.__init__()=Bio.DocSQL.IterationCursor-class.html#__init__,Method Bio.DocSQL.Query.__init__()=Bio.DocSQL.Query-class.html#__init__,Method Bio.DocSQL.QueryAll.__init__()=Bio.DocSQL.QueryAll-class.html#__init__,Method Bio.DocSQL.QueryGeneric.__init__()=Bio.DocSQL.QueryGeneric-class.html#__init__,Method Bio.DocSQL.QueryRow.__init__()=Bio.DocSQL.QueryRow-class.html#__init__,Method Bio.DocSQL.QuerySingle.__init__()=Bio.DocSQL.QuerySingle-class.html#__init__,Method Bio.ECell.ECellError.__init__()=Bio.ECell.ECellError-class.html#__init__,Method Bio.ECell.Error.__init__()=Bio.ECell.Error-class.html#__init__,Method Bio.ECell.Iterator.__init__()=Bio.ECell.Iterator-class.html#__init__,Method Bio.ECell.Record.Record.__init__()=Bio.ECell.Record.Record-class.html#__init__,Method Bio.ECell.RecordParser.__init__()=Bio.ECell.RecordParser-class.html#__init__,Method Bio.ECell._RecordConsumer.__init__()=Bio.ECell._RecordConsumer-class.html#__init__,Method Bio.ECell._Scanner.__init__()=Bio.ECell._Scanner-class.html#__init__,Method Bio.EUtils.Config.DatabaseInfo.__init__()=Bio.EUtils.Config.DatabaseInfo-class.html#__init__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsClient.__init__()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsLookup.__init__()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#__init__,Method Bio.EUtils.Datatypes.BinaryOp.__init__()=Bio.EUtils.Datatypes.BinaryOp-class.html#__init__,Method Bio.EUtils.Datatypes.CheckLinkSet.__init__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.DBIds.__init__()=Bio.EUtils.Datatypes.DBIds-class.html#__init__,Method Bio.EUtils.Datatypes.Date.__init__()=Bio.EUtils.Datatypes.Date-class.html#__init__,Method Bio.EUtils.Datatypes.DateRange.__init__()=Bio.EUtils.Datatypes.DateRange-class.html#__init__,Method Bio.EUtils.Datatypes.EUtilsSearchError.__init__()=Bio.EUtils.Datatypes.EUtilsSearchError-class.html#__init__,Method Bio.EUtils.Datatypes.IdCheck.__init__()=Bio.EUtils.Datatypes.IdCheck-class.html#__init__,Method Bio.EUtils.Datatypes.IdUrlSet.__init__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__init__,Method Bio.EUtils.Datatypes.Link.__init__()=Bio.EUtils.Datatypes.Link-class.html#__init__,Method Bio.EUtils.Datatypes.LinkSetDb.__init__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__init__,Method Bio.EUtils.Datatypes.LinksLinkSet.__init__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__init__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.ObjUrl.__init__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__init__,Method Bio.EUtils.Datatypes.PostResult.__init__()=Bio.EUtils.Datatypes.PostResult-class.html#__init__,Method Bio.EUtils.Datatypes.Problem.__init__()=Bio.EUtils.Datatypes.Problem-class.html#__init__,Method Bio.EUtils.Datatypes.Provider.__init__()=Bio.EUtils.Datatypes.Provider-class.html#__init__,Method Bio.EUtils.Datatypes.Range.__init__()=Bio.EUtils.Datatypes.Range-class.html#__init__,Method Bio.EUtils.Datatypes.SearchResult.__init__()=Bio.EUtils.Datatypes.SearchResult-class.html#__init__,Method Bio.EUtils.Datatypes.Summary.__init__()=Bio.EUtils.Datatypes.Summary-class.html#__init__,Method Bio.EUtils.Datatypes.Term.__init__()=Bio.EUtils.Datatypes.Term-class.html#__init__,Method Bio.EUtils.Datatypes.WithinNDays.__init__()=Bio.EUtils.Datatypes.WithinNDays-class.html#__init__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryClient.__init__()=Bio.EUtils.HistoryClient.HistoryClient-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryCookie.__init__()=Bio.EUtils.HistoryClient.HistoryCookie-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryLookup.__init__()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryRecord.__init__()=Bio.EUtils.HistoryClient.HistoryRecord-class.html#__init__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__init__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__init__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__init__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__init__,Method Bio.EUtils.POM.Comment.__init__()=Bio.EUtils.POM.Comment-class.html#__init__,Method Bio.EUtils.POM.ContentModel.__init__()=Bio.EUtils.POM.ContentModel-class.html#__init__,Method Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__()=Bio.EUtils.POM.DTDConsumerForSourceGeneration-class.html#__init__,Method Bio.EUtils.POM.ElementNode.__init__()=Bio.EUtils.POM.ElementNode-class.html#__init__,Method Bio.EUtils.POM.IndentedText.__init__()=Bio.EUtils.POM.IndentedText-class.html#__init__,Method Bio.EUtils.POM.ObjectParserHandler.__init__()=Bio.EUtils.POM.ObjectParserHandler-class.html#__init__,Method Bio.EUtils.POM.POMDocument.__init__()=Bio.EUtils.POM.POMDocument-class.html#__init__,Method Bio.EUtils.POM.XMLAttribute.__init__()=Bio.EUtils.POM.XMLAttribute-class.html#__init__,Method Bio.EUtils.POM._ContentModelGenerator.__init__()=Bio.EUtils.POM._ContentModelGenerator-class.html#__init__,Method Bio.EUtils.ReseekFile.ReseekFile.__init__()=Bio.EUtils.ReseekFile.ReseekFile-class.html#__init__,Method Bio.EUtils.ThinClient.ThinClient.__init__()=Bio.EUtils.ThinClient.ThinClient-class.html#__init__,Method Bio.EUtils.parse.UsePOMParser.__init__()=Bio.EUtils.parse.UsePOMParser-class.html#__init__,Method Bio.EUtils.sourcegen.ClassHolder.__init__()=Bio.EUtils.sourcegen.ClassHolder-class.html#__init__,Method Bio.EUtils.sourcegen.FunctionHolder.__init__()=Bio.EUtils.sourcegen.FunctionHolder-class.html#__init__,Method Bio.EUtils.sourcegen.MethodHolder.__init__()=Bio.EUtils.sourcegen.MethodHolder-class.html#__init__,Method Bio.EUtils.sourcegen.SourceFile.__init__()=Bio.EUtils.sourcegen.SourceFile-class.html#__init__,Method Bio.EUtils.sourcegen.SourceGen.__init__()=Bio.EUtils.sourcegen.SourceGen-class.html#__init__,Method Bio.Emboss.Applications.EConsenseCommandline.__init__()=Bio.Emboss.Applications.EConsenseCommandline-class.html#__init__,Method Bio.Emboss.Applications.EInvertedCommandline.__init__()=Bio.Emboss.Applications.EInvertedCommandline-class.html#__init__,Method Bio.Emboss.Applications.ENeighborCommandline.__init__()=Bio.Emboss.Applications.ENeighborCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtDistCommandline.__init__()=Bio.Emboss.Applications.EProtDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtParsCommandline.__init__()=Bio.Emboss.Applications.EProtParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.ESeqBootCommandline.__init__()=Bio.Emboss.Applications.ESeqBootCommandline-class.html#__init__,Method Bio.Emboss.Applications.ETandemCommandline.__init__()=Bio.Emboss.Applications.ETandemCommandline-class.html#__init__,Method Bio.Emboss.Applications.Est2GenomeCommandline.__init__()=Bio.Emboss.Applications.Est2GenomeCommandline-class.html#__init__,Method Bio.Emboss.Applications.FuzznucCommandline.__init__()=Bio.Emboss.Applications.FuzznucCommandline-class.html#__init__,Method Bio.Emboss.Applications.PalindromeCommandline.__init__()=Bio.Emboss.Applications.PalindromeCommandline-class.html#__init__,Method Bio.Emboss.Applications.Primer3Commandline.__init__()=Bio.Emboss.Applications.Primer3Commandline-class.html#__init__,Method Bio.Emboss.Applications.PrimerSearchCommandline.__init__()=Bio.Emboss.Applications.PrimerSearchCommandline-class.html#__init__,Method Bio.Emboss.Applications.TranalignCommandline.__init__()=Bio.Emboss.Applications.TranalignCommandline-class.html#__init__,Method Bio.Emboss.Applications.WaterCommandline.__init__()=Bio.Emboss.Applications.WaterCommandline-class.html#__init__,Method Bio.Emboss.Primer.Primer3Parser.__init__()=Bio.Emboss.Primer.Primer3Parser-class.html#__init__,Method Bio.Emboss.Primer.Primer3Primers.__init__()=Bio.Emboss.Primer.Primer3Primers-class.html#__init__,Method Bio.Emboss.Primer.Primer3Record.__init__()=Bio.Emboss.Primer.Primer3Record-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchAmplifier.__init__()=Bio.Emboss.Primer.PrimerSearchAmplifier-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchInputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchInputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchParser.__init__()=Bio.Emboss.Primer.PrimerSearchParser-class.html#__init__,Method Bio.Emboss.Primer._Primer3RecordConsumer.__init__()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#__init__,Method Bio.Emboss.Primer._Primer3Scanner.__init__()=Bio.Emboss.Primer._Primer3Scanner-class.html#__init__,Method 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Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
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Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
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Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
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Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
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Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
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Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
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Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
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Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
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Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
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Bio.PDB.HSExposure._AbstractHSExposure.__init__
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Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
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Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
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Bio.SCOP.FileIndex.defaultdict.__init__
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Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
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Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
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Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
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Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
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Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
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Bio.Sequencing.Ace.Reads.__init__
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Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
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Bio.Sequencing.Ace.ds.__init__
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Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
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Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
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Bio.UniGene.UnigeneProtsimRecord.__init__
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Bio.UniGene.UnigeneSTSRecord.__init__
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Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
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Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
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Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
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Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
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Bio.config._support.make_rate_limited_function.__init__
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Bio.pairwise2.affine_penalty.__init__
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Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
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BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
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Martel.Generate.print_info.__init__
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Martel.Iterator.HeaderFooterEventStream.__init__
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Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
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Martel.test.support.Dump.__init__
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Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-184', '__init__', 'link-184');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-185" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-185', 'start', 'link-46');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AST</tt> <tt class="py-op">=</tt> <tt class="py-name">AST</tt> </tt>
</div><a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line"> </tt>
<a name="GenericASTBuilder.preprocess"></a><div id="GenericASTBuilder.preprocess-def"><a name="L415"></a><tt class="py-lineno">415</tt> <a class="py-toggle" href="#" id="GenericASTBuilder.preprocess-toggle" onclick="return toggle('GenericASTBuilder.preprocess');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTBuilder-class.html#preprocess">preprocess</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">rule</tt><tt class="py-op">,</tt> <tt class="py-param">func</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTBuilder.preprocess-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTBuilder.preprocess-expanded"><a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">        <tt class="py-name">rebind</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">:</tt> \ </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">                <tt class="py-keyword">lambda</tt> <tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-name">lhs</tt><tt class="py-op">=</tt><tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">:</tt> \ </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name" targets="Method Bio.Parsers.spark.GenericASTBuilder.buildASTNode()=Bio.Parsers.spark.GenericASTBuilder-class.html#buildASTNode"><a title="Bio.Parsers.spark.GenericASTBuilder.buildASTNode" class="py-name" href="#" onclick="return doclink('link-186', 'buildASTNode', 'link-186');">buildASTNode</a></tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-name">lhs</tt><tt class="py-op">)</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line">        <tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">rhs</tt> <tt class="py-op">=</tt> <tt id="link-187" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-187', 'rule', 'link-49');">rule</a></tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-188" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-188', 'rule', 'link-49');">rule</a></tt><tt class="py-op">,</tt> <tt class="py-name">rebind</tt><tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">)</tt> </tt>
</div><a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line"> </tt>
<a name="GenericASTBuilder.buildASTNode"></a><div id="GenericASTBuilder.buildASTNode-def"><a name="L422"></a><tt class="py-lineno">422</tt> <a class="py-toggle" href="#" id="GenericASTBuilder.buildASTNode-toggle" onclick="return toggle('GenericASTBuilder.buildASTNode');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTBuilder-class.html#buildASTNode">buildASTNode</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-param">lhs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTBuilder.buildASTNode-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTBuilder.buildASTNode-expanded"><a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">        <tt id="link-189" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-189', 'children', 'link-155');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">arg</tt> <tt class="py-keyword">in</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">arg</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AST</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line">                <tt id="link-190" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-190', 'children', 'link-155');">children</a></tt><tt class="py-op">.</tt><tt id="link-191" 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-191', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">arg</tt><tt class="py-op">)</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">                <tt id="link-192" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-192', 'children', 'link-155');">children</a></tt><tt class="py-op">.</tt><tt id="link-193" 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-193', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name" targets="Method Bio.Parsers.spark.GenericASTBuilder.terminal()=Bio.Parsers.spark.GenericASTBuilder-class.html#terminal"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-194', 'terminal', 'link-194');">terminal</a></tt><tt class="py-op">(</tt><tt class="py-name">arg</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name" targets="Method Bio.Parsers.spark.GenericASTBuilder.nonterminal()=Bio.Parsers.spark.GenericASTBuilder-class.html#nonterminal"><a title="Bio.Parsers.spark.GenericASTBuilder.nonterminal" class="py-name" href="#" onclick="return doclink('link-195', 'nonterminal', 'link-195');">nonterminal</a></tt><tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt id="link-196" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-196', 'children', 'link-155');">children</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line"> </tt>
<a name="GenericASTBuilder.terminal"></a><div id="GenericASTBuilder.terminal-def"><a name="L431"></a><tt class="py-lineno">431</tt> <a class="py-toggle" href="#" id="GenericASTBuilder.terminal-toggle" onclick="return toggle('GenericASTBuilder.terminal');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTBuilder-class.html#terminal">terminal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">token</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  <tt class="py-keyword">return</tt> <tt class="py-name">token</tt> </tt>
</div><a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line"> </tt>
<a name="GenericASTBuilder.nonterminal"></a><div id="GenericASTBuilder.nonterminal-def"><a name="L433"></a><tt class="py-lineno">433</tt> <a class="py-toggle" href="#" id="GenericASTBuilder.nonterminal-toggle" onclick="return toggle('GenericASTBuilder.nonterminal');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTBuilder-class.html#nonterminal">nonterminal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">type</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTBuilder.nonterminal-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTBuilder.nonterminal-expanded"><a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">        <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">AST</tt><tt class="py-op">(</tt><tt id="link-197" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-197', 'type', 'link-197');">type</a></tt><tt class="py-op">)</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">        <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt> </tt>
</div></div><a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line"> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  GenericASTTraversal is a Visitor pattern according to Design Patterns.  For</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  each node it attempts to invoke the method n_&lt;node type&gt;, falling</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  back onto the default() method if the n_* can't be found.  The preorder</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  traversal also looks for an exit hook named n_&lt;node type&gt;_exit (no default</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  routine is called if it's not found).  To prematurely halt traversal</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  of a subtree, call the prune() method -- this only makes sense for a</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  preorder traversal.  Node type is determined via the typestring() method.</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="GenericASTTraversalPruningException"></a><div id="GenericASTTraversalPruningException-def"><a name="L448"></a><tt class="py-lineno">448</tt> <a class="py-toggle" href="#" id="GenericASTTraversalPruningException-toggle" onclick="return toggle('GenericASTTraversalPruningException');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversalPruningException-class.html">GenericASTTraversalPruningException</a><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTTraversalPruningException-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenericASTTraversalPruningException-expanded"><a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
</div><a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line"> </tt>
<a name="GenericASTTraversal"></a><div id="GenericASTTraversal-def"><a name="L451"></a><tt class="py-lineno">451</tt> <a class="py-toggle" href="#" id="GenericASTTraversal-toggle" onclick="return toggle('GenericASTTraversal');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversal-class.html">GenericASTTraversal</a><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTTraversal-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenericASTTraversal-expanded"><a name="GenericASTTraversal.__init__"></a><div id="GenericASTTraversal.__init__-def"><a name="L452"></a><tt class="py-lineno">452</tt> <a class="py-toggle" href="#" id="GenericASTTraversal.__init__-toggle" onclick="return toggle('GenericASTTraversal.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversal-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">ast</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTTraversal.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTTraversal.__init__-expanded"><a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ast</tt> <tt class="py-op">=</tt> <tt class="py-name">ast</tt> </tt>
</div><a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line"> </tt>
<a name="GenericASTTraversal.typestring"></a><div id="GenericASTTraversal.typestring-def"><a name="L455"></a><tt class="py-lineno">455</tt> <a class="py-toggle" href="#" id="GenericASTTraversal.typestring-toggle" onclick="return toggle('GenericASTTraversal.typestring');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversal-class.html#typestring">typestring</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTTraversal.typestring-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTTraversal.typestring-expanded"><a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-198" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.node()=Bio.EUtils.POM.ElementNode-class.html#node,Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-198', 'node', 'link-198');">node</a></tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-199', 'type', 'link-197');">type</a></tt> </tt>
</div><a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line"> </tt>
<a name="GenericASTTraversal.prune"></a><div id="GenericASTTraversal.prune-def"><a name="L458"></a><tt class="py-lineno">458</tt> <a class="py-toggle" href="#" id="GenericASTTraversal.prune-toggle" onclick="return toggle('GenericASTTraversal.prune');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversal-class.html#prune">prune</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="GenericASTTraversal.prune-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTTraversal.prune-expanded"><a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt id="link-200" class="py-name" targets="Class Bio.Parsers.spark.GenericASTTraversalPruningException=Bio.Parsers.spark.GenericASTTraversalPruningException-class.html"><a title="Bio.Parsers.spark.GenericASTTraversalPruningException" class="py-name" href="#" onclick="return doclink('link-200', 'GenericASTTraversalPruningException', 'link-200');">GenericASTTraversalPruningException</a></tt> </tt>
</div><a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line"> </tt>
<a name="GenericASTTraversal.preorder"></a><div id="GenericASTTraversal.preorder-def"><a name="L461"></a><tt class="py-lineno">461</tt> <a class="py-toggle" href="#" id="GenericASTTraversal.preorder-toggle" onclick="return toggle('GenericASTTraversal.preorder');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversal-class.html#preorder">preorder</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</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="GenericASTTraversal.preorder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTTraversal.preorder-expanded"><a name="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-201" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-201', 'node', 'link-198');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line">            <tt id="link-202" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-202', 'node', 'link-198');">node</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ast</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line"> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line">            <tt id="link-203" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-203', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'n_'</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.typestring
Bio.Parsers.spark.GenericParser.typestring" class="py-name" href="#" onclick="return doclink('link-204', 'typestring', 'link-136');">typestring</a></tt><tt class="py-op">(</tt><tt id="link-205" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-205', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-206" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-206', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt>  <tt class="py-line">                <tt class="py-name">func</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-207" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-207', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line">                <tt class="py-name">func</tt><tt class="py-op">(</tt><tt id="link-208" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-208', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.default()=Bio.Parsers.spark.GenericASTTraversal-class.html#default"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-209', 'default', 'link-209');">default</a></tt><tt class="py-op">(</tt><tt id="link-210" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-210', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt id="link-211" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversalPruningException" class="py-name" href="#" onclick="return doclink('link-211', 'GenericASTTraversalPruningException', 'link-200');">GenericASTTraversalPruningException</a></tt><tt class="py-op">:</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt>  <tt class="py-line"> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kid</tt> <tt class="py-keyword">in</tt> <tt id="link-212" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-212', 'node', 'link-198');">node</a></tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-213" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.preorder()=Bio.Parsers.spark.GenericASTTraversal-class.html#preorder"><a title="Bio.Parsers.spark.GenericASTTraversal.preorder" class="py-name" href="#" onclick="return doclink('link-213', 'preorder', 'link-213');">preorder</a></tt><tt class="py-op">(</tt><tt class="py-name">kid</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line"> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt>  <tt class="py-line">        <tt id="link-214" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-214', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-215" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-215', 'name', 'link-2');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-string">'_exit'</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-216" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-216', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt>  <tt class="py-line">            <tt class="py-name">func</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-217" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-217', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">            <tt class="py-name">func</tt><tt class="py-op">(</tt><tt id="link-218" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-218', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L482"></a><tt class="py-lineno">482</tt>  <tt class="py-line"> </tt>
<a name="GenericASTTraversal.postorder"></a><div id="GenericASTTraversal.postorder-def"><a name="L483"></a><tt class="py-lineno">483</tt> <a class="py-toggle" href="#" id="GenericASTTraversal.postorder-toggle" onclick="return toggle('GenericASTTraversal.postorder');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversal-class.html#postorder">postorder</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</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="GenericASTTraversal.postorder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTTraversal.postorder-expanded"><a name="L484"></a><tt class="py-lineno">484</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-219" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-219', 'node', 'link-198');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt>  <tt class="py-line">            <tt id="link-220" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-220', 'node', 'link-198');">node</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ast</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line"> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kid</tt> <tt class="py-keyword">in</tt> <tt id="link-221" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-221', 'node', 'link-198');">node</a></tt><tt class="py-op">:</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.postorder()=Bio.Parsers.spark.GenericASTTraversal-class.html#postorder"><a title="Bio.Parsers.spark.GenericASTTraversal.postorder" class="py-name" href="#" onclick="return doclink('link-222', 'postorder', 'link-222');">postorder</a></tt><tt class="py-op">(</tt><tt class="py-name">kid</tt><tt class="py-op">)</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt>  <tt class="py-line"> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt>  <tt class="py-line">        <tt id="link-223" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-223', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'n_'</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.typestring
Bio.Parsers.spark.GenericParser.typestring" class="py-name" href="#" onclick="return doclink('link-224', 'typestring', 'link-136');">typestring</a></tt><tt class="py-op">(</tt><tt id="link-225" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-225', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-226" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-226', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line">            <tt class="py-name">func</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-227" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-227', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line">            <tt class="py-name">func</tt><tt class="py-op">(</tt><tt id="link-228" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-228', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-229', 'default', 'link-209');">default</a></tt><tt class="py-op">(</tt><tt id="link-230" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-230', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L496"></a><tt class="py-lineno">496</tt>  <tt class="py-line"> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt>  <tt class="py-line"> </tt>
<a name="GenericASTTraversal.default"></a><div id="GenericASTTraversal.default-def"><a name="L498"></a><tt class="py-lineno">498</tt> <a class="py-toggle" href="#" id="GenericASTTraversal.default-toggle" onclick="return toggle('GenericASTTraversal.default');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTTraversal-class.html#default">default</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTTraversal.default-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTTraversal.default-expanded"><a name="L499"></a><tt class="py-lineno">499</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L500"></a><tt class="py-lineno">500</tt>  <tt class="py-line"> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  GenericASTMatcher.  AST nodes must have "__getitem__" and "__cmp__"</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  implemented.</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  XXX - makes assumptions about how GenericParser walks the parse tree.</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="GenericASTMatcher"></a><div id="GenericASTMatcher-def"><a name="L508"></a><tt class="py-lineno">508</tt> <a class="py-toggle" href="#" id="GenericASTMatcher-toggle" onclick="return toggle('GenericASTMatcher');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTMatcher-class.html">GenericASTMatcher</a><tt class="py-op">(</tt><tt class="py-base-class">GenericParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTMatcher-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenericASTMatcher-expanded"><a name="GenericASTMatcher.__init__"></a><div id="GenericASTMatcher.__init__-def"><a name="L509"></a><tt class="py-lineno">509</tt> <a class="py-toggle" href="#" id="GenericASTMatcher.__init__-toggle" onclick="return toggle('GenericASTMatcher.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTMatcher-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">start</tt><tt class="py-op">,</tt> <tt class="py-param">ast</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTMatcher.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTMatcher.__init__-expanded"><a name="L510"></a><tt class="py-lineno">510</tt>  <tt class="py-line">        <tt id="link-231" class="py-name"><a title="Bio.Parsers.spark.GenericParser" class="py-name" href="#" onclick="return doclink('link-231', 'GenericParser', 'link-183');">GenericParser</a></tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
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<a name="GenericASTMatcher.preprocess"></a><div id="GenericASTMatcher.preprocess-def"><a name="L513"></a><tt class="py-lineno">513</tt> <a class="py-toggle" href="#" id="GenericASTMatcher.preprocess-toggle" onclick="return toggle('GenericASTMatcher.preprocess');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTMatcher-class.html#preprocess">preprocess</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">rule</tt><tt class="py-op">,</tt> <tt class="py-param">func</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTMatcher.preprocess-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTMatcher.preprocess-expanded"><a name="L514"></a><tt class="py-lineno">514</tt>  <tt class="py-line">        <tt class="py-name">rebind</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">func</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">:</tt> \ </tt>
<a name="L515"></a><tt class="py-lineno">515</tt>  <tt class="py-line">                <tt class="py-keyword">lambda</tt> <tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-name">func</tt><tt class="py-op">=</tt><tt class="py-name">func</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">:</tt> \ </tt>
<a name="L516"></a><tt class="py-lineno">516</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-234" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.foundMatch()=Bio.Parsers.spark.GenericASTMatcher-class.html#foundMatch"><a title="Bio.Parsers.spark.GenericASTMatcher.foundMatch" class="py-name" href="#" onclick="return doclink('link-234', 'foundMatch', 'link-234');">foundMatch</a></tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-name">func</tt><tt class="py-op">)</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt>  <tt class="py-line">        <tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">rhs</tt> <tt class="py-op">=</tt> <tt id="link-235" class="py-name"><a title="Bio.Prosite._RecordConsumer.rule" class="py-name" href="#" onclick="return doclink('link-235', 'rule', 'link-49');">rule</a></tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt>  <tt class="py-line">        <tt class="py-name">rhslist</tt> <tt class="py-op">=</tt> <tt id="link-236" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-236', 'list', 'link-177');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt>  <tt class="py-line">        <tt class="py-name">rhslist</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name" targets="Method Bio.GFF.easy.Location.reverse()=Bio.GFF.easy.Location-class.html#reverse,Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse,Function Bio.SeqUtils.reverse()=Bio.SeqUtils-module.html#reverse"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-237', 'reverse', 'link-237');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt>  <tt class="py-line"> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">rhslist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">rebind</tt><tt class="py-op">(</tt><tt class="py-name">func</tt><tt class="py-op">)</tt> </tt>
</div><a name="L522"></a><tt class="py-lineno">522</tt>  <tt class="py-line"> </tt>
<a name="GenericASTMatcher.foundMatch"></a><div id="GenericASTMatcher.foundMatch-def"><a name="L523"></a><tt class="py-lineno">523</tt> <a class="py-toggle" href="#" id="GenericASTMatcher.foundMatch-toggle" onclick="return toggle('GenericASTMatcher.foundMatch');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTMatcher-class.html#foundMatch">foundMatch</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-param">func</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTMatcher.foundMatch-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTMatcher.foundMatch-expanded"><a name="L524"></a><tt class="py-lineno">524</tt>  <tt class="py-line">        <tt class="py-name">func</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="L526"></a><tt class="py-lineno">526</tt>  <tt class="py-line"> </tt>
<a name="GenericASTMatcher.match_r"></a><div id="GenericASTMatcher.match_r-def"><a name="L527"></a><tt class="py-lineno">527</tt> <a class="py-toggle" href="#" id="GenericASTMatcher.match_r-toggle" onclick="return toggle('GenericASTMatcher.match_r');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTMatcher-class.html#match_r">match_r</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTMatcher.match_r-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTMatcher.match_r-expanded"><a name="L528"></a><tt class="py-lineno">528</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">input</tt><tt class="py-op">.</tt><tt id="link-238" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-238', 'insert', 'link-154');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-239" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-239', 'node', 'link-198');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt>  <tt class="py-line">        <tt id="link-240" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-240', 'children', 'link-155');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt>  <tt class="py-line"> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt id="link-241" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-241', 'node', 'link-198');">node</a></tt><tt class="py-op">:</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-242" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-242', 'children', 'link-155');">children</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">input</tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-243', 'insert', 'link-154');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'('</tt><tt class="py-op">)</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt>  <tt class="py-line">            <tt id="link-244" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-244', 'children', 'link-155');">children</a></tt> <tt class="py-op">=</tt> <tt id="link-245" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-245', 'children', 'link-155');">children</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match_r()=Bio.Parsers.spark.GenericASTMatcher-class.html#match_r"><a title="Bio.Parsers.spark.GenericASTMatcher.match_r" class="py-name" href="#" onclick="return doclink('link-246', 'match_r', 'link-246');">match_r</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt>  <tt class="py-line"> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-247" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-247', 'children', 'link-155');">children</a></tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">input</tt><tt class="py-op">.</tt><tt id="link-248" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-248', 'insert', 'link-154');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">')'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L539"></a><tt class="py-lineno">539</tt>  <tt class="py-line"> </tt>
<a name="GenericASTMatcher.match"></a><div id="GenericASTMatcher.match-def"><a name="L540"></a><tt class="py-lineno">540</tt> <a class="py-toggle" href="#" id="GenericASTMatcher.match-toggle" onclick="return toggle('GenericASTMatcher.match');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTMatcher-class.html#match">match</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ast</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="GenericASTMatcher.match-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTMatcher.match-expanded"><a name="L541"></a><tt class="py-lineno">541</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">ast</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt>  <tt class="py-line">            <tt class="py-name">ast</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ast</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">input</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt>  <tt class="py-line"> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match_r" class="py-name" href="#" onclick="return doclink('link-249', 'match_r', 'link-246');">match_r</a></tt><tt class="py-op">(</tt><tt class="py-name">ast</tt><tt class="py-op">)</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-250" 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-250', 'parse', 'link-250');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">input</tt><tt class="py-op">)</tt> </tt>
</div><a name="L547"></a><tt class="py-lineno">547</tt>  <tt class="py-line"> </tt>
<a name="GenericASTMatcher.resolve"></a><div id="GenericASTMatcher.resolve-def"><a name="L548"></a><tt class="py-lineno">548</tt> <a class="py-toggle" href="#" id="GenericASTMatcher.resolve-toggle" onclick="return toggle('GenericASTMatcher.resolve');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark.GenericASTMatcher-class.html#resolve">resolve</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTMatcher.resolve-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GenericASTMatcher.resolve-expanded"><a name="L549"></a><tt class="py-lineno">549</tt>  <tt class="py-line">        <tt class="py-comment">#</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#  Resolve ambiguity in favor of the longest RHS.</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">return</tt> <tt id="link-251" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-251', 'list', 'link-177');">list</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L553"></a><tt class="py-lineno">553</tt>  <tt class="py-line"> </tt>
<a name="_dump"></a><div id="_dump-def"><a name="L554"></a><tt class="py-lineno">554</tt> <a class="py-toggle" href="#" id="_dump-toggle" onclick="return toggle('_dump');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Parsers.spark-module.html#_dump">_dump</a><tt class="py-op">(</tt><tt class="py-param">tokens</tt><tt class="py-op">,</tt> <tt class="py-param">states</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_dump-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_dump-expanded"><a name="L555"></a><tt class="py-lineno">555</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-252" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-252', 'i', 'link-34');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">states</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-string">'state'</tt><tt class="py-op">,</tt> <tt id="link-253" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-253', 'i', 'link-34');">i</a></tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-name">rhs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt> <tt class="py-keyword">in</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-254" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-254', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'\t'</tt><tt class="py-op">,</tt> <tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt class="py-string">'::='</tt><tt class="py-op">,</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt>  <tt class="py-line">            <tt class="py-keyword">print</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">rhs</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'.'</tt><tt class="py-op">,</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt>  <tt class="py-line">            <tt class="py-keyword">print</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">rhs</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">','</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-255" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-255', 'i', 'link-34');">i</a></tt> <tt class="py-op">&lt;</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-string">'token'</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt id="link-256" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-256', 'i', 'link-34');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> </tt>
</div><a name="L567"></a><tt class="py-lineno">567</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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