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Module 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>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><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"># 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"># "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"># 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"># 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"># 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"># 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>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><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"># 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>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><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"># 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"># 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"># 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"># 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"># 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"># 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>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">"""Copy of John Aycock's SPARK parser included with Biopython (DEPRECATED).</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">To clarify, when we say deprecated we just mean to warn you that Biopython will</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">in a future release no longer include this module. This does not affect the</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">status of John Aycock's SPARK parser which can be installed separately from:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">http://pages.cpsc.ucalgary.ca/~aycock/spark/</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">Biopython included this copy of SPARK purely for parsing GenBank/EMBL feature</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">location strings using Bio.GenBank.LocationParser, and that code has now been</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">replaced with something simpler and faster using regular expressions.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"># Don't issue a deprecation warning here, but via Bio.Parsers instead</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"># This avoids the user seeing multiple deprecation warnings.</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-string">'SPARK-0.6.1'</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="_namelist"></a><div id="_namelist-def"><a name="L41"></a><tt class="py-lineno"> 41</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="L42"></a><tt class="py-lineno"> 42</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="L43"></a><tt class="py-lineno"> 43</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="L44"></a><tt class="py-lineno"> 44</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="L45"></a><tt class="py-lineno"> 45</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.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-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"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.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="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-2" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.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="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-3" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-3', 'name', 'link-2');">name</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">namedict</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">namelist</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-4', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-5', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">namedict</tt><tt class="py-op">[</tt><tt id="link-6" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-6', '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="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">namelist</tt> </tt>
</div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="GenericScanner"></a><div id="GenericScanner-def"><a name="L52"></a><tt class="py-lineno"> 52</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 class="py-base-class">object</tt><tt class="py-op">)</tt><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="L53"></a><tt class="py-lineno"> 53</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="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">pattern</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" 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-7', 'reflect', 'link-7');">reflect</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-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 class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-name">pattern</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="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-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="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-8" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-8', '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-9" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.Phylo.PhyloXML.Events.items()=Bio.Phylo.PhyloXML.Events-class.html#items,Method Bio.SeqIO._index._IndexedSeqFileDict.items()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.Phylo.PhyloXML.Events.items
Bio.SeqIO._index._IndexedSeqFileDict.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items" class="py-name" href="#" onclick="return doclink('link-9', 'items', 'link-9');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt 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-10" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="GenericScanner.makeRE"></a><div id="GenericScanner.makeRE-def"><a name="L61"></a><tt class="py-lineno"> 61</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="L62"></a><tt class="py-lineno"> 62</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-11" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-11', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-string">'(?P<%s>%s)'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-12', '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="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt> </tt>
</div><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="GenericScanner.reflect"></a><div id="GenericScanner.reflect-def"><a name="L66"></a><tt class="py-lineno"> 66</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="L67"></a><tt class="py-lineno"> 67</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="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-13" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-2');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-14" 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-14', '_namelist', 'link-14');">_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="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-15" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.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 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-16" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-16', '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="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-17', '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-18" 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-18', 'makeRE', 'link-18');">makeRE</a></tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-19', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-20', '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-21" class="py-name"><a title="Bio.Parsers.spark.GenericScanner.makeRE" class="py-name" href="#" onclick="return doclink('link-21', 'makeRE', 'link-18');">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="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'|'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">rv</tt><tt class="py-op">)</tt> </tt>
</div><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="GenericScanner.error"></a><div id="GenericScanner.error-def"><a name="L75"></a><tt class="py-lineno"> 75</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="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</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="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">SystemExit</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
<a name="GenericScanner.tokenize"></a><div id="GenericScanner.tokenize-def"><a name="L79"></a><tt class="py-lineno"> 79</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="L80"></a><tt class="py-lineno"> 80</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="L81"></a><tt class="py-lineno"> 81</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 class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">pos</tt> <tt class="py-op"><</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">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-22" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-22', 'match', 'link-22');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" 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"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error" class="py-name" href="#" onclick="return doclink('link-23', 'error', 'link-23');">error</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">groups</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">groups</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-keyword">for</tt> <tt id="link-24" 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-24', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-25" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-25', 'range', 'link-25');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">groups</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-keyword">if</tt> <tt class="py-name">groups</tt><tt class="py-op">[</tt><tt id="link-26" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-26', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index2func</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">index2func</tt><tt class="py-op">[</tt><tt id="link-28" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-28', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-name">groups</tt><tt class="py-op">[</tt><tt id="link-29" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-29', 'i', 'link-24');">i</a></tt><tt class="py-op">]</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">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Variable Bio.SeqFeature.FeatureLocation.end=Bio.SeqFeature.FeatureLocation-class.html#end"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-30', 'end', 'link-30');">end</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="GenericScanner.t_default"></a><div id="GenericScanner.t_default-def"><a name="L93"></a><tt class="py-lineno"> 93</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="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-docstring">r'( . | \n )+'</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="GenericParser"></a><div id="GenericParser-def"><a name="L97"></a><tt class="py-lineno"> 97</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 class="py-base-class">object</tt><tt class="py-op">)</tt><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="L98"></a><tt class="py-lineno"> 98</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="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">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="L101"></a><tt class="py-lineno">101</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="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'collectRules', 'link-31');">collectRules</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">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-32" 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-32', 'augment', 'link-32');">augment</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Variable Bio.SeqFeature.FeatureLocation.start=Bio.SeqFeature.FeatureLocation-class.html#start"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-33', 'start', 'link-33');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-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="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt id="link-34" 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-34', '_START', 'link-34');">_START</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'START'</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt id="link-35" 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-35', '_EOF', 'link-35');">_EOF</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'EOF'</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-comment"># A hook for GenericASTBuilder and GenericASTMatcher.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="GenericParser.preprocess"></a><div id="GenericParser.preprocess-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="GenericParser.preprocess-toggle" onclick="return toggle('GenericParser.preprocess');">-</a><tt class="py-line"> <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 class="py-name">rule</tt><tt class="py-op">,</tt> <tt class="py-name">func</tt> </tt>
</div><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="GenericParser.addRule"></a><div id="GenericParser.addRule-def"><a name="L114"></a><tt class="py-lineno">114</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="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">rules</tt> <tt class="py-op">=</tt> <tt class="py-name">doc</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-36', 'split', 'link-36');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt id="link-37" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-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,Function Bio.SeqIO.index()=Bio.SeqIO-module.html#index"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-37', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-39" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-39', 'range', 'link-25');">range</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 class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</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-40" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-40', 'i', 'link-24');">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="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-41', 'index', 'link-37');">index</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-42', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-24');">i</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-44', 'index', 'link-37');">index</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-45', '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="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-46', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-47" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-47', 'range', 'link-25');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-48" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-48', 'index', 'link-37');">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="L124"></a><tt class="py-lineno">124</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-49" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-49', 'index', 'link-37');">index</a></tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</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-51" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-51', 'index', 'link-37');">index</a></tt><tt class="py-op">[</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-24');">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-53" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-53', 'index', 'link-37');">index</a></tt><tt class="py-op">[</tt><tt id="link-54" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-54', 'i', 'link-24');">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="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">rule</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="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">rule</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-55" 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-55', 'preprocess', 'link-55');">preprocess</a></tt><tt class="py-op">(</tt><tt class="py-name">rule</tt><tt class="py-op">,</tt> <tt class="py-name">func</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lhs</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>
<a name="L131"></a><tt class="py-lineno">131</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-56" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-56', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">rule</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">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 class="py-name">rule</tt> <tt class="py-op">]</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rule2func</tt><tt class="py-op">[</tt><tt class="py-name">rule</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">fn</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rule2name</tt><tt class="py-op">[</tt><tt class="py-name">rule</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="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ruleschanged</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="GenericParser.collectRules"></a><div id="GenericParser.collectRules-def"><a name="L138"></a><tt class="py-lineno">138</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="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-57" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-57', 'name', 'link-2');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-58" class="py-name"><a title="Bio.Parsers.spark._namelist" class="py-name" href="#" onclick="return doclink('link-58', '_namelist', 'link-14');">_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="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-59" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-59', '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="L141"></a><tt class="py-lineno">141</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-60" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-60', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-name">func</tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" 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-61', 'addRule', 'link-61');">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="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="GenericParser.augment"></a><div id="GenericParser.augment-def"><a name="L145"></a><tt class="py-lineno">145</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="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-comment"># Tempting though it is, this isn't made into a call</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-comment"># to self.addRule() because the start rule shouldn't</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-comment"># be subject to preprocessing.</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <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-62" class="py-name"><a title="Bio.Parsers.spark.GenericParser._START" class="py-name" href="#" onclick="return doclink('link-62', '_START', 'link-34');">_START</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt> <tt id="link-63" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-63', 'start', 'link-33');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Parsers.spark.GenericParser._EOF" class="py-name" href="#" onclick="return doclink('link-64', '_EOF', 'link-35');">_EOF</a></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 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="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rules</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Parsers.spark.GenericParser._START" class="py-name" href="#" onclick="return doclink('link-65', '_START', 'link-34');">_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="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">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="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">startRule</tt> </tt>
</div><a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> </tt>
<a name="GenericParser.makeFIRST"></a><div id="GenericParser.makeFIRST-def"><a name="L157"></a><tt class="py-lineno">157</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="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt id="link-66" 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-66', 'union', 'link-66');">union</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
<a name="L161"></a><tt class="py-lineno">161</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-67" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.Phylo.PhyloXML.Events.values()=Bio.Phylo.PhyloXML.Events-class.html#values,Method Bio.SeqIO._index._IndexedSeqFileDict.values()=Bio.SeqIO._index._IndexedSeqFileDict-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"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-67', 'values', 'link-67');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</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="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lhs</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">first</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt 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="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</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="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">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="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</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="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sym</tt> <tt class="py-keyword">not</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>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt 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="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.union" class="py-name" href="#" onclick="return doclink('link-68', 'union', 'link-66');">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="L175"></a><tt class="py-lineno">175</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="L176"></a><tt class="py-lineno">176</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="L177"></a><tt class="py-lineno">177</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="L178"></a><tt class="py-lineno">178</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-69" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.union" class="py-name" href="#" onclick="return doclink('link-69', 'union', 'link-66');">union</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Phylo.PhyloXML.Events.keys()=Bio.Phylo.PhyloXML.Events-class.html#keys,Method Bio.SeqIO._index._IndexedSeqFileDict.keys()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#keys,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.keys()=Bio.SeqIO._index._SQLiteManySeqFilesDict-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"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-70', 'keys', 'link-70');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</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="L180"></a><tt class="py-lineno">180</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-71" class="py-name" targets="Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SeqIO._index._IndexedSeqFileDict.update()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#update,Method Bio.SeqRecord._RestrictedDict.update()=Bio.SeqRecord._RestrictedDict-class.html#update"><a title="Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SeqIO._index._IndexedSeqFileDict.update
Bio.SeqRecord._RestrictedDict.update" class="py-name" href="#" onclick="return doclink('link-71', 'update', 'link-71');">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="L181"></a><tt class="py-lineno">181</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="L182"></a><tt class="py-lineno">182</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="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment"># An Earley parser, as per J. Earley, "An Efficient Context-Free</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment"># Parsing Algorithm", CACM 13(2), pp. 94-102. Also J. C. Earley,</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment"># "An Efficient Context-Free Parsing Algorithm", Ph.D. thesis,</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-comment"># Carnegie-Mellon University, August 1968, p. 27.</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="GenericParser.typestring"></a><div id="GenericParser.typestring-def"><a name="L191"></a><tt class="py-lineno">191</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="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="GenericParser.error"></a><div id="GenericParser.error-def"><a name="L194"></a><tt class="py-lineno">194</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="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</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="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">SystemExit</tt> </tt>
</div><a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="GenericParser.parse"></a><div id="GenericParser.parse-def"><a name="L198"></a><tt class="py-lineno">198</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="L199"></a><tt class="py-lineno">199</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="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">tokens</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-72', '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-73" class="py-name"><a title="Bio.Parsers.spark.GenericParser._EOF" class="py-name" href="#" onclick="return doclink('link-73', '_EOF', 'link-35');">_EOF</a></tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</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="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
<a name="L203"></a><tt class="py-lineno">203</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="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-74" 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-74', 'makeFIRST', 'link-74');">makeFIRST</a></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>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-75" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-75', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</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="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-76" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-76', 'i', 'link-24');">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="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-77" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-77', 'i', 'link-24');">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="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" 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-78', 'buildState', 'link-78');">buildState</a></tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt id="link-79" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-79', 'i', 'link-24');">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-80" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-80', 'i', 'link-24');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">tree</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-comment">#_dump(tokens, states)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-81" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-81', 'i', 'link-24');">i</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-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-82" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-82', 'i', 'link-24');">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="L216"></a><tt class="py-lineno">216</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="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error" class="py-name" href="#" onclick="return doclink('link-83', 'error', 'link-23');">error</a></tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">[</tt><tt id="link-84" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-84', 'i', 'link-24');">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="L218"></a><tt class="py-lineno">218</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-85" 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-85', 'buildTree', 'link-85');">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-86" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-86', 'i', 'link-24');">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="L219"></a><tt class="py-lineno">219</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="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt> </tt>
</div><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> </tt>
<a name="GenericParser.buildState"></a><div id="GenericParser.buildState-def"><a name="L222"></a><tt class="py-lineno">222</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="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-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-87" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-87', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</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="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">state</tt><tt class="py-op">:</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">rule</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-name">item</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</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 class="py-name">rule</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-comment"># A -> a . (completer)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <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="L235"></a><tt class="py-lineno">235</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="L236"></a><tt class="py-lineno">236</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 class="py-name">item</tt><tt class="py-op">,</tt> <tt id="link-88" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-88', 'i', 'link-24');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</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="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pitem</tt> <tt class="py-keyword">is</tt> <tt class="py-name">item</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="L242"></a><tt class="py-lineno">242</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="L243"></a><tt class="py-lineno">243</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="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-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="L246"></a><tt class="py-lineno">246</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="L247"></a><tt class="py-lineno">247</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="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">pparent</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">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="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-89', '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="L251"></a><tt class="py-lineno">251</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-90" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-90', 'i', 'link-24');">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 class="py-name">item</tt><tt class="py-op">,</tt> <tt id="link-91" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-91', 'i', 'link-24');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</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-92" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-92', 'i', 'link-24');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-93', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">,</tt> <tt id="link-94" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-94', 'i', 'link-24');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt 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="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-comment"># A -> a . B (predictor)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nextSym</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>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-comment"># Work on completer step some more; for rules</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-comment"># with empty RHS, the "parent state" is the</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-comment"># current state we're adding Earley items to,</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-comment"># so the Earley items the completer step needs</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-comment"># may not all be present when it runs.</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nextSym</tt> <tt class="py-keyword">in</tt> <tt class="py-name">needsCompletion</tt><tt class="py-op">:</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</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">rule</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="L271"></a><tt class="py-lineno">271</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="L272"></a><tt class="py-lineno">272</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="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.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">new</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</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-96" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-96', 'i', 'link-24');">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="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</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-97" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-97', 'i', 'link-24');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-98', '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="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-comment"># Has this been predicted already?</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nextSym</tt> <tt class="py-keyword">in</tt> <tt class="py-name">predicted</tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</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="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
<a name="L285"></a><tt class="py-lineno">285</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-99" class="py-name"><a title="Bio.Parsers.spark.GenericParser._EOF" class="py-name" href="#" onclick="return doclink('link-99', '_EOF', 'link-35');">_EOF</a></tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-100" 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-100', 'typestring', 'link-100');">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="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">None</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">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="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-comment"># Even smarter predictor, when the</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-comment"># token's type is known. The code is</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-comment"># grungy, but runs pretty fast. Three</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-comment"># cases are looked for: rules with</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-comment"># empty RHS; first symbol on RHS is a</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-comment"># terminal; first symbol on RHS is a</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-comment"># nonterminal (and isn't nullable).</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</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="L299"></a><tt class="py-lineno">299</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-101" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-101', 'i', 'link-24');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</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="L301"></a><tt class="py-lineno">301</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="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-102" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-102', '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 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="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">prhs0</tt> <tt class="py-keyword">not</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>
<a name="L306"></a><tt class="py-lineno">306</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="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-103', '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="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</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="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">None</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">first</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-name">ttype</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">first</tt><tt class="py-op">:</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-104', '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="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">continue</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-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="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-comment"># Smarter predictor, as per Grune &</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-comment"># Jacobs' _Parsing Techniques_. Not</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-comment"># as good as FIRST sets though.</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</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="L325"></a><tt class="py-lineno">325</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-keyword">and</tt> \ </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <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-keyword">not</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-keyword">and</tt> \ </tt>
<a name="L327"></a><tt class="py-lineno">327</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="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-105', '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-106" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-106', 'i', 'link-24');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-comment"># A -> a . c (scanner)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <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="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-comment">#assert new not in states[i+1]</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">states</tt><tt class="py-op">[</tt><tt id="link-107" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-107', 'i', 'link-24');">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-108" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-108', 'append', 'link-1');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">rule</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="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> </tt>
<a name="GenericParser.buildTree"></a><div id="GenericParser.buildTree-def"><a name="L338"></a><tt class="py-lineno">338</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="L339"></a><tt class="py-lineno">339</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="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <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_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-109', 'buildTree_r', 'link-109');">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 id="link-110" class="py-name" targets="Variable Bio.Phylo.BaseTree.Clade.root=Bio.Phylo.BaseTree.Clade-class.html#root"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-110', 'root', 'link-110');">root</a></tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</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="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> </tt>
<a name="GenericParser.buildTree_r"></a><div id="GenericParser.buildTree_r-def"><a name="L343"></a><tt class="py-lineno">343</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="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">rule</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 id="link-111" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-111', 'root', 'link-110');">root</a></tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">pos</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</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 class="py-name">rule</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="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">want</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tree</tt><tt class="py-op">:</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-comment"># Since pos > 0, it didn't come from closure,</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-comment"># and if it isn't in tree[], then there must</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-comment"># be a terminal symbol to the left of the dot.</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-comment"># (It must be from a "scanner" step.)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</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="L356"></a><tt class="py-lineno">356</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="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">stack</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-112', 'insert', 'link-112');">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="L358"></a><tt class="py-lineno">358</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="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-comment">#</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-comment"># There's a NT to the left of the dot.</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-comment"># Follow the tree pointer recursively (>1</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-comment"># tree pointers from it indicates ambiguity).</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-comment"># Since the item must have come about from a</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-comment"># "completer" step, the state where the item</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-comment"># came from must be the parent state of the</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-comment"># item the tree pointer points to.</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt id="link-113" 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-113', 'children', 'link-113');">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="L370"></a><tt class="py-lineno">370</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-114" 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-114', 'children', 'link-113');">children</a></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="L371"></a><tt class="py-lineno">371</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-115" 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-115', 'ambiguity', 'link-115');">ambiguity</a></tt><tt class="py-op">(</tt><tt id="link-116" 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-116', 'children', 'link-113');">children</a></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">else</tt><tt class="py-op">:</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">child</tt> <tt class="py-op">=</tt> <tt id="link-117" 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-117', 'children', 'link-113');">children</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> </tt>
<a name="L375"></a><tt class="py-lineno">375</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-118" class="py-name"><a title="Bio.Parsers.spark.GenericParser.buildTree_r" class="py-name" href="#" onclick="return doclink('link-118', 'buildTree_r', 'link-109');">buildTree_r</a></tt><tt class="py-op">(</tt><tt class="py-name">stack</tt><tt class="py-op">,</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</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="L377"></a><tt class="py-lineno">377</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="L378"></a><tt class="py-lineno">378</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="L379"></a><tt class="py-lineno">379</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="L380"></a><tt class="py-lineno">380</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="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> </tt>
<a name="L382"></a><tt class="py-lineno">382</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 class="py-name">rule</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</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 class="py-name">rule</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="L384"></a><tt class="py-lineno">384</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="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tokpos</tt> </tt>
</div><a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="GenericParser.ambiguity"></a><div id="GenericParser.ambiguity-def"><a name="L387"></a><tt class="py-lineno">387</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="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-comment"># XXX - problem here and in collectRules() if the same</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-comment"># rule appears in >1 method. But in that case the</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-comment"># user probably gets what they deserve :-) Also</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-comment"># undefined results if rules causing the ambiguity</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-comment"># appear in the same method.</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-name">sortlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</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="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-119" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-119', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-120" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-120', 'range', 'link-25');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-121" 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-121', 'children', 'link-113');">children</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">rule</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-122" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-122', 'index', 'link-37');">index</a></tt><tt class="py-op">)</tt> <tt class="py-op">=</tt> <tt id="link-123" 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-123', 'children', 'link-113');">children</a></tt><tt class="py-op">[</tt><tt id="link-124" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-124', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</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 class="py-name">rule</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt id="link-125" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-125', '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 class="py-name">rule</tt><tt class="py-op">]</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-name">sortlist</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-126', '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-127" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-127', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-name">name2index</tt><tt class="py-op">[</tt><tt id="link-128" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-128', 'name', 'link-2');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-129" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-129', 'i', 'link-24');">i</a></tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">sortlist</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.sort()=Bio.Align.MultipleSeqAlignment-class.html#sort,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.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-130', 'sort', 'link-130');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt id="link-131" 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-131', 'list', 'link-131');">list</a></tt> <tt class="py-op">=</tt> <tt class="py-name">map</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="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-132" 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-132', 'children', 'link-113');">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-133" 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"><a title="Bio.Parsers.spark.GenericASTMatcher.resolve
Bio.Parsers.spark.GenericParser.resolve" class="py-name" href="#" onclick="return doclink('link-133', 'resolve', 'link-133');">resolve</a></tt><tt class="py-op">(</tt><tt id="link-134" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-134', 'list', 'link-131');">list</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
</div><a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> </tt>
<a name="GenericParser.resolve"></a><div id="GenericParser.resolve-def"><a name="L407"></a><tt class="py-lineno">407</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="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-comment"># Resolve ambiguity in favor of the shortest RHS.</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-comment"># Since we walk the tree from the top down, this</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-comment"># should effectively resolve in favor of a "shift".</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-135" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-135', 'list', 'link-131');">list</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-comment"># GenericASTBuilder automagically constructs a concrete/abstract syntax tree</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-comment"># for a given input. The extra argument is a class (not an instance!)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-comment"># which supports the "__setslice__" and "__len__" methods.</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-comment"># XXX - silently overrides any user code in methods.</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> </tt>
<a name="GenericASTBuilder"></a><div id="GenericASTBuilder-def"><a name="L423"></a><tt class="py-lineno">423</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="L424"></a><tt class="py-lineno">424</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="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt id="link-136" 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-136', 'GenericParser', 'link-136');">GenericParser</a></tt><tt class="py-op">.</tt><tt id="link-137" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Affy.CelFile.CelScanner.__init__()=Bio.Affy.CelFile.CelScanner-class.html#__init__,Method Bio.Affy.CelFile.Record.__init__()=Bio.Affy.CelFile.Record-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__()=Bio.Align.Applications._Clustalw.ClustalwCommandline-class.html#__init__,Method Bio.Align.Applications._Dialign.DialignCommandline.__init__()=Bio.Align.Applications._Dialign.DialignCommandline-class.html#__init__,Method Bio.Align.Applications._Mafft.MafftCommandline.__init__()=Bio.Align.Applications._Mafft.MafftCommandline-class.html#__init__,Method Bio.Align.Applications._Muscle.MuscleCommandline.__init__()=Bio.Align.Applications._Muscle.MuscleCommandline-class.html#__init__,Method Bio.Align.Applications._Prank.PrankCommandline.__init__()=Bio.Align.Applications._Prank.PrankCommandline-class.html#__init__,Method Bio.Align.Applications._Probcons.ProbconsCommandline.__init__()=Bio.Align.Applications._Probcons.ProbconsCommandline-class.html#__init__,Method Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__()=Bio.Align.Applications._TCoffee.TCoffeeCommandline-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.Align.MultipleSeqAlignment.__init__()=Bio.Align.MultipleSeqAlignment-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationError.__init__()=Bio.Application.ApplicationError-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Application._Argument.__init__()=Bio.Application._Argument-class.html#__init__,Method Bio.Application._Option.__init__()=Bio.Application._Option-class.html#__init__,Method Bio.Application._Switch.__init__()=Bio.Application._Switch-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.BlastpgpCommandline.__init__()=Bio.Blast.Applications.BlastpgpCommandline-class.html#__init__,Method 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Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.Seq.UnknownSeq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.UnknownPosition.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhdIO.PhdWriter.__init__
Bio.SeqIO.QualityIO.QualPhredWriter.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__
Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__
Bio.SeqIO.SffIO.SffWriter.__init__
Bio.SeqIO.SffIO._AddTellHandle.__init__
Bio.SeqIO.UniprotIO.Parser.__init__
Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__
Bio.SeqIO._index.SeqFileRandomAccess.__init__
Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__
Bio.SeqIO._index.SffRandomAccess.__init__
Bio.SeqIO._index._IndexedSeqFileDict.__init__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqRecord._RestrictedDict.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.Record.__init__
Bio.SwissProt.Reference.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.ProtsimLine.__init__
Bio.UniGene.Record.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.STSLine.__init__
Bio.UniGene.SequenceLine.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.UniGene._Scanner.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-137', '__init__', 'link-137');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-138" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-138', 'start', 'link-33');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</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="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> </tt>
<a name="GenericASTBuilder.preprocess"></a><div id="GenericASTBuilder.preprocess-def"><a name="L428"></a><tt class="py-lineno">428</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="L429"></a><tt class="py-lineno">429</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="L430"></a><tt class="py-lineno">430</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="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-139" 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-139', 'buildASTNode', 'link-139');">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="L432"></a><tt class="py-lineno">432</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 class="py-name">rule</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rule</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="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> </tt>
<a name="GenericASTBuilder.buildASTNode"></a><div id="GenericASTBuilder.buildASTNode-def"><a name="L435"></a><tt class="py-lineno">435</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="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt id="link-140" 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-140', 'children', 'link-113');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</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="L438"></a><tt class="py-lineno">438</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="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt id="link-141" 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-141', 'children', 'link-113');">children</a></tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-142', '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="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt id="link-143" 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-143', 'children', 'link-113');">children</a></tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-144', '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-145" 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-145', 'terminal', 'link-145');">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="L442"></a><tt class="py-lineno">442</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-146" 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-146', 'nonterminal', 'link-146');">nonterminal</a></tt><tt class="py-op">(</tt><tt class="py-name">lhs</tt><tt class="py-op">,</tt> <tt id="link-147" 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-147', 'children', 'link-113');">children</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> </tt>
<a name="GenericASTBuilder.terminal"></a><div id="GenericASTBuilder.terminal-def"><a name="L444"></a><tt class="py-lineno">444</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="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> </tt>
<a name="GenericASTBuilder.nonterminal"></a><div id="GenericASTBuilder.nonterminal-def"><a name="L446"></a><tt class="py-lineno">446</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="L447"></a><tt class="py-lineno">447</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-148" 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,Method Bio.Phylo.PhyloXMLIO.Writer.type()=Bio.Phylo.PhyloXMLIO.Writer-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-148', 'type', 'link-148');">type</a></tt><tt class="py-op">)</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</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="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt> </tt>
</div></div><a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-comment"># GenericASTTraversal is a Visitor pattern according to Design Patterns. For</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-comment"># each node it attempts to invoke the method n_<node type>, falling</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-comment"># back onto the default() method if the n_* can't be found. The preorder</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-comment"># traversal also looks for an exit hook named n_<node type>_exit (no default</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-comment"># routine is called if it's not found). To prematurely halt traversal</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-comment"># of a subtree, call the prune() method -- this only makes sense for a</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-comment"># preorder traversal. Node type is determined via the typestring() method.</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> </tt>
<a name="GenericASTTraversalPruningException"></a><div id="GenericASTTraversalPruningException-def"><a name="L461"></a><tt class="py-lineno">461</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 class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GenericASTTraversalPruningException-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenericASTTraversalPruningException-expanded"><a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> </tt>
<a name="GenericASTTraversal"></a><div id="GenericASTTraversal-def"><a name="L464"></a><tt class="py-lineno">464</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 class="py-base-class">object</tt><tt class="py-op">)</tt><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="L465"></a><tt class="py-lineno">465</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="L466"></a><tt class="py-lineno">466</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="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> </tt>
<a name="GenericASTTraversal.typestring"></a><div id="GenericASTTraversal.typestring-def"><a name="L468"></a><tt class="py-lineno">468</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="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-149" class="py-name" targets="Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-149', 'node', 'link-149');">node</a></tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-150', 'type', 'link-148');">type</a></tt> </tt>
</div><a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> </tt>
<a name="GenericASTTraversal.prune"></a><div id="GenericASTTraversal.prune-def"><a name="L471"></a><tt class="py-lineno">471</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="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-151" 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-151', 'GenericASTTraversalPruningException', 'link-151');">GenericASTTraversalPruningException</a></tt> </tt>
</div><a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> </tt>
<a name="GenericASTTraversal.preorder"></a><div id="GenericASTTraversal.preorder-def"><a name="L474"></a><tt class="py-lineno">474</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="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-152" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-152', 'node', 'link-149');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt id="link-153" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-153', 'node', 'link-149');">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="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 class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt id="link-154" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-154', '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-155" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.typestring
Bio.Parsers.spark.GenericParser.typestring" class="py-name" href="#" onclick="return doclink('link-155', 'typestring', 'link-100');">typestring</a></tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-156', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</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-157" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-157', 'name', 'link-2');">name</a></tt><tt class="py-op">)</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 class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-158" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-158', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-name">func</tt><tt class="py-op">(</tt><tt id="link-159" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-159', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-160" 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-160', 'default', 'link-160');">default</a></tt><tt class="py-op">(</tt><tt id="link-161" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-161', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-162" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversalPruningException" class="py-name" href="#" onclick="return doclink('link-162', 'GenericASTTraversalPruningException', 'link-151');">GenericASTTraversalPruningException</a></tt><tt class="py-op">:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> </tt>
<a name="L488"></a><tt class="py-lineno">488</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-163" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-163', 'node', 'link-149');">node</a></tt><tt class="py-op">:</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-164" 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-164', 'preorder', 'link-164');">preorder</a></tt><tt class="py-op">(</tt><tt class="py-name">kid</tt><tt class="py-op">)</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt id="link-165" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-165', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-166" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-166', 'name', 'link-2');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-string">'_exit'</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</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-167" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-167', 'name', 'link-2');">name</a></tt><tt class="py-op">)</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 class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-168" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-168', 'name', 'link-2');">name</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-name">func</tt><tt class="py-op">(</tt><tt id="link-169" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-169', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> </tt>
<a name="GenericASTTraversal.postorder"></a><div id="GenericASTTraversal.postorder-def"><a name="L496"></a><tt class="py-lineno">496</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="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-170" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-170', 'node', 'link-149');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt id="link-171" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-171', 'node', 'link-149');">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="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> </tt>
<a name="L500"></a><tt class="py-lineno">500</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-172" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-172', 'node', 'link-149');">node</a></tt><tt class="py-op">:</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-173" 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-173', 'postorder', 'link-173');">postorder</a></tt><tt class="py-op">(</tt><tt class="py-name">kid</tt><tt class="py-op">)</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt id="link-174" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-174', '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-175" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.typestring
Bio.Parsers.spark.GenericParser.typestring" class="py-name" href="#" onclick="return doclink('link-175', 'typestring', 'link-100');">typestring</a></tt><tt class="py-op">(</tt><tt id="link-176" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-176', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</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-177" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-177', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</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-178" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-178', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-name">func</tt><tt class="py-op">(</tt><tt id="link-179" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-179', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-180', 'default', 'link-160');">default</a></tt><tt class="py-op">(</tt><tt id="link-181" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-181', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> </tt>
<a name="GenericASTTraversal.default"></a><div id="GenericASTTraversal.default-def"><a name="L511"></a><tt class="py-lineno">511</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="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"><tt class="py-comment"># GenericASTMatcher. AST nodes must have "__getitem__" and "__cmp__"</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"><tt class="py-comment"># implemented.</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"><tt class="py-comment"># XXX - makes assumptions about how GenericParser walks the parse tree.</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> </tt>
<a name="GenericASTMatcher"></a><div id="GenericASTMatcher-def"><a name="L521"></a><tt class="py-lineno">521</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="L522"></a><tt class="py-lineno">522</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="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt id="link-182" class="py-name"><a title="Bio.Parsers.spark.GenericParser" class="py-name" href="#" onclick="return doclink('link-182', 'GenericParser', 'link-136');">GenericParser</a></tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Affy.CelFile.CelScanner.__init__
Bio.Affy.CelFile.Record.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__
Bio.Align.Applications._Dialign.DialignCommandline.__init__
Bio.Align.Applications._Mafft.MafftCommandline.__init__
Bio.Align.Applications._Muscle.MuscleCommandline.__init__
Bio.Align.Applications._Prank.PrankCommandline.__init__
Bio.Align.Applications._Probcons.ProbconsCommandline.__init__
Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__
Bio.Align.Generic.Alignment.__init__
Bio.Align.MultipleSeqAlignment.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationError.__init__
Bio.Application._AbstractParameter.__init__
Bio.Application._Argument.__init__
Bio.Application._Option.__init__
Bio.Application._Switch.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.BlastpgpCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.Applications.NcbiblastformatterCommandline.__init__
Bio.Blast.Applications.NcbiblastnCommandline.__init__
Bio.Blast.Applications.NcbiblastpCommandline.__init__
Bio.Blast.Applications.NcbiblastxCommandline.__init__
Bio.Blast.Applications.NcbipsiblastCommandline.__init__
Bio.Blast.Applications.NcbirpsblastCommandline.__init__
Bio.Blast.Applications.NcbirpstblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastnCommandline.__init__
Bio.Blast.Applications.NcbitblastxCommandline.__init__
Bio.Blast.Applications.RpsBlastCommandline.__init__
Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__
Bio.Blast.Applications._BlastCommandLine.__init__
Bio.Blast.Applications._NcbibaseblastCommandline.__init__
Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__
Bio.Blast.Applications._NcbiblastCommandline.__init__
Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
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BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-183', '__init__', 'link-137');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-184" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-184', 'start', 'link-33');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</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="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> </tt>
<a name="GenericASTMatcher.preprocess"></a><div id="GenericASTMatcher.preprocess-def"><a name="L526"></a><tt class="py-lineno">526</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="L527"></a><tt class="py-lineno">527</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="L528"></a><tt class="py-lineno">528</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="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-185" 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-185', 'foundMatch', 'link-185');">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="L530"></a><tt class="py-lineno">530</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 class="py-name">rule</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-name">rhslist</tt> <tt class="py-op">=</tt> <tt id="link-186" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-186', 'list', 'link-131');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">rhs</tt><tt class="py-op">)</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-name">rhslist</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name" targets="Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-187', 'reverse', 'link-187');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> </tt>
<a name="L534"></a><tt class="py-lineno">534</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="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> </tt>
<a name="GenericASTMatcher.foundMatch"></a><div id="GenericASTMatcher.foundMatch-def"><a name="L536"></a><tt class="py-lineno">536</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="L537"></a><tt class="py-lineno">537</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="L538"></a><tt class="py-lineno">538</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="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> </tt>
<a name="GenericASTMatcher.match_r"></a><div id="GenericASTMatcher.match_r-def"><a name="L540"></a><tt class="py-lineno">540</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="L541"></a><tt class="py-lineno">541</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-188" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-188', 'insert', 'link-112');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-189" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-189', 'node', 'link-149');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</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-113');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> </tt>
<a name="L544"></a><tt class="py-lineno">544</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-191" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-191', 'node', 'link-149');">node</a></tt><tt class="py-op">:</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <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-113');">children</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</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 class="py-name">input</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-193', 'insert', 'link-112');">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="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt id="link-194" 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-194', 'children', 'link-113');">children</a></tt> <tt class="py-op">=</tt> <tt id="link-195" 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-195', 'children', 'link-113');">children</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-196" 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-196', 'match_r', 'link-196');">match_r</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-197" 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-197', 'children', 'link-113');">children</a></tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</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-198" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-198', 'insert', 'link-112');">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="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> </tt>
<a name="GenericASTMatcher.match"></a><div id="GenericASTMatcher.match-def"><a name="L553"></a><tt class="py-lineno">553</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="L554"></a><tt class="py-lineno">554</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="L555"></a><tt class="py-lineno">555</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="L556"></a><tt class="py-lineno">556</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="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match_r" class="py-name" href="#" onclick="return doclink('link-199', 'match_r', 'link-196');">match_r</a></tt><tt class="py-op">(</tt><tt class="py-name">ast</tt><tt class="py-op">)</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-200" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-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,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.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,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,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.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.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-200', 'parse', 'link-200');">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="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> </tt>
<a name="GenericASTMatcher.resolve"></a><div id="GenericASTMatcher.resolve-def"><a name="L561"></a><tt class="py-lineno">561</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="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-comment"># Resolve ambiguity in favor of the longest RHS.</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-201" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-201', 'list', 'link-131');">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="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> </tt>
<a name="_dump"></a><div id="_dump-def"><a name="L567"></a><tt class="py-lineno">567</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="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-202" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-202', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-203" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-203', 'range', 'link-25');">range</a></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="L569"></a><tt class="py-lineno">569</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-204" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-204', 'i', 'link-24');">i</a></tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</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-205" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-205', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</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="L572"></a><tt class="py-lineno">572</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">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="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'.'</tt><tt class="py-op">,</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</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">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="L575"></a><tt class="py-lineno">575</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="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-206" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-206', 'i', 'link-24');">i</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>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</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-207" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-207', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
</div><a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> </tt><script type="text/javascript">
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