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<a href="Bio-module.html">Package Bio</a> ::
Module ParserSupport
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<h1 class="epydoc">Source Code for <a href="Bio.ParserSupport-module.html">Module Bio.ParserSupport</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 1999 by Jeffrey Chang. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Code to support writing parsers.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">AbstractParser Base class for parsers.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">AbstractConsumer Base class of all Consumers.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">TaggingConsumer Consumer that tags output with its event. For debugging</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">SGMLStrippingConsumer Consumer that strips SGML tags from output.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">EventGenerator Generate Biopython Events from Martel XML output</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">Functions:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">safe_readline Read a line from a handle, with check for EOF.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">safe_peekline Peek at next line, with check for EOF.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">read_and_call Read a line from a handle and pass it to a method.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">read_and_call_while Read many lines, as long as a condition is met.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">read_and_call_until Read many lines, until a condition is met.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">attempt_read_and_call Like read_and_call, but forgiving of errors.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">is_blank_line Test whether a line is blank.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">traceback</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"># XML from python 2.0</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> <tt class="py-keyword">import</tt> <tt class="py-name">handler</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt id="link-2" class="py-name" targets="Variable Bio.AlignAce.AlignAceStandalone.xml_support=Bio.AlignAce.AlignAceStandalone-module.html#xml_support,Variable Bio.AlignAce.Parser.xml_support=Bio.AlignAce.Parser-module.html#xml_support,Variable Bio.Blast.NCBIStandalone.xml_support=Bio.Blast.NCBIStandalone-module.html#xml_support,Variable Bio.Blast.NCBIWWW.xml_support=Bio.Blast.NCBIWWW-module.html#xml_support,Variable Bio.Compass.xml_support=Bio.Compass-module.html#xml_support,Variable Bio.Enzyme.xml_support=Bio.Enzyme-module.html#xml_support,Variable Bio.Gobase.xml_support=Bio.Gobase-module.html#xml_support,Variable Bio.MEME.Parser.xml_support=Bio.MEME.Parser-module.html#xml_support,Variable Bio.Medline.xml_support=Bio.Medline-module.html#xml_support,Variable Bio.Ndb.xml_support=Bio.Ndb-module.html#xml_support,Variable Bio.ParserSupport.xml_support=Bio.ParserSupport-module.html#xml_support,Variable Bio.PopGen.FDist.xml_support=Bio.PopGen.FDist-module.html#xml_support,Variable Bio.PopGen.GenePop.xml_support=Bio.PopGen.GenePop-module.html#xml_support,Variable Bio.Prosite.Prodoc.xml_support=Bio.Prosite.Prodoc-module.html#xml_support,Variable Bio.Prosite.xml_support=Bio.Prosite-module.html#xml_support,Variable Bio.Rebase.xml_support=Bio.Rebase-module.html#xml_support,Variable Bio.Sequencing.Ace.xml_support=Bio.Sequencing.Ace-module.html#xml_support,Variable Bio.Sequencing.Phd.xml_support=Bio.Sequencing.Phd-module.html#xml_support,Variable Bio.SwissProt.KeyWList.xml_support=Bio.SwissProt.KeyWList-module.html#xml_support,Variable Bio.SwissProt.SProt.xml_support=Bio.SwissProt.SProt-module.html#xml_support,Variable Bio.UniGene.xml_support=Bio.UniGene-module.html#xml_support"><a title="Bio.AlignAce.AlignAceStandalone.xml_support
Bio.AlignAce.Parser.xml_support
Bio.Blast.NCBIStandalone.xml_support
Bio.Blast.NCBIWWW.xml_support
Bio.Compass.xml_support
Bio.Enzyme.xml_support
Bio.Gobase.xml_support
Bio.MEME.Parser.xml_support
Bio.Medline.xml_support
Bio.Ndb.xml_support
Bio.ParserSupport.xml_support
Bio.PopGen.FDist.xml_support
Bio.PopGen.GenePop.xml_support
Bio.Prosite.Prodoc.xml_support
Bio.Prosite.xml_support
Bio.Rebase.xml_support
Bio.Sequencing.Ace.xml_support
Bio.Sequencing.Phd.xml_support
Bio.SwissProt.KeyWList.xml_support
Bio.SwissProt.SProt.xml_support
Bio.UniGene.xml_support" class="py-name" href="#" onclick="return doclink('link-2', 'xml_support', 'link-2');">xml_support</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-3', 'write', 'link-3');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"Warning: Could not import SAX for dealing with XML.\n"</tt> <tt class="py-op">+</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-string">"This causes problems with some ParserSupport modules\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-4" class="py-name"><a title="Bio.AlignAce.AlignAceStandalone.xml_support
Bio.AlignAce.Parser.xml_support
Bio.Blast.NCBIStandalone.xml_support
Bio.Blast.NCBIWWW.xml_support
Bio.Compass.xml_support
Bio.Enzyme.xml_support
Bio.Gobase.xml_support
Bio.MEME.Parser.xml_support
Bio.Medline.xml_support
Bio.Ndb.xml_support
Bio.ParserSupport.xml_support
Bio.PopGen.FDist.xml_support
Bio.PopGen.GenePop.xml_support
Bio.Prosite.Prodoc.xml_support
Bio.Prosite.xml_support
Bio.Rebase.xml_support
Bio.Sequencing.Ace.xml_support
Bio.Sequencing.Phd.xml_support
Bio.SwissProt.KeyWList.xml_support
Bio.SwissProt.SProt.xml_support
Bio.UniGene.xml_support" class="py-name" href="#" onclick="return doclink('link-4', 'xml_support', 'link-2');">xml_support</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="AbstractParser"></a><div id="AbstractParser-def"><a name="L44"></a><tt class="py-lineno"> 44</tt> <a class="py-toggle" href="#" id="AbstractParser-toggle" onclick="return toggle('AbstractParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractParser-class.html">AbstractParser</a><tt class="py-op">:</tt> </tt>
</div><div id="AbstractParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AbstractParser-expanded"><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for other parsers.</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="AbstractParser.parse"></a><div id="AbstractParser.parse-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="AbstractParser.parse-toggle" onclick="return toggle('AbstractParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractParser.parse-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"Please implement in a derived class"</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="AbstractParser.parse_str"></a><div id="AbstractParser.parse_str-def"><a name="L51"></a><tt class="py-lineno"> 51</tt> <a class="py-toggle" href="#" id="AbstractParser.parse_str-toggle" onclick="return toggle('AbstractParser.parse_str');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractParser-class.html#parse_str">parse_str</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractParser.parse_str-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractParser.parse_str-expanded"><a name="L52"></a><tt class="py-lineno"> 52</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-5" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-5', 'parse', 'link-5');">parse</a></tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-6', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="AbstractParser.parse_file"></a><div id="AbstractParser.parse_file-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="AbstractParser.parse_file-toggle" onclick="return toggle('AbstractParser.parse_file');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractParser-class.html#parse_file">parse_file</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractParser.parse_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractParser.parse_file-expanded"><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">h</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-7', 'open', 'link-7');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">retval</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-8', 'parse', 'link-5');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">h</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">finally</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">h</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-9', 'close', 'link-9');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">retval</tt> </tt>
</div></div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="AbstractConsumer"></a><div id="AbstractConsumer-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="AbstractConsumer-toggle" onclick="return toggle('AbstractConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractConsumer-class.html">AbstractConsumer</a><tt class="py-op">:</tt> </tt>
</div><div id="AbstractConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AbstractConsumer-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for other Consumers.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> Derive Consumers from this class and implement appropriate</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> methods for each event that you want to receive.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="AbstractConsumer._unhandled_section"></a><div id="AbstractConsumer._unhandled_section-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="AbstractConsumer._unhandled_section-toggle" onclick="return toggle('AbstractConsumer._unhandled_section');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractConsumer-class.html#_unhandled_section">_unhandled_section</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="AbstractConsumer._unhandled_section-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractConsumer._unhandled_section-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="AbstractConsumer._unhandled"></a><div id="AbstractConsumer._unhandled-def"><a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="AbstractConsumer._unhandled-toggle" onclick="return toggle('AbstractConsumer._unhandled');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractConsumer-class.html#_unhandled">_unhandled</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractConsumer._unhandled-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractConsumer._unhandled-expanded"><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="AbstractConsumer.__getattr__"></a><div id="AbstractConsumer.__getattr__-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="AbstractConsumer.__getattr__-toggle" onclick="return toggle('AbstractConsumer.__getattr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.AbstractConsumer-class.html#__getattr__">__getattr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractConsumer.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractConsumer.__getattr__-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">attr</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'start_'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">attr</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'end_'</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">method</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.ParserSupport.AbstractConsumer._unhandled_section()=Bio.ParserSupport.AbstractConsumer-class.html#_unhandled_section"><a title="Bio.ParserSupport.AbstractConsumer._unhandled_section" class="py-name" href="#" onclick="return doclink('link-10', '_unhandled_section', 'link-10');">_unhandled_section</a></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">method</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.ParserSupport.AbstractConsumer._unhandled()=Bio.ParserSupport.AbstractConsumer-class.html#_unhandled"><a title="Bio.ParserSupport.AbstractConsumer._unhandled" class="py-name" href="#" onclick="return doclink('link-11', '_unhandled', 'link-11');">_unhandled</a></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">method</tt> </tt>
</div></div><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="TaggingConsumer"></a><div id="TaggingConsumer-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="TaggingConsumer-toggle" onclick="return toggle('TaggingConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.ParserSupport.TaggingConsumer-class.html">TaggingConsumer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractConsumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TaggingConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TaggingConsumer-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-docstring">"""A Consumer that tags the data stream with the event and</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> prints it to a handle. Useful for debugging.</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="TaggingConsumer.__init__"></a><div id="TaggingConsumer.__init__-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="TaggingConsumer.__init__-toggle" onclick="return toggle('TaggingConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.TaggingConsumer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">colwidth</tt><tt class="py-op">=</tt><tt class="py-number">15</tt><tt class="py-op">,</tt> <tt class="py-param">maxwidth</tt><tt class="py-op">=</tt><tt class="py-number">80</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TaggingConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggingConsumer.__init__-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-docstring">"""TaggingConsumer(handle=sys.stdout, colwidth=15, maxwidth=80)"""</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-comment"># I can't assign sys.stdout to handle in the argument list.</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># If I do that, handle will be assigned the value of sys.stdout</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the first time this function is called. This will fail if</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the user has assigned sys.stdout to some other file, which may</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># be closed or invalid at a later time.</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-12" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-12', 'handle', 'link-12');">handle</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-13', 'handle', 'link-12');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdout</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-14', 'handle', 'link-12');">handle</a></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_colwidth</tt> <tt class="py-op">=</tt> <tt class="py-name">colwidth</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_maxwidth</tt> <tt class="py-op">=</tt> <tt class="py-name">maxwidth</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="TaggingConsumer.unhandled_section"></a><div id="TaggingConsumer.unhandled_section-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="TaggingConsumer.unhandled_section-toggle" onclick="return toggle('TaggingConsumer.unhandled_section');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.TaggingConsumer-class.html#unhandled_section">unhandled_section</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="TaggingConsumer.unhandled_section-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggingConsumer.unhandled_section-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 id="link-15" class="py-name" targets="Method Bio.ParserSupport.TaggingConsumer._print_name()=Bio.ParserSupport.TaggingConsumer-class.html#_print_name"><a title="Bio.ParserSupport.TaggingConsumer._print_name" class="py-name" href="#" onclick="return doclink('link-15', '_print_name', 'link-15');">_print_name</a></tt><tt class="py-op">(</tt><tt class="py-string">'unhandled_section'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="TaggingConsumer.unhandled"></a><div id="TaggingConsumer.unhandled-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="TaggingConsumer.unhandled-toggle" onclick="return toggle('TaggingConsumer.unhandled');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.TaggingConsumer-class.html#unhandled">unhandled</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TaggingConsumer.unhandled-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggingConsumer.unhandled-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.ParserSupport.TaggingConsumer._print_name" class="py-name" href="#" onclick="return doclink('link-16', '_print_name', 'link-15');">_print_name</a></tt><tt class="py-op">(</tt><tt class="py-string">'unhandled'</tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-17', 'data', 'link-17');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="TaggingConsumer._print_name"></a><div id="TaggingConsumer._print_name-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="TaggingConsumer._print_name-toggle" onclick="return toggle('TaggingConsumer._print_name');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.TaggingConsumer-class.html#_print_name">_print_name</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-param">data</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="TaggingConsumer._print_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggingConsumer._print_name-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-18" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-18', 'data', 'link-17');">data</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-comment"># Write the name of a section.</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-19', 'write', 'link-3');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-string">"*"</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_colwidth</tt><tt class="py-op">,</tt> <tt id="link-20" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-20');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-comment"># Write the tag and line.</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-21', 'write', 'link-3');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%-*s: %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_colwidth</tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-22', 'name', 'link-20');">name</a></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">_colwidth</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-23', 'data', 'link-17');">data</a></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">_maxwidth</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_colwidth</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-op">)</tt> </tt>
</div><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="TaggingConsumer.__getattr__"></a><div id="TaggingConsumer.__getattr__-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="TaggingConsumer.__getattr__-toggle" onclick="return toggle('TaggingConsumer.__getattr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.TaggingConsumer-class.html#__getattr__">__getattr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TaggingConsumer.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TaggingConsumer.__getattr__-expanded"><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">attr</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'start_'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">attr</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'end_'</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">method</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">attr</tt><tt class="py-op">,</tt> <tt id="link-24" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-24', 's', 'link-24');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">:</tt> <tt id="link-25" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-25', 's', 'link-24');">s</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.ParserSupport.TaggingConsumer._print_name" class="py-name" href="#" onclick="return doclink('link-26', '_print_name', 'link-15');">_print_name</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">method</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt id="link-27" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-27', 'x', 'link-27');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">a</tt><tt class="py-op">=</tt><tt class="py-name">attr</tt><tt class="py-op">,</tt> <tt id="link-28" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-28', 's', 'link-24');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">:</tt> <tt id="link-29" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-29', 's', 'link-24');">s</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.ParserSupport.TaggingConsumer._print_name" class="py-name" href="#" onclick="return doclink('link-30', '_print_name', 'link-15');">_print_name</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt> <tt id="link-31" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-31', 'x', 'link-27');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">method</tt> </tt>
</div></div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="SGMLStrippingConsumer"></a><div id="SGMLStrippingConsumer-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="SGMLStrippingConsumer-toggle" onclick="return toggle('SGMLStrippingConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.ParserSupport.SGMLStrippingConsumer-class.html">SGMLStrippingConsumer</a><tt class="py-op">:</tt> </tt>
</div><div id="SGMLStrippingConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SGMLStrippingConsumer-expanded"><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-docstring">"""A consumer that strips off SGML tags.</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> This is meant to be used as a decorator for other consumers.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="SGMLStrippingConsumer.__init__"></a><div id="SGMLStrippingConsumer.__init__-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="SGMLStrippingConsumer.__init__-toggle" onclick="return toggle('SGMLStrippingConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.SGMLStrippingConsumer-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">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SGMLStrippingConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SGMLStrippingConsumer.__init__-expanded"><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-32" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-32', 'type', 'link-32');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">consumer</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">InstanceType</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"consumer should be an instance"</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt class="py-name">consumer</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">_prev_attr</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stripper</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-33', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Class Bio.File.SGMLStripper=Bio.File.SGMLStripper-class.html"><a title="Bio.File.SGMLStripper" class="py-name" href="#" onclick="return doclink('link-34', 'SGMLStripper', 'link-34');">SGMLStripper</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="SGMLStrippingConsumer._apply_clean_data"></a><div id="SGMLStrippingConsumer._apply_clean_data-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="SGMLStrippingConsumer._apply_clean_data-toggle" onclick="return toggle('SGMLStrippingConsumer._apply_clean_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.SGMLStrippingConsumer-class.html#_apply_clean_data">_apply_clean_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SGMLStrippingConsumer._apply_clean_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SGMLStrippingConsumer._apply_clean_data-expanded"><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt id="link-35" class="py-name" targets="Method Bio.AlignIO.Interfaces.AlignmentWriter.clean()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#clean,Method Bio.SeqIO.Interfaces.SequenceWriter.clean()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#clean"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-35', 'clean', 'link-35');">clean</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_stripper</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-36', 'strip', 'link-36');">strip</a></tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-37', 'data', 'link-17');">data</a></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">_prev_attr</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-38', 'clean', 'link-35');">clean</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="SGMLStrippingConsumer.__getattr__"></a><div id="SGMLStrippingConsumer.__getattr__-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="SGMLStrippingConsumer.__getattr__-toggle" onclick="return toggle('SGMLStrippingConsumer.__getattr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.SGMLStrippingConsumer-class.html#__getattr__">__getattr__</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="SGMLStrippingConsumer.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SGMLStrippingConsumer.__getattr__-expanded"><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-39" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-39', 'name', 'link-20');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'_prev_attr'</tt><tt class="py-op">,</tt> <tt class="py-string">'_stripper'</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">return</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-40" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-40', 'name', 'link-20');">name</a></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">attr</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-name">_consumer</tt><tt class="py-op">,</tt> <tt id="link-41" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-41', 'name', 'link-20');">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-comment"># If this is not a method, then return it as is.</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-42" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-42', 'type', 'link-32');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">attr</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">MethodType</tt><tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">attr</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-comment"># If it's a section method, then return it.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-43" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-43', 'name', 'link-20');">name</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'start_'</tt> <tt class="py-keyword">or</tt> <tt id="link-44" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-44', 'name', 'link-20');">name</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'end_'</tt><tt class="py-op">:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">attr</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-comment"># Otherwise, it's an info event, and return my method.</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_prev_attr</tt> <tt class="py-op">=</tt> <tt class="py-name">attr</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</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-45" class="py-name" targets="Method Bio.ParserSupport.SGMLStrippingConsumer._apply_clean_data()=Bio.ParserSupport.SGMLStrippingConsumer-class.html#_apply_clean_data"><a title="Bio.ParserSupport.SGMLStrippingConsumer._apply_clean_data" class="py-name" href="#" onclick="return doclink('link-45', '_apply_clean_data', 'link-45');">_apply_clean_data</a></tt> </tt>
</div></div><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"># onle use the Event Generator if XML handling is okay</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">if</tt> <tt id="link-46" class="py-name"><a title="Bio.AlignAce.AlignAceStandalone.xml_support
Bio.AlignAce.Parser.xml_support
Bio.Blast.NCBIStandalone.xml_support
Bio.Blast.NCBIWWW.xml_support
Bio.Compass.xml_support
Bio.Enzyme.xml_support
Bio.Gobase.xml_support
Bio.MEME.Parser.xml_support
Bio.Medline.xml_support
Bio.Ndb.xml_support
Bio.ParserSupport.xml_support
Bio.PopGen.FDist.xml_support
Bio.PopGen.GenePop.xml_support
Bio.Prosite.Prodoc.xml_support
Bio.Prosite.xml_support
Bio.Rebase.xml_support
Bio.Sequencing.Ace.xml_support
Bio.Sequencing.Phd.xml_support
Bio.SwissProt.KeyWList.xml_support
Bio.SwissProt.SProt.xml_support
Bio.UniGene.xml_support" class="py-name" href="#" onclick="return doclink('link-46', 'xml_support', 'link-2');">xml_support</a></tt><tt class="py-op">:</tt> </tt>
<a name="EventGenerator"></a><div id="EventGenerator-def"><a name="L154"></a><tt class="py-lineno">154</tt> <a class="py-toggle" href="#" id="EventGenerator-toggle" onclick="return toggle('EventGenerator');">-</a><tt class="py-line"> <tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.ParserSupport.EventGenerator-class.html">EventGenerator</a><tt class="py-op">(</tt><tt class="py-base-class">handler</tt><tt class="py-op">.</tt><tt class="py-base-class">ContentHandler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="EventGenerator-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EventGenerator-expanded"><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-docstring">"""Handler to generate events associated with a Martel parsed file.</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> This acts like a normal SAX handler, and accepts XML generated by</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> Martel during parsing. These events are then converted into</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> 'Biopython events', which can then be caught by a standard</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> biopython consumer</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="EventGenerator.__init__"></a><div id="EventGenerator.__init__-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="EventGenerator.__init__-toggle" onclick="return toggle('EventGenerator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.EventGenerator-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">consumer</tt><tt class="py-op">,</tt> <tt class="py-param">interest_tags</tt><tt class="py-op">,</tt> <tt class="py-param">callback_finalizer</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-param">exempt_tags</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>
</div><div id="EventGenerator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="EventGenerator.__init__-expanded"><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize to begin catching and firing off events.</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> o consumer - The consumer that we'll send Biopython events to.</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> o interest_tags - A listing of all the tags we are interested in.</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> o callback_finalizer - A function to deal with the collected</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> information before passing it on to the consumer. By default</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> the collected information is a list of all of the lines read</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> for a particular tag -- if there are multiple tags in a row</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"> like:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> <some_info>Spam<some_info></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> <some_info>More Spam<some_info></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> In this case the list of information would be:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> ['Spam', 'More Spam']</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> This list of lines will be passed to the callback finalizer if</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> it is present. Otherwise the consumer will be called with the</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> list of content information.</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> o exempt_tags - A listing of particular tags that are exempt from</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> being processed by the callback_finalizer. This allows you to</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> use a finalizer to deal with most tags, but leave those you don't</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> want touched.</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt class="py-name">consumer</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">=</tt> <tt class="py-name">interest_tags</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_finalizer</tt> <tt class="py-op">=</tt> <tt class="py-name">callback_finalizer</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_exempt_tags</tt> <tt class="py-op">=</tt> <tt class="py-name">exempt_tags</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-comment"># a dictionary of content for each tag of interest</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the information for each tag is held as a list of the lines.</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># This allows us to collect information from multiple tags</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in a row, and return it all at once.</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-47" class="py-name" targets="Variable Martel.Time.tag=Martel.Time-module.html#tag"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-47', 'tag', 'link-47');">tag</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">:</tt> </tt>
<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 class="py-name">info</tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-48', 'tag', 'link-47');">tag</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="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-comment"># the previous tag we were collecting information for.</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># We set a delay in sending info to the consumer so that we can</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># collect a bunch of tags in a row and append all of the info</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># together.</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_previous_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-comment"># the current character information for a tag</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_content</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-comment"># whether we should be collecting information</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_collect_characters</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="EventGenerator.startElement"></a><div id="EventGenerator.startElement-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="EventGenerator.startElement-toggle" onclick="return toggle('EventGenerator.startElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.EventGenerator-class.html#startElement">startElement</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-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="EventGenerator.startElement-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="EventGenerator.startElement-expanded"><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-docstring">"""Determine if we should collect characters from this tag.</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-49" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-49', 'name', 'link-20');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_collect_characters</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> </tt>
<a name="EventGenerator.characters"></a><div id="EventGenerator.characters-def"><a name="L223"></a><tt class="py-lineno">223</tt> <a class="py-toggle" href="#" id="EventGenerator.characters-toggle" onclick="return toggle('EventGenerator.characters');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.EventGenerator-class.html#characters">characters</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="EventGenerator.characters-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="EventGenerator.characters-expanded"><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-docstring">"""Extract the information if we are interested in it.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_collect_characters</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_content</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-50', 'append', 'link-50');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">content</tt><tt class="py-op">)</tt> </tt>
</div><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> </tt>
<a name="EventGenerator.endElement"></a><div id="EventGenerator.endElement-def"><a name="L229"></a><tt class="py-lineno">229</tt> <a class="py-toggle" href="#" id="EventGenerator.endElement-toggle" onclick="return toggle('EventGenerator.endElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.EventGenerator-class.html#endElement">endElement</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="EventGenerator.endElement-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="EventGenerator.endElement-expanded"><a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-docstring">"""Send the information to the consumer.</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-docstring"> Once we've got the end element we've collected up all of the</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-docstring"> character information we need, and we need to send this on to</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"> the consumer to do something with it.</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> We have a delay of one tag on doing this, so that we can collect</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> all of the info from multiple calls to the same element at once.</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-comment"># only deal with the tag if it is something we are</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># interested in and potentially have information for</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_collect_characters</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-comment"># add all of the information collected inside this tag</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">[</tt><tt id="link-51" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-51', 'name', 'link-20');">name</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-52', 'append', 'link-50');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_content</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-comment"># reset our information and flags</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cur_content</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_collect_characters</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-comment"># if we are at a new tag, pass on the info from the last tag</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_previous_tag</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_previous_tag</tt> <tt class="py-op">!=</tt> <tt id="link-53" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-53', 'name', 'link-20');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.ParserSupport.EventGenerator._make_callback()=Bio.ParserSupport.EventGenerator-class.html#_make_callback"><a title="Bio.ParserSupport.EventGenerator._make_callback" class="py-name" href="#" onclick="return doclink('link-54', '_make_callback', 'link-54');">_make_callback</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_previous_tag</tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-comment"># set this tag as the next to be passed</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_previous_tag</tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-55', 'name', 'link-20');">name</a></tt> </tt>
</div><a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> </tt>
<a name="EventGenerator._make_callback"></a><div id="EventGenerator._make_callback-def"><a name="L255"></a><tt class="py-lineno">255</tt> <a class="py-toggle" href="#" id="EventGenerator._make_callback-toggle" onclick="return toggle('EventGenerator._make_callback');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.EventGenerator-class.html#_make_callback">_make_callback</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="EventGenerator._make_callback-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="EventGenerator._make_callback-expanded"><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-docstring">"""Call the callback function with the info with the given name.</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-comment"># strip off whitespace and call the consumer</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">callback_function</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-name">_consumer</tt><tt class="py-op">,</tt> <tt id="link-56" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-56', 'name', 'link-20');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-comment"># --- pass back the information</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># if there is a finalizer, use that</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_finalizer</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt id="link-57" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-57', 'name', 'link-20');">name</a></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">_exempt_tags</tt><tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">info_to_pass</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_finalizer</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">[</tt><tt id="link-58" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-58', 'name', 'link-20');">name</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-comment"># otherwise pass back the entire list of information</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">info_to_pass</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">[</tt><tt id="link-59" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-59', 'name', 'link-20');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">callback_function</tt><tt class="py-op">(</tt><tt class="py-name">info_to_pass</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-comment"># reset the information for the tag</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-60', 'name', 'link-20');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="EventGenerator.endDocument"></a><div id="EventGenerator.endDocument-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="EventGenerator.endDocument-toggle" onclick="return toggle('EventGenerator.endDocument');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport.EventGenerator-class.html#endDocument">endDocument</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="EventGenerator.endDocument-collapsed" style="display:none;" pad="+++" indent="++++++++++++++++"></div><div id="EventGenerator.endDocument-expanded"><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-docstring">"""Make sure all of our information has been passed.</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"> This just flushes out any stored tags that need to be passed.</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</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">_previous_tag</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.ParserSupport.EventGenerator._make_callback" class="py-name" href="#" onclick="return doclink('link-61', '_make_callback', 'link-54');">_make_callback</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_previous_tag</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> </tt>
<a name="read_and_call"></a><div id="read_and_call-def"><a name="L282"></a><tt class="py-lineno">282</tt> <a class="py-toggle" href="#" id="read_and_call-toggle" onclick="return toggle('read_and_call');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#read_and_call">read_and_call</a><tt class="py-op">(</tt><tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read_and_call-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read_and_call-expanded"><a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-docstring">"""read_and_call(uhandle, method[, start][, end][, contains][, blank][, has_re])</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-docstring"> Read a line from uhandle, check it, and pass it to the method.</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-docstring"> Raises a ValueError if the line does not pass the checks.</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-docstring"> start, end, contains, blank, and has_re specify optional conditions</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-docstring"> that the line must pass. start and end specifies what the line must</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"> begin or end with (not counting EOL characters). contains</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-docstring"> specifies a substring that must be found in the line. If blank</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-docstring"> is a true value, then the line must be blank. has_re should be</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"> a regular expression object with a pattern that the line must match</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"> somewhere.</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name" targets="Function Bio.ParserSupport.safe_readline()=Bio.ParserSupport-module.html#safe_readline"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-62', 'safe_readline', 'link-62');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">errmsg</tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name" targets="Function Bio.ParserSupport._fails_conditions()=Bio.ParserSupport-module.html#_fails_conditions"><a title="Bio.ParserSupport._fails_conditions" class="py-name" href="#" onclick="return doclink('link-63', '_fails_conditions', 'link-63');">_fails_conditions</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">errmsg</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="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-name">errmsg</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">method</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> </tt>
<a name="read_and_call_while"></a><div id="read_and_call_while-def"><a name="L303"></a><tt class="py-lineno">303</tt> <a class="py-toggle" href="#" id="read_and_call_while-toggle" onclick="return toggle('read_and_call_while');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#read_and_call_while">read_and_call_while</a><tt class="py-op">(</tt><tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read_and_call_while-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read_and_call_while-expanded"><a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-docstring">"""read_and_call_while(uhandle, method[, start][, end][, contains][, blank][, has_re]) -> number of lines</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> Read a line from uhandle and pass it to the method as long as</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-docstring"> some condition is true. Returns the number of lines that were read.</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-docstring"> See the docstring for read_and_call for a description of the parameters.</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">nlines</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-64', 'safe_readline', 'link-62');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-comment"># If I've failed the condition, then stop reading the line.</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-65" class="py-name"><a title="Bio.ParserSupport._fails_conditions" class="py-name" href="#" onclick="return doclink('link-65', '_fails_conditions', 'link-63');">_fails_conditions</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Method Bio.File.UndoHandle.saveline()=Bio.File.UndoHandle-class.html#saveline"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-66', 'saveline', 'link-66');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">method</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">nlines</tt> <tt class="py-op">=</tt> <tt class="py-name">nlines</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">nlines</tt> </tt>
</div><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="read_and_call_until"></a><div id="read_and_call_until-def"><a name="L323"></a><tt class="py-lineno">323</tt> <a class="py-toggle" href="#" id="read_and_call_until-toggle" onclick="return toggle('read_and_call_until');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#read_and_call_until">read_and_call_until</a><tt class="py-op">(</tt><tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read_and_call_until-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read_and_call_until-expanded"><a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-docstring">"""read_and_call_until(uhandle, method, </tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> start=None, end=None, contains=None, blank=None) -> number of lines</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-docstring"> Read a line from uhandle and pass it to the method until</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-docstring"> some condition is true. Returns the number of lines that were read.</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-docstring"> See the docstring for read_and_call for a description of the parameters.</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-name">nlines</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-67', 'safe_readline', 'link-62');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-comment"># If I've met the condition, then stop reading the line.</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-68" class="py-name"><a title="Bio.ParserSupport._fails_conditions" class="py-name" href="#" onclick="return doclink('link-68', '_fails_conditions', 'link-63');">_fails_conditions</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-69', 'saveline', 'link-66');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">method</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-name">nlines</tt> <tt class="py-op">=</tt> <tt class="py-name">nlines</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">nlines</tt> </tt>
</div><a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> </tt>
<a name="attempt_read_and_call"></a><div id="attempt_read_and_call-def"><a name="L344"></a><tt class="py-lineno">344</tt> <a class="py-toggle" href="#" id="attempt_read_and_call-toggle" onclick="return toggle('attempt_read_and_call');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#attempt_read_and_call">attempt_read_and_call</a><tt class="py-op">(</tt><tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">method</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="attempt_read_and_call-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="attempt_read_and_call-expanded"><a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-docstring">"""attempt_read_and_call(uhandle, method, **keywds) -> boolean</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-docstring"> Similar to read_and_call, but returns a boolean specifying</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-docstring"> whether the line has passed the checks. Does not raise</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"> exceptions.</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-docstring"> See docs for read_and_call for a description of the function</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-docstring"> arguments.</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-70" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-70', 'safe_readline', 'link-62');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-name">passed</tt> <tt class="py-op">=</tt> <tt class="py-keyword">not</tt> <tt id="link-71" class="py-name"><a title="Bio.ParserSupport._fails_conditions" class="py-name" href="#" onclick="return doclink('link-71', '_fails_conditions', 'link-63');">_fails_conditions</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">passed</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">method</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-72', 'saveline', 'link-66');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">passed</tt> </tt>
</div><a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> </tt>
<a name="_fails_conditions"></a><div id="_fails_conditions-def"><a name="L363"></a><tt class="py-lineno">363</tt> <a class="py-toggle" href="#" id="_fails_conditions-toggle" onclick="return toggle('_fails_conditions');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#_fails_conditions">_fails_conditions</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">contains</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">blank</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-param">has_re</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="_fails_conditions-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_fails_conditions-expanded"><a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-73" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-73', 'start', 'link-73');">start</a></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="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-74', 'start', 'link-73');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-75" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-75', 'start', 'link-73');">start</a></tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Line does not start with '%s':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-76', 'start', 'link-73');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-77" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-77', 'end', 'link-77');">end</a></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="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-78', 'end', 'link-77');">end</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-79" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-79', 'end', 'link-77');">end</a></tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Line does not end with '%s':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-80', 'end', 'link-77');">end</a></tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-81" class="py-name" targets="Method Bio.Alphabet.Alphabet.contains()=Bio.Alphabet.Alphabet-class.html#contains,Method Bio.Alphabet.AlphabetEncoder.contains()=Bio.Alphabet.AlphabetEncoder-class.html#contains,Method Bio.Alphabet.Gapped.contains()=Bio.Alphabet.Gapped-class.html#contains,Method Bio.Alphabet.HasStopCodon.contains()=Bio.Alphabet.HasStopCodon-class.html#contains,Method Bio.Pathway.Rep.HashSet.HashSet.contains()=Bio.Pathway.Rep.HashSet.HashSet-class.html#contains,Method Bio.biblio.Biblio.contains()=Bio.biblio.Biblio-class.html#contains"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-81', 'contains', 'link-81');">contains</a></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="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-82', 'find', 'link-82');">find</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-83', 'contains', 'link-81');">contains</a></tt><tt class="py-op">)</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="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Line does not contain '%s':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-84" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-84', 'contains', 'link-81');">contains</a></tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-85" class="py-name" targets="Variable Bio.MetaTool.metatool_format.blank=Bio.MetaTool.metatool_format-module.html#blank"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-85', 'blank', 'link-85');">blank</a></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="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-86" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-86', 'blank', 'link-85');">blank</a></tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-87" class="py-name" targets="Function Bio.ParserSupport.is_blank_line()=Bio.ParserSupport-module.html#is_blank_line"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-87', 'is_blank_line', 'link-87');">is_blank_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Expected blank line, but got:\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-88" class="py-name"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-88', 'is_blank_line', 'link-87');">is_blank_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Expected non-blank line, but got a blank one"</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">has_re</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="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">has_re</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-89', 'search', 'link-89');">search</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Line does not match regex '%s':\n%s"</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">has_re</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name" targets="Method Bio.Prosite._RecordConsumer.pattern()=Bio.Prosite._RecordConsumer-class.html#pattern"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-90', 'pattern', 'link-90');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-name">line</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">None</tt> </tt>
</div><a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="is_blank_line"></a><div id="is_blank_line-def"><a name="L387"></a><tt class="py-lineno">387</tt> <a class="py-toggle" href="#" id="is_blank_line-toggle" onclick="return toggle('is_blank_line');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#is_blank_line">is_blank_line</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">,</tt> <tt class="py-param">allow_spaces</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="is_blank_line-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="is_blank_line-expanded"><a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-docstring">"""is_blank_line(line, allow_spaces=0) -> boolean</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-docstring"> Return whether a line is blank. allow_spaces specifies whether to</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-docstring"> allow whitespaces in a blank line. A true value signifies that a</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-docstring"> line containing whitespaces as well as end-of-line characters</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"> should be considered blank.</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">allow_spaces</tt><tt class="py-op">:</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</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-string">'\n'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">line</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-string">'\r'</tt> </tt>
</div><a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> </tt>
<a name="safe_readline"></a><div id="safe_readline-def"><a name="L402"></a><tt class="py-lineno">402</tt> <a class="py-toggle" href="#" id="safe_readline-toggle" onclick="return toggle('safe_readline');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#safe_readline">safe_readline</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="safe_readline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="safe_readline-expanded"><a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-docstring">"""safe_readline(handle) -> line</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"> Read a line from an UndoHandle and return it. If there are no more</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-docstring"> lines to read, I will raise a ValueError.</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-91" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-91', 'handle', 'link-12');">handle</a></tt><tt class="py-op">.</tt><tt id="link-92" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-92', 'readline', 'link-92');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unexpected end of stream."</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> </tt>
<a name="safe_peekline"></a><div id="safe_peekline-def"><a name="L414"></a><tt class="py-lineno">414</tt> <a class="py-toggle" href="#" id="safe_peekline-toggle" onclick="return toggle('safe_peekline');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.ParserSupport-module.html#safe_peekline">safe_peekline</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="safe_peekline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="safe_peekline-expanded"><a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-docstring">"""safe_peekline(handle) -> line</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-docstring"> Peek at the next line in an UndoHandle and return it. If there are no</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-docstring"> more lines to peek, I will raise a ValueError.</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-93" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-93', 'handle', 'link-12');">handle</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method Bio.File.UndoHandle.peekline()=Bio.File.UndoHandle-class.html#peekline"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-94', 'peekline', 'link-94');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unexpected end of stream."</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> </tt><script type="text/javascript">
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