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<a href="Martel-module.html">Package Martel</a> ::
Module IterParser
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<h1 class="epydoc">Source Code for <a href="Martel.IterParser-module.html">Module Martel.IterParser</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 2000-2001, Dalke Scientific Software, LLC</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"># Distributed under the Biopython License Agreement (see the LICENSE file).</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">"""Implement Martel parsers.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">The classes in this module are used by other Martel modules and not</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">typically by external users.</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">There are two major parsers, 'Parser' and 'RecordParser.' The first</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">is the standard one, which parses the file as one string in memory</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">then generates the SAX events. The other reads a record at a time</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">using a RecordReader and generates events after each read. The</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">generated event callbacks are identical.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">At some level, both parsers use "_do_callback" to convert mxTextTools</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">tags into SAX events.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">XXX finish this documentation</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">XXX need a better way to get closer to the likely error position when</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">parsing.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">XXX need to implement Locator</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"></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-keyword">from</tt> <tt class="py-name">__future__</tt> <tt class="py-keyword">import</tt> <tt class="py-name">generators</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">urllib</tt><tt class="py-op">,</tt> <tt class="py-name">traceback</tt><tt class="py-op">,</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">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 class="py-op">,</tt> <tt class="py-name">saxutils</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.AlignAce.Parser=Bio.AlignAce.Parser-module.html,Module Bio.Entrez.Parser=Bio.Entrez.Parser-module.html,Module Bio.MEME.Parser=Bio.MEME.Parser-module.html,Class Bio.SCOP.Cla.Parser=Bio.SCOP.Cla.Parser-class.html,Class Bio.SCOP.Des.Parser=Bio.SCOP.Des.Parser-class.html,Class Bio.SCOP.Dom.Parser=Bio.SCOP.Dom.Parser-class.html,Class Bio.SCOP.Hie.Parser=Bio.SCOP.Hie.Parser-class.html,Class Bio.SCOP.Raf.Parser=Bio.SCOP.Raf.Parser-class.html,Module Martel.Parser=Martel.Parser-module.html,Class Martel.Parser.Parser=Martel.Parser.Parser-class.html"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-0', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-1', 'RecordReader', 'link-1');">RecordReader</a></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</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="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="IterRecords"></a><div id="IterRecords-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="IterRecords-toggle" onclick="return toggle('IterRecords');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.IterParser.IterRecords-class.html">IterRecords</a><tt class="py-op">:</tt> </tt>
</div><div id="IterRecords-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IterRecords-expanded"><a name="IterRecords.__init__"></a><div id="IterRecords.__init__-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="IterRecords.__init__-toggle" onclick="return toggle('IterRecords.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterRecords-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">record_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_reader</tt><tt class="py-op">,</tt> <tt class="py-param">reader_args</tt><tt class="py-op">,</tt> <tt class="py-param">marker_tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IterRecords.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterRecords.__init__-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">record_parser</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_reader</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reader_args</tt> <tt class="py-op">=</tt> <tt class="py-name">reader_args</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">marker_tag</tt> </tt>
</div><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="IterRecords.copy"></a><div id="IterRecords.copy-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="IterRecords.copy-toggle" onclick="return toggle('IterRecords.copy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterRecords-class.html#copy">copy</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="IterRecords.copy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterRecords.copy-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-2" class="py-name" targets="Class Martel.IterParser.IterRecords=Martel.IterParser.IterRecords-class.html"><a title="Martel.IterParser.IterRecords" class="py-name" href="#" onclick="return doclink('link-2', 'IterRecords', 'link-2');">IterRecords</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-3', 'copy', 'link-3');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_reader</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reader_args</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt><tt class="py-op">)</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="IterRecords.iterate"></a><div id="IterRecords.iterate-def"><a name="L51"></a><tt class="py-lineno"> 51</tt> <a class="py-toggle" href="#" id="IterRecords.iterate-toggle" onclick="return toggle('IterRecords.iterate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterRecords-class.html#iterate">iterate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</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="IterRecords.iterate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterRecords.iterate-expanded"><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-4', 'source', 'link-4');">source</a></tt> <tt class="py-op">=</tt> <tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Function Bio.EUtils.ReseekFile.prepare_input_source()=Bio.EUtils.ReseekFile-module.html#prepare_input_source"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-5', 'prepare_input_source', 'link-5');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-6', 'source', 'link-4');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-7', 'source', 'link-4');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-8" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-8', 'source', 'link-4');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</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-9" class="py-name" targets="Method Martel.IterParser.IterHeaderFooter.iterateFile()=Martel.IterParser.IterHeaderFooter-class.html#iterateFile,Method Martel.IterParser.IterRecords.iterateFile()=Martel.IterParser.IterRecords-class.html#iterateFile,Method Martel.Iterator.Iterator.iterateFile()=Martel.Iterator.Iterator-class.html#iterateFile,Method Martel.Iterator.IteratorHeaderFooter.iterateFile()=Martel.Iterator.IteratorHeaderFooter-class.html#iterateFile,Method Martel.Iterator.IteratorRecords.iterateFile()=Martel.Iterator.IteratorRecords-class.html#iterateFile"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-9', 'iterateFile', 'link-9');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
<a name="IterRecords.iterateString"></a><div id="IterRecords.iterateString-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="IterRecords.iterateString-toggle" onclick="return toggle('IterRecords.iterateString');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterRecords-class.html#iterateString">iterateString</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</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="IterRecords.iterateString-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterRecords.iterateString-expanded"><a name="L57"></a><tt class="py-lineno"> 57</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-10" class="py-name"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-10', 'iterateFile', 'link-9');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-11" 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-11', 's', 'link-11');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="IterRecords.iterateFile"></a><div id="IterRecords.iterateFile-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="IterRecords.iterateFile-toggle" onclick="return toggle('IterRecords.iterateFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterRecords-class.html#iterateFile">iterateFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fileobj</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</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="IterRecords.iterateFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterRecords.iterateFile-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cont_handler</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Module Martel.LAX=Martel.LAX-module.html,Class Martel.LAX.LAX=Martel.LAX.LAX-class.html"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-12', 'LAX', 'link-12');">LAX</a></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">cont_handler</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-13', 'LAX', 'link-12');">LAX</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-14', 'LAX', 'link-12');">LAX</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_reader</tt><tt class="py-op">(</tt><tt class="py-name">fileobj</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">reader_args</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</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="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-15', 'next', 'link-15');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-16" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-16', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Class Martel.RecordReader.ReaderError=Martel.RecordReader.ReaderError-class.html"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-17', 'ReaderError', 'link-17');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-18" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-18', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Class Martel.Parser.ParserPositionException=Martel.Parser.ParserPositionException-class.html"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-19', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Martel.Parser.HeaderFooterParser.parseString()=Martel.Parser.HeaderFooterParser-class.html#parseString,Method Martel.Parser.Parser.parseString()=Martel.Parser.Parser-class.html#parseString,Method Martel.Parser.RecordParser.parseString()=Martel.Parser.RecordParser-class.html#parseString"><a title="Martel.Parser.HeaderFooterParser.parseString
Martel.Parser.Parser.parseString
Martel.Parser.RecordParser.parseString" class="py-name" href="#" onclick="return doclink('link-20', 'parseString', 'link-20');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-21" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-21', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-22', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">,</tt> <tt class="py-name">exc</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">cont_handler</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Variable Bio.Affy.CelFile.remainder=Bio.Affy.CelFile-module.html#remainder,Variable Bio.LogisticRegression.remainder=Bio.LogisticRegression-module.html#remainder,Variable Bio.MarkovModel.remainder=Bio.MarkovModel-module.html#remainder,Variable Bio.MaxEntropy.remainder=Bio.MaxEntropy-module.html#remainder,Variable Bio.NaiveBayes.remainder=Bio.NaiveBayes-module.html#remainder,Variable Bio.Statistics.lowess.remainder=Bio.Statistics.lowess-module.html#remainder,Variable Bio.distance.remainder=Bio.distance-module.html#remainder,Variable Bio.kNN.remainder=Bio.kNN-module.html#remainder,Method Martel.RecordReader.CountLines.remainder()=Martel.RecordReader.CountLines-class.html#remainder,Method Martel.RecordReader.EndsWith.remainder()=Martel.RecordReader.EndsWith-class.html#remainder,Method Martel.RecordReader.Everything.remainder()=Martel.RecordReader.Everything-class.html#remainder,Method Martel.RecordReader.Nothing.remainder()=Martel.RecordReader.Nothing-class.html#remainder,Method Martel.RecordReader.RecordReader.remainder()=Martel.RecordReader.RecordReader-class.html#remainder,Method Martel.RecordReader.StartsWith.remainder()=Martel.RecordReader.StartsWith-class.html#remainder,Method Martel.RecordReader.Until.remainder()=Martel.RecordReader.Until-class.html#remainder"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-23', 'remainder', 'link-23');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lookahead</tt> <tt class="py-keyword">or</tt> <tt class="py-name">fileobj</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-24', 'read', 'link-24');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-25" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-25', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-26', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="IterHeaderFooter"></a><div id="IterHeaderFooter-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="IterHeaderFooter-toggle" onclick="return toggle('IterHeaderFooter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.IterParser.IterHeaderFooter-class.html">IterHeaderFooter</a><tt class="py-op">:</tt> </tt>
</div><div id="IterHeaderFooter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IterHeaderFooter-expanded"><a name="IterHeaderFooter.__init__"></a><div id="IterHeaderFooter.__init__-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="IterHeaderFooter.__init__-toggle" onclick="return toggle('IterHeaderFooter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterHeaderFooter-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-param">header_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_header_reader</tt><tt class="py-op">,</tt> <tt class="py-param">header_args</tt><tt class="py-op">,</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-param">record_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_record_reader</tt><tt class="py-op">,</tt> <tt class="py-param">record_args</tt><tt class="py-op">,</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-param">footer_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_footer_reader</tt><tt class="py-op">,</tt> <tt class="py-param">footer_args</tt><tt class="py-op">,</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-param">marker_tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IterHeaderFooter.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterHeaderFooter.__init__-expanded"><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">header_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">header_parser</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">make_header_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_header_reader</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_args</tt> <tt class="py-op">=</tt> <tt class="py-name">header_args</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">record_parser</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_record_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_record_reader</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_args</tt> <tt class="py-op">=</tt> <tt class="py-name">record_args</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">footer_parser</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_footer_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_footer_reader</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_args</tt> <tt class="py-op">=</tt> <tt class="py-name">footer_args</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">marker_tag</tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="IterHeaderFooter.copy"></a><div id="IterHeaderFooter.copy-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="IterHeaderFooter.copy-toggle" onclick="return toggle('IterHeaderFooter.copy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterHeaderFooter-class.html#copy">copy</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="IterHeaderFooter.copy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterHeaderFooter.copy-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">header_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_parser</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">header_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">header_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">header_parser</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-27', 'copy', 'link-3');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">record_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-28', 'copy', 'link-3');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">footer_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">footer_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">footer_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">footer_parser</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-29', 'copy', 'link-3');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-30" class="py-name" targets="Class Martel.IterParser.IterHeaderFooter=Martel.IterParser.IterHeaderFooter-class.html"><a title="Martel.IterParser.IterHeaderFooter" class="py-name" href="#" onclick="return doclink('link-30', 'IterHeaderFooter', 'link-30');">IterHeaderFooter</a></tt><tt class="py-op">(</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">header_parser</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_header_reader</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_args</tt><tt class="py-op">,</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">record_parser</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_record_reader</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_args</tt><tt class="py-op">,</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">footer_parser</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_footer_reader</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_args</tt><tt class="py-op">,</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt><tt class="py-op">)</tt> </tt>
</div><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
<a name="IterHeaderFooter.iterate"></a><div id="IterHeaderFooter.iterate-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="IterHeaderFooter.iterate-toggle" onclick="return toggle('IterHeaderFooter.iterate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterHeaderFooter-class.html#iterate">iterate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</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="IterHeaderFooter.iterate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterHeaderFooter.iterate-expanded"><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-docstring">"""parse using the URL or file handle"""</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-31', 'source', 'link-4');">source</a></tt> <tt class="py-op">=</tt> <tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-32', 'prepare_input_source', 'link-5');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-33', 'source', 'link-4');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-34', 'source', 'link-4');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-35" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-35', 'source', 'link-4');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</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-36" class="py-name"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-36', 'iterateFile', 'link-9');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="IterHeaderFooter.iterateString"></a><div id="IterHeaderFooter.iterateString-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="IterHeaderFooter.iterateString-toggle" onclick="return toggle('IterHeaderFooter.iterateString');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterHeaderFooter-class.html#iterateString">iterateString</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</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="IterHeaderFooter.iterateString-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterHeaderFooter.iterateString-expanded"><a name="L131"></a><tt class="py-lineno">131</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-37" class="py-name"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-37', 'iterateFile', 'link-9');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-38', 's', 'link-11');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="IterHeaderFooter.iterateFile"></a><div id="IterHeaderFooter.iterateFile-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="IterHeaderFooter.iterateFile-toggle" onclick="return toggle('IterHeaderFooter.iterateFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.IterParser.IterHeaderFooter-class.html#iterateFile">iterateFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fileobj</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</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="IterHeaderFooter.iterateFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IterHeaderFooter.iterateFile-expanded"><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cont_handler</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-39" class="py-name"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-39', 'LAX', 'link-12');">LAX</a></tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">cont_handler</tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-40', 'LAX', 'link-12');">LAX</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-41', 'LAX', 'link-12');">LAX</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment"># By construction, we never need events from the header</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># nor from the footer</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</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">header_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_header_reader</tt><tt class="py-op">(</tt><tt class="py-name">fileobj</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">header_args</tt><tt class="py-op">,</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-op">{</tt><tt class="py-string">"lookahead"</tt><tt class="py-op">:</tt> <tt class="py-name">lookahead</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-42', 'next', 'link-15');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-43" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-43', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-44', 'ReaderError', 'link-17');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-45" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-45', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-46', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_parser</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Martel.Parser.HeaderFooterParser.parseString
Martel.Parser.Parser.parseString
Martel.Parser.RecordParser.parseString" class="py-name" href="#" onclick="return doclink('link-47', 'parseString', 'link-20');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-48', 'remainder', 'link-23');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_record_reader</tt><tt class="py-op">(</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_args</tt><tt class="py-op">,</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-op">{</tt><tt class="py-string">"lookahead"</tt><tt class="py-op">:</tt> <tt class="py-name">lookahead</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt><tt class="py-op">:</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</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="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-49', 'next', 'link-15');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-50" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-50', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-51', 'ReaderError', 'link-17');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-52" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-52', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-53', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Martel.Parser.HeaderFooterParser.parseString
Martel.Parser.Parser.parseString
Martel.Parser.RecordParser.parseString" class="py-name" href="#" onclick="return doclink('link-54', 'parseString', 'link-20');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-55" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-55', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-56', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">,</tt> <tt class="py-name">exc</tt><tt class="py-op">:</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">cont_handler</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-comment"># This one is tedious</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-57', 'next', 'link-15');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-58" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-58', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-59', 'ReaderError', 'link-17');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-comment"># we may have stumbled into the footer</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-60', 'remainder', 'link-23');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rec</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment"># maybe there's a footer left</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-61', 'remainder', 'link-23');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Martel.Parser.HeaderFooterParser.parseString
Martel.Parser.Parser.parseString
Martel.Parser.RecordParser.parseString" class="py-name" href="#" onclick="return doclink('link-62', 'parseString', 'link-20');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-63" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-63', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Class Martel.Parser.ParserException=Martel.Parser.ParserException-class.html"><a title="Martel.Parser.ParserException" class="py-name" href="#" onclick="return doclink('link-64', 'ParserException', 'link-64');">ParserException</a></tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-comment"># we may have tried to parse the footer</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-65', 'remainder', 'link-23');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">rec</tt> <tt class="py-op">+</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">cont_handler</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-comment"># Try to read the footer</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_footer_reader</tt><tt class="py-op">(</tt><tt class="py-name">fileobj</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">footer_args</tt><tt class="py-op">,</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-op">{</tt><tt class="py-string">"lookahead"</tt><tt class="py-op">:</tt> <tt class="py-name">lookahead</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-66', 'next', 'link-15');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-67" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-67', 'RecordReader', 'link-1');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-68', 'ReaderError', 'link-17');">ReaderError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-69" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-69', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-70', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-comment"># Could read any footer</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt id="link-71" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-71', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-72', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Martel.Parser.HeaderFooterParser.parseString
Martel.Parser.Parser.parseString
Martel.Parser.RecordParser.parseString" class="py-name" href="#" onclick="return doclink('link-73', 'parseString', 'link-20');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-74" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-74', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-75', 'ParserPositionException', 'link-19');">ParserPositionException</a></tt><tt class="py-op">,</tt> <tt class="py-name">exc</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-76', 'remainder', 'link-23');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lookahead</tt> <tt class="py-keyword">or</tt> <tt class="py-name">fileobj</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-77', 'read', 'link-24');">read</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-78" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-78', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-79" class="py-name" targets="Class Martel.Parser.ParserIncompleteException=Martel.Parser.ParserIncompleteException-class.html"><a title="Martel.Parser.ParserIncompleteException" class="py-name" href="#" onclick="return doclink('link-79', 'ParserIncompleteException', 'link-79');">ParserIncompleteException</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt><script type="text/javascript">
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