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        <a href="Martel-module.html">Package&nbsp;Martel</a> ::
        <a href="Martel.test-module.html">Package&nbsp;test</a> ::
        Module&nbsp;test_Parser
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<h1 class="epydoc">Source Code for <a href="Martel.test.test_Parser-module.html">Module Martel.test.test_Parser</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">,</tt> <tt id="link-3" 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-3', 'Parser', 'link-3');">Parser</a></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"> </tt>
<a name="L4"></a><tt class="py-lineno">  4</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="L5"></a><tt class="py-lineno">  5</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="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"># NOTE: Do not write formats like this, eg, with "(.|\n)*".  Those</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># depend on the implementation using a RecordReader-like interface.</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Instead, you need to write them so they could be used even as one</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># huge regexp.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="test_reader_parser"></a><div id="test_reader_parser-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="test_reader_parser-toggle" onclick="return toggle('test_reader_parser');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_reader_parser">test_reader_parser</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_reader_parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_reader_parser-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line">    <tt id="link-4" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-4', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-5', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Class Martel.Expression.Group=Martel.Expression.Group-class.html,Function Martel.Group()=Martel-module.html#Group"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-6', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"start"</tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-7', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Package Bio.Pathway.Rep=Bio.Pathway.Rep-module.html,Function Martel.Rep()=Martel-module.html#Rep"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-8', 'Rep', 'link-8');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-9', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-10', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"abc"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line">             <tt id="link-11" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-11', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-12', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-13', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-14', 'Rep', 'link-8');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-15', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-16', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"xyz"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-17', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_parser()=Bio.config.FormatRegistry.FormatObject-class.html#make_parser,Method Bio.config._support.make_cached_expression.make_parser()=Bio.config._support.make_cached_expression-class.html#make_parser,Method Martel.Expression.Expression.make_parser()=Martel.Expression.Expression-class.html#make_parser,Method Martel.Expression.HeaderFooter.make_parser()=Martel.Expression.HeaderFooter-class.html#make_parser,Method Martel.Expression.ParseRecords.make_parser()=Martel.Expression.ParseRecords-class.html#make_parser"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-18', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-19" 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-19', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'parseString', 'link-21');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-string">"abc"</tt> <tt class="py-op">*</tt> <tt class="py-number">10</tt> <tt class="py-op">+</tt> <tt class="py-string">"xyz"</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">        <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-22" 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-22', 'parseString', 'link-21');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-string">"abc"</tt> <tt class="py-op">*</tt> <tt class="py-number">10</tt> <tt class="py-op">+</tt> <tt class="py-string">"xyzQ"</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt id="link-23" 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-23', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-24" 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-24', 'ParserPositionException', 'link-24');">ParserPositionException</a></tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"didn't get a position exception"</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">        <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'parseString', 'link-21');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-string">"abc"</tt> <tt class="py-op">*</tt> <tt class="py-number">10</tt> <tt class="py-op">+</tt> <tt class="py-string">"x"</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt id="link-26" 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-26', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-27', 'ParserPositionException', 'link-24');">ParserPositionException</a></tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"didn't get a position exception"</tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"> </tt>
<a name="CountErrors"></a><div id="CountErrors-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="CountErrors-toggle" onclick="return toggle('CountErrors');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.test.test_Parser.CountErrors-class.html">CountErrors</a><tt class="py-op">(</tt><tt class="py-base-class">handler</tt><tt class="py-op">.</tt><tt class="py-base-class">ErrorHandler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountErrors-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CountErrors-expanded"><a name="CountErrors.__init__"></a><div id="CountErrors.__init__-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="CountErrors.__init__-toggle" onclick="return toggle('CountErrors.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser.CountErrors-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountErrors.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountErrors.__init__-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="CountErrors.error"></a><div id="CountErrors.error-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="CountErrors.error-toggle" onclick="return toggle('CountErrors.error');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser.CountErrors-class.html#error">error</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountErrors.error-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountErrors.error-expanded"><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">error_count</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
</div><a name="CountErrors.fatalError"></a><div id="CountErrors.fatalError-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="CountErrors.fatalError-toggle" onclick="return toggle('CountErrors.fatalError');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser.CountErrors-class.html#fatalError">fatalError</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountErrors.fatalError-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountErrors.fatalError-expanded"><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">fatal_error_count</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
</div></div><a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"> </tt>
<a name="CountRecords"></a><div id="CountRecords-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="CountRecords-toggle" onclick="return toggle('CountRecords');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.test.test_Parser.CountRecords-class.html">CountRecords</a><tt class="py-op">(</tt><tt class="py-base-class">handler</tt><tt class="py-op">.</tt><tt class="py-base-class">ContentHandler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountRecords-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CountRecords-expanded"><a name="CountRecords.__init__"></a><div id="CountRecords.__init__-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="CountRecords.__init__-toggle" onclick="return toggle('CountRecords.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser.CountRecords-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">tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountRecords.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountRecords.__init__-expanded"><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 id="link-28" class="py-name" targets="Variable Martel.Time.tag=Martel.Time-module.html#tag"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-28', 'tag', 'link-28');">tag</a></tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-29', 'tag', 'link-28');">tag</a></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 id="link-30" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-30', 'count', 'link-30');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="CountRecords.startElement"></a><div id="CountRecords.startElement-def"><a name="L49"></a><tt class="py-lineno"> 49</tt> <a class="py-toggle" href="#" id="CountRecords.startElement-toggle" onclick="return toggle('CountRecords.startElement');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser.CountRecords-class.html#startElement">startElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountRecords.startElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountRecords.startElement-expanded"><a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-31" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-31', 'tag', 'link-28');">tag</a></tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-32', 'tag', 'link-28');">tag</a></tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-33', 'count', 'link-30');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-34', 'count', 'link-30');">count</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
</div></div><a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">         </tt>
<a name="test_record_parser"></a><div id="test_record_parser-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="test_record_parser-toggle" onclick="return toggle('test_record_parser');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_record_parser">test_record_parser</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_record_parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_record_parser-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt id="link-35" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-35', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-36', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-37', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-38', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-39', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"X\n"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-40" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-40', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Function Martel.Re()=Martel-module.html#Re"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-41', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"a*\n"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-42', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-43', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-44" 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-44', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Class Bio.CDD.RecordParser=Bio.CDD.RecordParser-class.html,Class Bio.Compass.RecordParser=Bio.Compass.RecordParser-class.html,Class Bio.ECell.RecordParser=Bio.ECell.RecordParser-class.html,Class Bio.Enzyme.RecordParser=Bio.Enzyme.RecordParser-class.html,Class Bio.Fasta.RecordParser=Bio.Fasta.RecordParser-class.html,Class Bio.GenBank.RecordParser=Bio.GenBank.RecordParser-class.html,Class Bio.Gobase.RecordParser=Bio.Gobase.RecordParser-class.html,Class Bio.IntelliGenetics.RecordParser=Bio.IntelliGenetics.RecordParser-class.html,Class Bio.LocusLink.RecordParser=Bio.LocusLink.RecordParser-class.html,Class Bio.Medline.RecordParser=Bio.Medline.RecordParser-class.html,Class Bio.MetaTool.RecordParser=Bio.MetaTool.RecordParser-class.html,Class Bio.NBRF.RecordParser=Bio.NBRF.RecordParser-class.html,Class Bio.PopGen.FDist.RecordParser=Bio.PopGen.FDist.RecordParser-class.html,Class Bio.PopGen.GenePop.RecordParser=Bio.PopGen.GenePop.RecordParser-class.html,Class Bio.Prosite.Prodoc.RecordParser=Bio.Prosite.Prodoc.RecordParser-class.html,Class Bio.Prosite.RecordParser=Bio.Prosite.RecordParser-class.html,Class Bio.Rebase.RecordParser=Bio.Rebase.RecordParser-class.html,Class Bio.Saf.RecordParser=Bio.Saf.RecordParser-class.html,Class Bio.Sequencing.Ace.RecordParser=Bio.Sequencing.Ace.RecordParser-class.html,Class Bio.Sequencing.Phd.RecordParser=Bio.Sequencing.Phd.RecordParser-class.html,Class Bio.SwissProt.SProt.RecordParser=Bio.SwissProt.SProt.RecordParser-class.html,Class Bio.UniGene.RecordParser=Bio.UniGene.RecordParser-class.html,Class Martel.Parser.RecordParser=Martel.Parser.RecordParser-class.html"><a title="Bio.CDD.RecordParser
Bio.Compass.RecordParser
Bio.ECell.RecordParser
Bio.Enzyme.RecordParser
Bio.Fasta.RecordParser
Bio.GenBank.RecordParser
Bio.Gobase.RecordParser
Bio.IntelliGenetics.RecordParser
Bio.LocusLink.RecordParser
Bio.Medline.RecordParser
Bio.MetaTool.RecordParser
Bio.NBRF.RecordParser
Bio.PopGen.FDist.RecordParser
Bio.PopGen.GenePop.RecordParser
Bio.Prosite.Prodoc.RecordParser
Bio.Prosite.RecordParser
Bio.Rebase.RecordParser
Bio.Saf.RecordParser
Bio.Sequencing.Ace.RecordParser
Bio.Sequencing.Phd.RecordParser
Bio.SwissProt.SProt.RecordParser
Bio.UniGene.RecordParser
Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-45', 'RecordParser', 'link-45');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-string">"blah"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">                                 <tt id="link-46" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-46', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Class Martel.RecordReader.StartsWith=Martel.RecordReader.StartsWith-class.html"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-47', 'StartsWith', 'link-47');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"X"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name" targets="Class Martel.test.test_Parser.CountErrors=Martel.test.test_Parser.CountErrors-class.html"><a title="Martel.test.test_Parser.CountErrors" class="py-name" href="#" onclick="return doclink('link-48', 'CountErrors', 'link-48');">CountErrors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt id="link-49" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-49', 'count', 'link-30');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name" targets="Class Martel.test.test_Parser.CountRecords=Martel.test.test_Parser.CountRecords-class.html"><a title="Martel.test.test_Parser.CountRecords" class="py-name" href="#" onclick="return doclink('link-50', 'CountRecords', 'link-50');">CountRecords</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-51', 'count', 'link-30');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">     </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-52" 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-52', 'parseString', 'link-21');">parseString</a></tt><tt class="py-op">(</tt><tt class="py-string">"X\na\nX\nb\nX\naaa\nX\naaaa\nX\nq\nX\na\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">     </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-53" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-53', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-54', 'count', 'link-30');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">4</tt><tt class="py-op">,</tt> <tt id="link-55" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-55', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-56', 'count', 'link-30');">count</a></tt> </tt>
</div><a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"> </tt>
<a name="test_header_footer1"></a><div id="test_header_footer1-def"><a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="test_header_footer1-toggle" onclick="return toggle('test_header_footer1');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer1">test_header_footer1</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer1-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer1-expanded"><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">    <tt id="link-57" 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-57', 's', 'link-57');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-string">header</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-string">XX</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-string">record 1</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-string">record 2</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-string">record 3</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-string">footer</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-name">gold</tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-string">&lt;?xml version="1.0" encoding="iso-8859-1"?&gt;</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-string">&lt;hf&gt;&lt;header&gt;header</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"><tt class="py-string">XX</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-string">&lt;/header&gt;&lt;record&gt;record 1</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;record&gt;record 2</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;record&gt;record 3</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;footer&gt;footer</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-string">&lt;/footer&gt;&lt;/hf&gt;"""</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">     </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">     </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-comment"># Don't use regexps like these in your code - for testing only!</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-58" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-58', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-59', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-60', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"header"</tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-61', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-62', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"header(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">    <tt id="link-63" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-63', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-64', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-65', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-66" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-66', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-67', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"rec(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-68', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-69', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"footer"</tt><tt class="py-op">,</tt> <tt id="link-70" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-70', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-71', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"footer(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">    <tt id="link-72" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-72', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-73', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-74', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">    <tt id="link-75" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-75', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-76', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-77', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-78', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</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">hf</tt> <tt class="py-op">=</tt> <tt id="link-79" 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-79', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Class Martel.Parser.HeaderFooterParser=Martel.Parser.HeaderFooterParser-class.html"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-80', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt id="link-81" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-81', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name" targets="Class Martel.RecordReader.EndsWith=Martel.RecordReader.EndsWith-class.html"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-82', 'EndsWith', 'link-82');">EndsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"XX\n"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-83', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt id="link-84" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-84', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-85', 'EndsWith', 'link-82');">EndsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"//\n"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-86" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-86', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">        <tt id="link-87" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-87', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-88', 'StartsWith', 'link-47');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"f"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt class="py-name">XMLGenerator</tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.parseFile()=Bio.EUtils.POM.POMDocument-class.html#parseFile,Method Martel.Parser.HeaderFooterParser.parseFile()=Martel.Parser.HeaderFooterParser-class.html#parseFile,Method Martel.Parser.Parser.parseFile()=Martel.Parser.Parser-class.html#parseFile,Method Martel.Parser.RecordParser.parseFile()=Martel.Parser.RecordParser-class.html#parseFile"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-89', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-90', 's', 'link-57');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">    <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">result</tt> <tt class="py-op">==</tt> <tt class="py-name">gold</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">result</tt><tt class="py-op">,</tt> <tt class="py-name">gold</tt><tt class="py-op">)</tt> </tt>
</div><a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"> </tt>
<a name="test_header_footer2"></a><div id="test_header_footer2-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="test_header_footer2-toggle" onclick="return toggle('test_header_footer2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer2">test_header_footer2</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer2-expanded"><a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">    <tt class="py-comment"># Have a header but no footer</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-91" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-91', 's', 'link-57');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-string">This is some misc. header text</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-string">that goes on until the end.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"><tt class="py-string">ID 1</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"><tt class="py-string">ID 2</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">    <tt class="py-name">gold</tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-string">&lt;?xml version="1.0" encoding="iso-8859-1"?&gt;</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-string">&lt;hf&gt;&lt;header&gt;</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-string">This is some misc. header text</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-string">that goes on until the end.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-string">&lt;/header&gt;&lt;record&gt;ID 1</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;record&gt;ID 2</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;/hf&gt;"""</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">     </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">    <tt class="py-comment"># Don't use a regexp like this in your code - for testing only!</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-92" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-92', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-93" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-93', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-94', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"header"</tt><tt class="py-op">,</tt> <tt id="link-95" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-95', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-96', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">    <tt id="link-97" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-97', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-98', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-99', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-100" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-100', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-101', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"ID \d+(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line"> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">    <tt id="link-102" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-102', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-103" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-103', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-104', 'make_parser', 'link-18');">make_parser</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 id="link-105" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-105', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-106', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-107', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-name">hf</tt> <tt class="py-op">=</tt> <tt id="link-108" 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-108', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-109', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt id="link-110" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-110', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-111" class="py-name" targets="Class Martel.RecordReader.Until=Martel.RecordReader.Until-class.html"><a title="Martel.RecordReader.Until" class="py-name" href="#" onclick="return doclink('link-111', 'Until', 'link-111');">Until</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-112" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-112', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">        <tt id="link-113" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-113', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-114', 'StartsWith', 'link-47');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-115" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-115', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt id="link-116" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-116', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-117" class="py-name" targets="Class Martel.RecordReader.Nothing=Martel.RecordReader.Nothing-class.html"><a title="Martel.RecordReader.Nothing" class="py-name" href="#" onclick="return doclink('link-117', 'Nothing', 'link-117');">Nothing</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt class="py-name">XMLGenerator</tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-118', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-119" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-119', 's', 'link-57');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line"> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">    <tt id="link-120" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-120', 'text', 'link-120');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-121" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-121', 'text', 'link-120');">text</a></tt> <tt class="py-op">==</tt> <tt class="py-name">gold</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-122" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-122', 'text', 'link-120');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">gold</tt><tt class="py-op">)</tt> </tt>
</div><a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"> </tt>
<a name="test_header_footer3"></a><div id="test_header_footer3-def"><a name="L166"></a><tt class="py-lineno">166</tt> <a class="py-toggle" href="#" id="test_header_footer3-toggle" onclick="return toggle('test_header_footer3');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer3">test_header_footer3</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer3-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer3-expanded"><a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">    <tt class="py-comment"># Have a footer but no header</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-123" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-123', 's', 'link-57');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-string">ID 1</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-string">ID 2</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-string">Okay, that was all of the data.</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">    <tt class="py-name">gold</tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"><tt class="py-string">&lt;?xml version="1.0" encoding="iso-8859-1"?&gt;</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"><tt class="py-string">&lt;hf&gt;&lt;record&gt;ID 1</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;record&gt;ID 2</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;footer&gt;Okay, that was all of the data.</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-string">&lt;/footer&gt;&lt;/hf&gt;"""</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">     </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-comment"># Don't use a regexp like this in your code - for testing only!</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-124" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-124', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-125" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-125', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-126', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-127" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-127', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-128', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"ID \d+(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">    <tt class="py-comment"># Require at least 5 characters (just to be safe)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt id="link-129" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-129', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-130', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"footer"</tt><tt class="py-op">,</tt> <tt id="link-131" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-131', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-132', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r".....(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">    <tt id="link-133" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-133', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-134" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-134', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-135', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-136', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">    <tt class="py-name">hf</tt> <tt class="py-op">=</tt> <tt id="link-137" 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-137', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-138', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt id="link-139" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-139', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Martel.RecordReader.Nothing" class="py-name" href="#" onclick="return doclink('link-140', 'Nothing', 'link-117');">Nothing</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt id="link-141" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-141', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-142', 'EndsWith', 'link-82');">EndsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"//\n"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-143" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-143', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">        <tt id="link-144" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-144', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-145" class="py-name" targets="Class Martel.RecordReader.Everything=Martel.RecordReader.Everything-class.html"><a title="Martel.RecordReader.Everything" class="py-name" href="#" onclick="return doclink('link-145', 'Everything', 'link-145');">Everything</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt class="py-name">XMLGenerator</tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-146', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-147" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-147', 's', 'link-57');">s</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>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">    <tt id="link-148" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-148', 'text', 'link-120');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-149" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-149', 'text', 'link-120');">text</a></tt> <tt class="py-op">==</tt> <tt class="py-name">gold</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-150" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-150', 'text', 'link-120');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">gold</tt><tt class="py-op">)</tt> </tt>
</div><a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">     </tt>
<a name="test_header_footer4"></a><div id="test_header_footer4-def"><a name="L211"></a><tt class="py-lineno">211</tt> <a class="py-toggle" href="#" id="test_header_footer4-toggle" onclick="return toggle('test_header_footer4');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer4">test_header_footer4</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer4-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer4-expanded"><a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">    <tt class="py-comment"># Have a header but no footer - and not footer reader</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-151" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-151', 's', 'link-57');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"><tt class="py-string">This is some misc. header text</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line"><tt class="py-string">that goes on until the end.</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"><tt class="py-string">ID 1</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"><tt class="py-string">ID 2</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">    <tt class="py-name">gold</tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"><tt class="py-string">&lt;?xml version="1.0" encoding="iso-8859-1"?&gt;</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line"><tt class="py-string">&lt;hf&gt;&lt;header&gt;</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line"><tt class="py-string">This is some misc. header text</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-string">that goes on until the end.</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-string">&lt;/header&gt;&lt;record&gt;ID 1</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;record&gt;ID 2</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"><tt class="py-string">&lt;/record&gt;&lt;/hf&gt;"""</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">    <tt class="py-comment"># Don't use a regexp like this in your code - for testing only!</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-152" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-152', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-153" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-153', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-154', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"header"</tt><tt class="py-op">,</tt> <tt id="link-155" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-155', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-156', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">    <tt id="link-157" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-157', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-158" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-158', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-159', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-160" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-160', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-161', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"ID \d+(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">    <tt id="link-162" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-162', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-163" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-163', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-164', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">    <tt id="link-165" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-165', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-166" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-166', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-167', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">    <tt class="py-name">hf</tt> <tt class="py-op">=</tt> <tt id="link-168" 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-168', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-169', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">        <tt id="link-170" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-170', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Martel.RecordReader.Until" class="py-name" href="#" onclick="return doclink('link-171', 'Until', 'link-111');">Until</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-172" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-172', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">        <tt id="link-173" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-173', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-174', 'StartsWith', 'link-47');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-175" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-175', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">        <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">    <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt class="py-name">XMLGenerator</tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ErrorHandler</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-176', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-177" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-177', 's', 'link-57');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line"> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">    <tt id="link-178" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-178', 'text', 'link-120');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-179" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-179', 'text', 'link-120');">text</a></tt> <tt class="py-op">==</tt> <tt class="py-name">gold</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-180" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-180', 'text', 'link-120');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">gold</tt><tt class="py-op">)</tt> </tt>
</div><a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"> </tt>
<a name="test_header_footer5"></a><div id="test_header_footer5-def"><a name="L253"></a><tt class="py-lineno">253</tt> <a class="py-toggle" href="#" id="test_header_footer5-toggle" onclick="return toggle('test_header_footer5');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer5">test_header_footer5</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer5-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer5-expanded"><a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">    <tt class="py-comment"># Make sure I can skip records when there are not footer records</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-181" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-181', 's', 'link-57');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"><tt class="py-string">This is some misc. header text</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"><tt class="py-string">that goes on until the end.</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-string">ID 1</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line"><tt class="py-string">ID A</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"><tt class="py-string">ID 3</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line"><tt class="py-string">This is again some more data</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line"><tt class="py-string">ID Q</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line"><tt class="py-string">This blah</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"><tt class="py-string">ID W</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"><tt class="py-string">QWE</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"><tt class="py-string">ID 987</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line"><tt class="py-string">To be</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line"><tt class="py-string">ID 897</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line"><tt class="py-string">Or not to be</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">    <tt id="link-182" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-182', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-183" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-183', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-184', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"header"</tt><tt class="py-op">,</tt> <tt id="link-185" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-185', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-186', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">    <tt id="link-187" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-187', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-188" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-188', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-189', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-190" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-190', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-191', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"ID \d+(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">    <tt id="link-192" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-192', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-193" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-193', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-194', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">    <tt id="link-195" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-195', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-196" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-196', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-197', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">    <tt class="py-name">hf</tt> <tt class="py-op">=</tt> <tt id="link-198" 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-198', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-199', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">        <tt id="link-200" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-200', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="Martel.RecordReader.Until" class="py-name" href="#" onclick="return doclink('link-201', 'Until', 'link-111');">Until</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-202" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-202', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">        <tt id="link-203" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-203', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-204', 'StartsWith', 'link-47');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-205" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-205', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">        <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">    <tt id="link-206" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-206', 'count', 'link-30');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-207" class="py-name"><a title="Martel.test.test_Parser.CountRecords" class="py-name" href="#" onclick="return doclink('link-207', 'CountRecords', 'link-50');">CountRecords</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt id="link-208" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-208', 'count', 'link-30');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">    <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt id="link-209" class="py-name"><a title="Martel.test.test_Parser.CountErrors" class="py-name" href="#" onclick="return doclink('link-209', 'CountErrors', 'link-48');">CountErrors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-210', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-211" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-211', 's', 'link-57');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-212" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-212', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-213" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-213', 'count', 'link-30');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">4</tt><tt class="py-op">,</tt> <tt id="link-214" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-214', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-215', 'count', 'link-30');">count</a></tt> </tt>
</div><a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line"> </tt>
<a name="test_header_footer6"></a><div id="test_header_footer6-def"><a name="L295"></a><tt class="py-lineno">295</tt> <a class="py-toggle" href="#" id="test_header_footer6-toggle" onclick="return toggle('test_header_footer6');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer6">test_header_footer6</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer6-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer6-expanded"><a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">    <tt class="py-comment"># Make sure I can skip records when there are footer records</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-216" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-216', 's', 'link-57');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line"><tt class="py-string">This is some misc. header text</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line"><tt class="py-string">that goes on until the end.</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line"><tt class="py-string">ID 1</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line"><tt class="py-string">This is some data</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line"><tt class="py-string">ID A</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line"><tt class="py-string">This is some more data</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line"><tt class="py-string">ID 3</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line"><tt class="py-string">This is again some more data</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"><tt class="py-string">ID Q</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line"><tt class="py-string">This blah</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line"><tt class="py-string">ID W</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line"><tt class="py-string">QWE</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line"><tt class="py-string">ID 987</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line"><tt class="py-string">To be</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line"><tt class="py-string">ID 897</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line"><tt class="py-string">Or not to be</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"><tt class="py-string">FOOTER</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">    <tt id="link-217" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-217', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-218" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-218', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-219', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"header"</tt><tt class="py-op">,</tt> <tt id="link-220" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-220', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-221', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">    <tt id="link-222" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-222', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-223" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-223', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-224', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-225" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-225', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-226" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-226', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"ID \d+(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt id="link-227" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-227', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-228" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-228', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"footer"</tt><tt class="py-op">,</tt> <tt id="link-229" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-229', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-230" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-230', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"FOOTER(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">    <tt id="link-231" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-231', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-232" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-232', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-233', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">    <tt id="link-234" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-234', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-235" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-235', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-236" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-236', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-237', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line"> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">    <tt class="py-name">hf</tt> <tt class="py-op">=</tt> <tt id="link-238" 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-238', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-239', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">        <tt id="link-240" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-240', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="Martel.RecordReader.Until" class="py-name" href="#" onclick="return doclink('link-241', 'Until', 'link-111');">Until</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ID"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-242" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-242', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">        <tt id="link-243" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-243', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-244" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-244', 'EndsWith', 'link-82');">EndsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"//"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-245" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-245', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">        <tt id="link-246" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-246', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-247', 'StartsWith', 'link-47');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"FOOTER"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">    <tt id="link-248" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-248', 'count', 'link-30');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-249" class="py-name"><a title="Martel.test.test_Parser.CountRecords" class="py-name" href="#" onclick="return doclink('link-249', 'CountRecords', 'link-50');">CountRecords</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt id="link-250" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-250', 'count', 'link-30');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">    <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt id="link-251" class="py-name"><a title="Martel.test.test_Parser.CountErrors" class="py-name" href="#" onclick="return doclink('link-251', 'CountErrors', 'link-48');">CountErrors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-252" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-252', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-253" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-253', 's', 'link-57');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line"> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-254" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-254', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-255', 'count', 'link-30');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">4</tt><tt class="py-op">,</tt> <tt id="link-256" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-256', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-257', 'count', 'link-30');">count</a></tt> </tt>
</div><a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line"> </tt>
<a name="test_header_footer7"></a><div id="test_header_footer7-def"><a name="L347"></a><tt class="py-lineno">347</tt> <a class="py-toggle" href="#" id="test_header_footer7-toggle" onclick="return toggle('test_header_footer7');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer7">test_header_footer7</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer7-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer7-expanded"><a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">    <tt class="py-comment"># header and footer but with no record data</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-258" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-258', 's', 'link-57');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""\</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line"><tt class="py-string">This is some misc. header text</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line"><tt class="py-string">that goes on until the end.</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line"><tt class="py-string">FOOTER</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">    <tt id="link-259" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-259', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-260" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-260', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-261', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"header"</tt><tt class="py-op">,</tt> <tt id="link-262" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-262', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-263" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-263', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">    <tt id="link-264" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-264', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-265" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-265', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-266" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-266', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-267" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-267', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-268" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-268', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"ID \d+(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt id="link-269" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-269', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-270', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"footer"</tt><tt class="py-op">,</tt> <tt id="link-271" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-271', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-272" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-272', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"FOOTER(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line"> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">    <tt id="link-273" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-273', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-274" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-274', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-275', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">    <tt id="link-276" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-276', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-277" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-277', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-278" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-278', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt id="link-279" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-279', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line"> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">    <tt class="py-name">hf</tt> <tt class="py-op">=</tt> <tt id="link-280" 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-280', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-281', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">        <tt id="link-282" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-282', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-283" class="py-name" targets="Class Martel.RecordReader.CountLines=Martel.RecordReader.CountLines-class.html"><a title="Martel.RecordReader.CountLines" class="py-name" href="#" onclick="return doclink('link-283', 'CountLines', 'link-283');">CountLines</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-284" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-284', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">        <tt id="link-285" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-285', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-286" class="py-name"><a title="Martel.RecordReader.EndsWith" class="py-name" href="#" onclick="return doclink('link-286', 'EndsWith', 'link-82');">EndsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"//"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-287" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-287', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">        <tt id="link-288" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-288', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-289', 'StartsWith', 'link-47');">StartsWith</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"FOOTER"</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">    <tt id="link-290" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-290', 'count', 'link-30');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-291" class="py-name"><a title="Martel.test.test_Parser.CountRecords" class="py-name" href="#" onclick="return doclink('link-291', 'CountRecords', 'link-50');">CountRecords</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt id="link-292" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-292', 'count', 'link-30');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">    <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt id="link-293" class="py-name"><a title="Martel.test.test_Parser.CountErrors" class="py-name" href="#" onclick="return doclink('link-293', 'CountErrors', 'link-48');">CountErrors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">    <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-294', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-295" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-295', 's', 'link-57');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line"> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-296" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-296', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-297" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-297', 'count', 'link-30');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-298" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-298', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-299" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-299', 'count', 'link-30');">count</a></tt> </tt>
</div><a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line"> </tt>
<a name="test_header_footer8"></a><div id="test_header_footer8-def"><a name="L378"></a><tt class="py-lineno">378</tt> <a class="py-toggle" href="#" id="test_header_footer8-toggle" onclick="return toggle('test_header_footer8');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test_header_footer8">test_header_footer8</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test_header_footer8-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test_header_footer8-expanded"><a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">    <tt class="py-comment"># header, record and footer, but with extra data</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-300" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-300', 's1', 'link-300');">s1</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""Two lines in</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line"><tt class="py-string">the header.</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line"><tt class="py-string">Data 1</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line"><tt class="py-string">Data 2</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line"><tt class="py-string">Data Q</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line"><tt class="py-string">Data 4</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line"><tt class="py-string">FOOTER Abc</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line"><tt class="py-string">FOOTER B</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">    <tt id="link-301" class="py-name" targets="Variable Martel.test.test_swissprot38.s2=Martel.test.test_swissprot38-module.html#s2"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-301', 's2', 'link-301');">s2</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""Two lines in</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line"><tt class="py-string">the header.</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line"><tt class="py-string">Data 1</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line"><tt class="py-string">Data 2</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line"><tt class="py-string">Data Q</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line"><tt class="py-string">Data 4</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line"><tt class="py-string">FOOTER Abc</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">    <tt id="link-302" class="py-name" targets="Variable Martel.test.test_swissprot38.s3=Martel.test.test_swissprot38-module.html#s3"><a title="Martel.test.test_swissprot38.s3" class="py-name" href="#" onclick="return doclink('link-302', 's3', 'link-302');">s3</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""Two lines in</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line"><tt class="py-string">the header.</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line"><tt class="py-string">Data 1</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line"><tt class="py-string">Data 4</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line"><tt class="py-string">FOOTER Abc</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line">    <tt class="py-name">s4</tt> <tt class="py-op">=</tt> <tt class="py-string">"""Two lines in</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line"><tt class="py-string">the header.</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line"><tt class="py-string">Data Q</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line"><tt class="py-string">FOOTER Abc</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">    <tt class="py-name">s5</tt> <tt class="py-op">=</tt> <tt class="py-string">"""Two lines in</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line"><tt class="py-string">the header.</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line"><tt class="py-string">FOOTER Abc</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">    <tt class="py-name">dataset</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> <tt class="py-op">(</tt><tt id="link-303" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-303', 's1', 'link-300');">s1</a></tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-number">1</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="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line">                <tt class="py-op">(</tt><tt id="link-304" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-304', 's2', 'link-301');">s2</a></tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line">                <tt class="py-op">(</tt><tt id="link-305" class="py-name"><a title="Martel.test.test_swissprot38.s3" class="py-name" href="#" onclick="return doclink('link-305', 's3', 'link-302');">s3</a></tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line">                <tt class="py-op">(</tt><tt class="py-name">s4</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">                <tt class="py-op">(</tt><tt class="py-name">s5</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">                <tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line">                 </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line">    <tt id="link-306" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-306', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-307" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-307', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-308" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-308', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"header"</tt><tt class="py-op">,</tt> <tt id="link-309" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-309', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-310" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-310', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"(.|\n)*"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">    <tt id="link-311" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-311', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-312" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-312', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-313" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-313', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt id="link-314" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-314', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-315', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"Data \d+\n"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt id="link-316" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-316', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-317" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-317', 'Group', 'link-6');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"footer"</tt><tt class="py-op">,</tt> <tt id="link-318" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-318', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-319" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-319', 'Re', 'link-41');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">"FOOTER \w+\n"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line"> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">    <tt id="link-320" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-320', 'header', 'link-58');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-321" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-321', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt id="link-322" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-322', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">    <tt id="link-323" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-323', 'record', 'link-4');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-324" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-324', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt id="link-325" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-325', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">    <tt class="py-name">footer</tt> <tt class="py-op">=</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt id="link-326" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-326', 'make_parser', 'link-18');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line"> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line">    <tt class="py-name">hf</tt> <tt class="py-op">=</tt> <tt id="link-327" 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-327', 'Parser', 'link-3');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-328" class="py-name"><a title="Martel.Parser.HeaderFooterParser" class="py-name" href="#" onclick="return doclink('link-328', 'HeaderFooterParser', 'link-80');">HeaderFooterParser</a></tt><tt class="py-op">(</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">        <tt class="py-string">"hf"</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line">        <tt id="link-329" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-329', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-330" class="py-name"><a title="Martel.RecordReader.CountLines" class="py-name" href="#" onclick="return doclink('link-330', 'CountLines', 'link-283');">CountLines</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-331" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-331', 'header', 'link-58');">header</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line">        <tt id="link-332" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-332', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-333" class="py-name"><a title="Martel.RecordReader.CountLines" class="py-name" href="#" onclick="return doclink('link-333', 'CountLines', 'link-283');">CountLines</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-334" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-334', 'record', 'link-4');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt>  <tt class="py-line">        <tt id="link-335" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-335', 'RecordReader', 'link-2');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-336" class="py-name"><a title="Martel.RecordReader.CountLines" class="py-name" href="#" onclick="return doclink('link-336', 'CountLines', 'link-283');">CountLines</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">footer</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">,</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-337" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-337', 's', 'link-57');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">rec_count</tt><tt class="py-op">,</tt> <tt class="py-name">err_count</tt><tt class="py-op">,</tt> <tt class="py-name">fatal_count</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataset</tt><tt class="py-op">:</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">        <tt id="link-338" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-338', 'count', 'link-30');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-339" class="py-name"><a title="Martel.test.test_Parser.CountRecords" class="py-name" href="#" onclick="return doclink('link-339', 'CountRecords', 'link-50');">CountRecords</a></tt><tt class="py-op">(</tt><tt class="py-string">"record"</tt><tt class="py-op">)</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">        <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt id="link-340" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-340', 'count', 'link-30');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line">        <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt id="link-341" class="py-name"><a title="Martel.test.test_Parser.CountErrors" class="py-name" href="#" onclick="return doclink('link-341', 'CountErrors', 'link-48');">CountErrors</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line">        <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">)</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line">        <tt class="py-name">hf</tt><tt class="py-op">.</tt><tt id="link-342" class="py-name"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-342', 'parseFile', 'link-89');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-343" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-343', 's', 'link-57');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line"> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt> <tt class="py-op">==</tt> <tt class="py-name">err_count</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-344" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-344', 's', 'link-57');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">error_count</tt><tt class="py-op">,</tt> <tt class="py-name">err_count</tt><tt class="py-op">)</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt> <tt class="py-op">==</tt> <tt class="py-name">fatal_count</tt><tt class="py-op">,</tt> \ </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line">               <tt class="py-op">(</tt><tt id="link-345" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-345', 's', 'link-57');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">.</tt><tt class="py-name">fatal_error_count</tt><tt class="py-op">,</tt> <tt class="py-name">fatal_count</tt><tt class="py-op">)</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt id="link-346" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-346', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-347" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-347', 'count', 'link-30');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-name">rec_count</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-348" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-348', 's', 'link-57');">s</a></tt><tt class="py-op">,</tt> <tt id="link-349" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-349', 'count', 'link-30');">count</a></tt><tt class="py-op">.</tt><tt id="link-350" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-350', 'count', 'link-30');">count</a></tt><tt class="py-op">,</tt> <tt class="py-name">rec_count</tt><tt class="py-op">)</tt> </tt>
</div><a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line"> </tt>
<a name="test"></a><div id="test-def"><a name="L445"></a><tt class="py-lineno">445</tt> <a class="py-toggle" href="#" id="test-toggle" onclick="return toggle('test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.test.test_Parser-module.html#test">test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test-expanded"><a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line">    <tt id="link-351" class="py-name" targets="Function Martel.test.test_Parser.test_reader_parser()=Martel.test.test_Parser-module.html#test_reader_parser"><a title="Martel.test.test_Parser.test_reader_parser" class="py-name" href="#" onclick="return doclink('link-351', 'test_reader_parser', 'link-351');">test_reader_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line">    <tt id="link-352" class="py-name" targets="Function Martel.test.test_Parser.test_record_parser()=Martel.test.test_Parser-module.html#test_record_parser,Function Martel.test.test_attrs.test_record_parser()=Martel.test.test_attrs-module.html#test_record_parser"><a title="Martel.test.test_Parser.test_record_parser
Martel.test.test_attrs.test_record_parser" class="py-name" href="#" onclick="return doclink('link-352', 'test_record_parser', 'link-352');">test_record_parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line">    <tt id="link-353" class="py-name" targets="Function Martel.test.test_Iterator.test_header_footer1()=Martel.test.test_Iterator-module.html#test_header_footer1,Function Martel.test.test_Parser.test_header_footer1()=Martel.test.test_Parser-module.html#test_header_footer1"><a title="Martel.test.test_Iterator.test_header_footer1
Martel.test.test_Parser.test_header_footer1" class="py-name" href="#" onclick="return doclink('link-353', 'test_header_footer1', 'link-353');">test_header_footer1</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line">    <tt id="link-354" class="py-name" targets="Function Martel.test.test_Iterator.test_header_footer2()=Martel.test.test_Iterator-module.html#test_header_footer2,Function Martel.test.test_Parser.test_header_footer2()=Martel.test.test_Parser-module.html#test_header_footer2"><a title="Martel.test.test_Iterator.test_header_footer2
Martel.test.test_Parser.test_header_footer2" class="py-name" href="#" onclick="return doclink('link-354', 'test_header_footer2', 'link-354');">test_header_footer2</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line">    <tt id="link-355" class="py-name" targets="Function Martel.test.test_Iterator.test_header_footer3()=Martel.test.test_Iterator-module.html#test_header_footer3,Function Martel.test.test_Parser.test_header_footer3()=Martel.test.test_Parser-module.html#test_header_footer3"><a title="Martel.test.test_Iterator.test_header_footer3
Martel.test.test_Parser.test_header_footer3" class="py-name" href="#" onclick="return doclink('link-355', 'test_header_footer3', 'link-355');">test_header_footer3</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt>  <tt class="py-line">    <tt id="link-356" class="py-name" targets="Function Martel.test.test_Iterator.test_header_footer4()=Martel.test.test_Iterator-module.html#test_header_footer4,Function Martel.test.test_Parser.test_header_footer4()=Martel.test.test_Parser-module.html#test_header_footer4"><a title="Martel.test.test_Iterator.test_header_footer4
Martel.test.test_Parser.test_header_footer4" class="py-name" href="#" onclick="return doclink('link-356', 'test_header_footer4', 'link-356');">test_header_footer4</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt>  <tt class="py-line">    <tt id="link-357" class="py-name" targets="Function Martel.test.test_Iterator.test_header_footer5()=Martel.test.test_Iterator-module.html#test_header_footer5,Function Martel.test.test_Parser.test_header_footer5()=Martel.test.test_Parser-module.html#test_header_footer5"><a title="Martel.test.test_Iterator.test_header_footer5
Martel.test.test_Parser.test_header_footer5" class="py-name" href="#" onclick="return doclink('link-357', 'test_header_footer5', 'link-357');">test_header_footer5</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line">    <tt id="link-358" class="py-name" targets="Function Martel.test.test_Iterator.test_header_footer7()=Martel.test.test_Iterator-module.html#test_header_footer7,Function Martel.test.test_Parser.test_header_footer7()=Martel.test.test_Parser-module.html#test_header_footer7"><a title="Martel.test.test_Iterator.test_header_footer7
Martel.test.test_Parser.test_header_footer7" class="py-name" href="#" onclick="return doclink('link-358', 'test_header_footer7', 'link-358');">test_header_footer7</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line">    <tt id="link-359" class="py-name" targets="Function Martel.test.test_Parser.test_header_footer8()=Martel.test.test_Parser-module.html#test_header_footer8"><a title="Martel.test.test_Parser.test_header_footer8" class="py-name" href="#" onclick="return doclink('link-359', 'test_header_footer8', 'link-359');">test_header_footer8</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line"> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line">    <tt id="link-360" class="py-name" targets="Function Bio.Decode.test()=Bio.Decode-module.html#test,Function Bio.EUtils.ReseekFile.test()=Bio.EUtils.ReseekFile-module.html#test,Package Martel.test=Martel.test-module.html,Method Martel.test.support.Storage.test()=Martel.test.support.Storage-class.html#test,Function Martel.test.test()=Martel.test-module.html#test,Function Martel.test.test_Expression.test()=Martel.test.test_Expression-module.html#test,Function Martel.test.test_Generate.test()=Martel.test.test_Generate-module.html#test,Function Martel.test.test_IterParser.test()=Martel.test.test_IterParser-module.html#test,Function Martel.test.test_Iterator.test()=Martel.test.test_Iterator-module.html#test,Function Martel.test.test_LAX.test()=Martel.test.test_LAX-module.html#test,Function Martel.test.test_ParseRecords.test()=Martel.test.test_ParseRecords-module.html#test,Function Martel.test.test_Parser.test()=Martel.test.test_Parser-module.html#test,Function Martel.test.test_RecordReader.test()=Martel.test.test_RecordReader-module.html#test,Function Martel.test.test_RecordReader2.test()=Martel.test.test_RecordReader2-module.html#test,Function Martel.test.test_Time.test()=Martel.test.test_Time-module.html#test,Function Martel.test.test_attrs.test()=Martel.test.test_attrs-module.html#test,Function Martel.test.test_convert_re.test()=Martel.test.test_convert_re-module.html#test,Function Martel.test.test_delimiter.test()=Martel.test.test_delimiter-module.html#test,Function Martel.test.test_macros.test()=Martel.test.test_macros-module.html#test,Function Martel.test.test_optimize.test()=Martel.test.test_optimize-module.html#test,Function Martel.test.test_swissprot38.test()=Martel.test.test_swissprot38-module.html#test"><a title="Bio.Decode.test
Bio.EUtils.ReseekFile.test
Martel.test
Martel.test.support.Storage.test
Martel.test.test
Martel.test.test_Expression.test
Martel.test.test_Generate.test
Martel.test.test_IterParser.test
Martel.test.test_Iterator.test
Martel.test.test_LAX.test
Martel.test.test_ParseRecords.test
Martel.test.test_Parser.test
Martel.test.test_RecordReader.test
Martel.test.test_RecordReader2.test
Martel.test.test_Time.test
Martel.test.test_attrs.test
Martel.test.test_convert_re.test
Martel.test.test_delimiter.test
Martel.test.test_macros.test
Martel.test.test_optimize.test
Martel.test.test_swissprot38.test" class="py-name" href="#" onclick="return doclink('link-360', 'test', 'link-360');">test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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</pre>
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