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<a href="Martel-module.html">Package Martel</a> ::
Module Iterator
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<h1 class="epydoc">Source Code for <a href="Martel.Iterator-module.html">Module Martel.Iterator</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2000-2001, Dalke Scientific Software, LLC</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Distributed under the Biopython License Agreement (see the LICENSE file).</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">"""Iterate over records of a XML parse tree.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">The standard parser is callback based over all the elements of a file.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">If the file contains records, many people would like to be able to</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">iterate over each record and only use the callback parser to analyze</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">the record.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">If the expression is a 'ParseRecords', then the code to do this is</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">easy; use its make_reader to grab records and its record_expression to</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">parse them. However, this isn't general enough. The use of a</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">ParseRecords in the format definition should be strictly a</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">implementation decision for better memory use. So there needs to be</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">an API which allows both full and record oriented parsers.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">Here's an example use of the API:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">>>> import sys</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">>>> import swissprot38 # one is in Martel/test/testformats</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">>>> from xml.dom import pulldom</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">>>> iterator = swissprot38.format.make_iterator("swissprot38_record")</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">>>> text = open("sample.swissprot").read()</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">>>> for record in iterator.iterateString(text, pulldom.SAX2DOM()):</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">.. print "Read a record with the following AC numbers:"</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">... for acc in record.document.getElementsByTagName("ac_number"):</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">... acc.writexml(sys.stdout)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring">... sys.stdout.write("\n")</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">...</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">There are several parts to this API. First is the 'Iterator</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring">There are two parts to the API. One is the EventStream. This</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">contains a single method called "next()" which returns a list of SAX</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring">events in the 2-ple (event_name, args). It is called multiple times</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring">to return successive event lists and returns None if no events are</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring">available.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring">The other is the Iterator</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring">Sean McGrath has a RAX parser (Record API for XML) which uses a</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring">concept similar to this.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">urllib</tt><tt class="py-op">,</tt> <tt class="py-name">traceback</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</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">saxutils</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.AlignAce.Parser=Bio.AlignAce.Parser-module.html,Module Bio.Entrez.Parser=Bio.Entrez.Parser-module.html,Module Bio.MEME.Parser=Bio.MEME.Parser-module.html,Class Bio.SCOP.Cla.Parser=Bio.SCOP.Cla.Parser-class.html,Class Bio.SCOP.Des.Parser=Bio.SCOP.Des.Parser-class.html,Class Bio.SCOP.Dom.Parser=Bio.SCOP.Dom.Parser-class.html,Class Bio.SCOP.Hie.Parser=Bio.SCOP.Hie.Parser-class.html,Class Bio.SCOP.Raf.Parser=Bio.SCOP.Raf.Parser-class.html,Module Martel.Parser=Martel.Parser-module.html,Class Martel.Parser.Parser=Martel.Parser.Parser-class.html"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-0', 'Parser', 'link-0');">Parser</a></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</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="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
<a name="StoreEvents"></a><div id="StoreEvents-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="StoreEvents-toggle" onclick="return toggle('StoreEvents');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-class.html">StoreEvents</a><tt class="py-op">:</tt> </tt>
</div><div id="StoreEvents-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StoreEvents-expanded"><a name="StoreEvents.__init__"></a><div id="StoreEvents.__init__-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="StoreEvents.__init__-toggle" onclick="return toggle('StoreEvents.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-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="StoreEvents.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StoreEvents.__init__-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.Blast.NCBIXML._XMLparser.characters()=Bio.Blast.NCBIXML._XMLparser-class.html#characters,Method Bio.EUtils.POM.ObjectParserHandler.characters()=Bio.EUtils.POM.ObjectParserHandler-class.html#characters,Method Bio.Entrez.Parser.DataHandler.characters()=Bio.Entrez.Parser.DataHandler-class.html#characters,Method Bio.Mindy.XPath.GrabXPathNodes.characters()=Bio.Mindy.XPath.GrabXPathNodes-class.html#characters,Method Bio.ParserSupport.EventGenerator.characters()=Bio.ParserSupport.EventGenerator-class.html#characters,Method Martel.Dispatch.Dispatcher.characters()=Martel.Dispatch.Dispatcher-class.html#characters,Method Martel.LAX.LAX.characters()=Martel.LAX.LAX-class.html#characters,Method Martel.test.support.Dump.characters()=Martel.test.support.Dump-class.html#characters,Method Martel.test.test_delimiter.CatchFields.characters()=Martel.test.test_delimiter.CatchFields-class.html#characters"><a title="Bio.Blast.NCBIXML._XMLparser.characters
Bio.EUtils.POM.ObjectParserHandler.characters
Bio.Entrez.Parser.DataHandler.characters
Bio.Mindy.XPath.GrabXPathNodes.characters
Bio.ParserSupport.EventGenerator.characters
Martel.Dispatch.Dispatcher.characters
Martel.LAX.LAX.characters
Martel.test.support.Dump.characters
Martel.test.test_delimiter.CatchFields.characters" class="py-name" href="#" onclick="return doclink('link-1', 'characters', 'link-1');">characters</a></tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">ch</tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-2', 'append', 'link-2');">append</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-3', 'append', 'link-2');">append</a></tt><tt class="py-op">:</tt> \ </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt id="link-4" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-4', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-string">"characters"</tt><tt class="py-op">,</tt> <tt class="py-name">ch</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="StoreEvents.startDocument"></a><div id="StoreEvents.startDocument-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="StoreEvents.startDocument-toggle" onclick="return toggle('StoreEvents.startDocument');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-class.html#startDocument">startDocument</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="StoreEvents.startDocument-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StoreEvents.startDocument-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="StoreEvents.endDocument"></a><div id="StoreEvents.endDocument-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="StoreEvents.endDocument-toggle" onclick="return toggle('StoreEvents.endDocument');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-class.html#endDocument">endDocument</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StoreEvents.endDocument-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StoreEvents.endDocument-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="StoreEvents.startElement"></a><div id="StoreEvents.startElement-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="StoreEvents.startElement-toggle" onclick="return toggle('StoreEvents.startElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-class.html#startElement">startElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StoreEvents.startElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StoreEvents.startElement-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-5', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-string">"startElement"</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment">## def characters(self, s):</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # Note: This doesn't store the args as a tuple!</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## self.events.append( ("characters", s) )</tt> </tt>
<a name="StoreEvents.endElement"></a><div id="StoreEvents.endElement-def"><a name="L72"></a><tt class="py-lineno"> 72</tt> <a class="py-toggle" href="#" id="StoreEvents.endElement-toggle" onclick="return toggle('StoreEvents.endElement');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-class.html#endElement">endElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StoreEvents.endElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StoreEvents.endElement-expanded"><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-6', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-string">"endElement"</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="StoreEvents.error"></a><div id="StoreEvents.error-def"><a name="L75"></a><tt class="py-lineno"> 75</tt> <a class="py-toggle" href="#" id="StoreEvents.error-toggle" onclick="return toggle('StoreEvents.error');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-class.html#error">error</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StoreEvents.error-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StoreEvents.error-expanded"><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-7', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-string">"error"</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="StoreEvents.fatalError"></a><div id="StoreEvents.fatalError-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="StoreEvents.fatalError-toggle" onclick="return toggle('StoreEvents.fatalError');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.StoreEvents-class.html#fatalError">fatalError</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StoreEvents.fatalError-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StoreEvents.fatalError-expanded"><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_error</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-8', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-string">"fatalError"</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div></div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="EventStream"></a><div id="EventStream-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="EventStream-toggle" onclick="return toggle('EventStream');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.EventStream-class.html">EventStream</a><tt class="py-op">:</tt> </tt>
</div><div id="EventStream-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="EventStream-expanded"><a name="EventStream.__init__"></a><div id="EventStream.__init__-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="EventStream.__init__-toggle" onclick="return toggle('EventStream.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.EventStream-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">event_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="EventStream.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EventStream.__init__-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">event_list</tt> </tt>
</div><a name="EventStream.next"></a><div id="EventStream.next-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="EventStream.next-toggle" onclick="return toggle('EventStream.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.EventStream-class.html#next">next</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="EventStream.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EventStream.next-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt id="link-9" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-9', 'x', 'link-9');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-10', 'x', 'link-9');">x</a></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div></div><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="Iterator"></a><div id="Iterator-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="Iterator-toggle" onclick="return toggle('Iterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.Iterator-class.html">Iterator</a><tt class="py-op">:</tt> </tt>
</div><div id="Iterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterator-expanded"><a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="Iterator.__init__-toggle" onclick="return toggle('Iterator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterator-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">parser</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="Iterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__init__-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'tag', 'link-11');">tag</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-12', 'tag', 'link-11');">tag</a></tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="Iterator.iterateString"></a><div id="Iterator.iterateString-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="Iterator.iterateString-toggle" onclick="return toggle('Iterator.iterateString');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterator-class.html#iterateString">iterateString</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterator.iterateString-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.iterateString-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-docstring">"""create an iterator over a string"""</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name" targets="Class Martel.Iterator.StoreEvents=Martel.Iterator.StoreEvents-class.html"><a title="Martel.Iterator.StoreEvents" class="py-name" href="#" onclick="return doclink('link-13', 'StoreEvents', 'link-13');">StoreEvents</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'parseString', 'link-14');">parseString</a></tt><tt class="py-op">(</tt><tt id="link-15" 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-15', 's', 'link-15');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-16" class="py-name" targets="Class Martel.Iterator.Iterate=Martel.Iterator.Iterate-class.html"><a title="Martel.Iterator.Iterate" class="py-name" href="#" onclick="return doclink('link-16', 'Iterate', 'link-16');">Iterate</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name" targets="Class Martel.Iterator.EventStream=Martel.Iterator.EventStream-class.html"><a title="Martel.Iterator.EventStream" class="py-name" href="#" onclick="return doclink('link-17', 'EventStream', 'link-17');">EventStream</a></tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-18', 'tag', 'link-11');">tag</a></tt><tt class="py-op">,</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="Iterator.iterateFile"></a><div id="Iterator.iterateFile-def"><a name="L106"></a><tt class="py-lineno">106</tt> <a class="py-toggle" href="#" id="Iterator.iterateFile-toggle" onclick="return toggle('Iterator.iterateFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterator-class.html#iterateFile">iterateFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fileobj</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterator.iterateFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.iterateFile-expanded"><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Martel.IterParser.IterHeaderFooter.iterateString()=Martel.IterParser.IterHeaderFooter-class.html#iterateString,Method Martel.IterParser.IterRecords.iterateString()=Martel.IterParser.IterRecords-class.html#iterateString,Method Martel.Iterator.Iterator.iterateString()=Martel.Iterator.Iterator-class.html#iterateString,Method Martel.Iterator.IteratorHeaderFooter.iterateString()=Martel.Iterator.IteratorHeaderFooter-class.html#iterateString,Method Martel.Iterator.IteratorRecords.iterateString()=Martel.Iterator.IteratorRecords-class.html#iterateString"><a title="Martel.IterParser.IterHeaderFooter.iterateString
Martel.IterParser.IterRecords.iterateString
Martel.Iterator.Iterator.iterateString
Martel.Iterator.IteratorHeaderFooter.iterateString
Martel.Iterator.IteratorRecords.iterateString" class="py-name" href="#" onclick="return doclink('link-19', 'iterateString', 'link-19');">iterateString</a></tt><tt class="py-op">(</tt><tt class="py-name">fileobj</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-20', 'read', 'link-20');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="Iterator.iterate"></a><div id="Iterator.iterate-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="Iterator.iterate-toggle" onclick="return toggle('Iterator.iterate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterator-class.html#iterate">iterate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterator.iterate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.iterate-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-docstring">"""parse using the URL or file handle"""</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt id="link-21" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-21', 'source', 'link-21');">source</a></tt> <tt class="py-op">=</tt> <tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Function Bio.EUtils.ReseekFile.prepare_input_source()=Bio.EUtils.ReseekFile-module.html#prepare_input_source"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-22', 'prepare_input_source', 'link-22');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-23', 'source', 'link-21');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-24', 'source', 'link-21');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-25" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-25', 'source', 'link-21');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Martel.IterParser.IterHeaderFooter.iterateFile()=Martel.IterParser.IterHeaderFooter-class.html#iterateFile,Method Martel.IterParser.IterRecords.iterateFile()=Martel.IterParser.IterRecords-class.html#iterateFile,Method Martel.Iterator.Iterator.iterateFile()=Martel.Iterator.Iterator-class.html#iterateFile,Method Martel.Iterator.IteratorHeaderFooter.iterateFile()=Martel.Iterator.IteratorHeaderFooter-class.html#iterateFile,Method Martel.Iterator.IteratorRecords.iterateFile()=Martel.Iterator.IteratorRecords-class.html#iterateFile"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-26', 'iterateFile', 'link-26');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="RecordEventStream"></a><div id="RecordEventStream-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="RecordEventStream-toggle" onclick="return toggle('RecordEventStream');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.RecordEventStream-class.html">RecordEventStream</a><tt class="py-op">:</tt> </tt>
</div><div id="RecordEventStream-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordEventStream-expanded"><a name="RecordEventStream.__init__"></a><div id="RecordEventStream.__init__-def"><a name="L116"></a><tt class="py-lineno">116</tt> <a class="py-toggle" href="#" id="RecordEventStream.__init__-toggle" onclick="return toggle('RecordEventStream.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.RecordEventStream-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">reader</tt><tt class="py-op">,</tt> <tt class="py-param">parser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordEventStream.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordEventStream.__init__-expanded"><a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt> </tt>
</div><a name="RecordEventStream.next"></a><div id="RecordEventStream.next-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="RecordEventStream.next-toggle" onclick="return toggle('RecordEventStream.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.RecordEventStream-class.html#next">next</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="RecordEventStream.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordEventStream.next-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-27" 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-27', 'text', 'link-27');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-28', 'next', 'link-28');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-29" 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-29', 'text', 'link-27');">text</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="Martel.Iterator.StoreEvents" class="py-name" href="#" onclick="return doclink('link-30', 'StoreEvents', 'link-13');">StoreEvents</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><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">events</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'parseString', 'link-14');">parseString</a></tt><tt class="py-op">(</tt><tt id="link-32" 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-32', 'text', 'link-27');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">events</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> </tt>
</div></div><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> </tt>
<a name="IteratorRecords"></a><div id="IteratorRecords-def"><a name="L129"></a><tt class="py-lineno">129</tt> <a class="py-toggle" href="#" id="IteratorRecords-toggle" onclick="return toggle('IteratorRecords');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.IteratorRecords-class.html">IteratorRecords</a><tt class="py-op">:</tt> </tt>
</div><div id="IteratorRecords-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IteratorRecords-expanded"><a name="IteratorRecords.__init__"></a><div id="IteratorRecords.__init__-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="IteratorRecords.__init__-toggle" onclick="return toggle('IteratorRecords.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorRecords-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_reader</tt><tt class="py-op">,</tt> <tt class="py-param">reader_args</tt><tt class="py-op">,</tt> <tt class="py-param">marker_tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorRecords.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorRecords.__init__-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">record_parser</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_reader</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reader_args</tt> <tt class="py-op">=</tt> <tt class="py-name">reader_args</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">marker_tag</tt> </tt>
</div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="IteratorRecords.copy"></a><div id="IteratorRecords.copy-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="IteratorRecords.copy-toggle" onclick="return toggle('IteratorRecords.copy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorRecords-class.html#copy">copy</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorRecords.copy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorRecords.copy-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> <tt class="py-comment"># This is (so far) an immutable object</tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="IteratorRecords.iterateString"></a><div id="IteratorRecords.iterateString-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="IteratorRecords.iterateString-toggle" onclick="return toggle('IteratorRecords.iterateString');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorRecords-class.html#iterateString">iterateString</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorRecords.iterateString-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorRecords.iterateString-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-33', 'iterateFile', 'link-26');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-34', 's', 'link-15');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="IteratorRecords.iterateFile"></a><div id="IteratorRecords.iterateFile-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="IteratorRecords.iterateFile-toggle" onclick="return toggle('IteratorRecords.iterateFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorRecords-class.html#iterateFile">iterateFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fileobj</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorRecords.iterateFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorRecords.iterateFile-expanded"><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">record_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_reader</tt><tt class="py-op">(</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reader_args</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-35" class="py-name"><a title="Martel.Iterator.Iterate" class="py-name" href="#" onclick="return doclink('link-35', 'Iterate', 'link-16');">Iterate</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt id="link-36" class="py-name" targets="Class Martel.Iterator.RecordEventStream=Martel.Iterator.RecordEventStream-class.html"><a title="Martel.Iterator.RecordEventStream" class="py-name" href="#" onclick="return doclink('link-36', 'RecordEventStream', 'link-36');">RecordEventStream</a></tt><tt class="py-op">(</tt><tt class="py-name">record_reader</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
<a name="IteratorRecords.iterate"></a><div id="IteratorRecords.iterate-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="IteratorRecords.iterate-toggle" onclick="return toggle('IteratorRecords.iterate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorRecords-class.html#iterate">iterate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorRecords.iterate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorRecords.iterate-expanded"><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-docstring">"""parse using the URL or file handle"""</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-37', 'source', 'link-21');">source</a></tt> <tt class="py-op">=</tt> <tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-38', 'prepare_input_source', 'link-22');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-39', 'source', 'link-21');">source</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-name">file</tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-40', 'source', 'link-21');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-41" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-41', 'source', 'link-21');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-42', 'iterateFile', 'link-26');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<a name="_get_next_text"></a><div id="_get_next_text-def"><a name="L155"></a><tt class="py-lineno">155</tt> <a class="py-toggle" href="#" id="_get_next_text-toggle" onclick="return toggle('_get_next_text');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator-module.html#_get_next_text">_get_next_text</a><tt class="py-op">(</tt><tt class="py-param">reader</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_next_text-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_next_text-expanded"><a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-43', 'next', 'link-28');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-op">(</tt><tt class="py-name">KeyboardInterrupt</tt><tt class="py-op">,</tt> <tt class="py-name">SystemExit</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-keyword">raise</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-comment"># Something unusual happened (couldn't find a record?)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># so call it a fatal error and stop</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> <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="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">traceback</tt><tt class="py-op">.</tt><tt class="py-name">print_exc</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">=</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">exc</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-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Class Martel.Parser.ParserRecordException=Martel.Parser.ParserRecordException-class.html"><a title="Martel.Parser.ParserRecordException" class="py-name" href="#" onclick="return doclink('link-45', 'ParserRecordException', 'link-45');">ParserRecordException</a></tt><tt class="py-op">(</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exc_info</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-op">(</tt><tt class="py-string">"fatalError"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">exc</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">]</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">events</tt> </tt>
</div><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt>
<a name="HeaderFooterEventStream"></a><div id="HeaderFooterEventStream-def"><a name="L171"></a><tt class="py-lineno">171</tt> <a class="py-toggle" href="#" id="HeaderFooterEventStream-toggle" onclick="return toggle('HeaderFooterEventStream');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.HeaderFooterEventStream-class.html">HeaderFooterEventStream</a><tt class="py-op">:</tt> </tt>
</div><div id="HeaderFooterEventStream-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HeaderFooterEventStream-expanded"><a name="HeaderFooterEventStream.__init__"></a><div id="HeaderFooterEventStream.__init__-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="HeaderFooterEventStream.__init__-toggle" onclick="return toggle('HeaderFooterEventStream.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.HeaderFooterEventStream-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">fileobj</tt><tt class="py-op">,</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-param">header_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_header_reader</tt><tt class="py-op">,</tt> <tt class="py-param">header_args</tt><tt class="py-op">,</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-param">record_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_record_reader</tt><tt class="py-op">,</tt> <tt class="py-param">record_args</tt><tt class="py-op">,</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-param">footer_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_footer_reader</tt><tt class="py-op">,</tt> <tt class="py-param">footer_args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HeaderFooterEventStream.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HeaderFooterEventStream.__init__-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt> <tt class="py-op">=</tt> <tt class="py-name">fileobj</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">header_parser</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_header_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_header_reader</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_args</tt> <tt class="py-op">=</tt> <tt class="py-name">header_args</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">record_parser</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_record_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_record_reader</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_args</tt> <tt class="py-op">=</tt> <tt class="py-name">record_args</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">footer_parser</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_footer_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">make_footer_reader</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_args</tt> <tt class="py-op">=</tt> <tt class="py-name">footer_args</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">"header"</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="HeaderFooterEventStream.next"></a><div id="HeaderFooterEventStream.next-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="HeaderFooterEventStream.next-toggle" onclick="return toggle('HeaderFooterEventStream.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.HeaderFooterEventStream-class.html#next">next</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="HeaderFooterEventStream.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HeaderFooterEventStream.next-expanded"><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">"header"</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt id="link-46" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-46', 'x', 'link-9');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Martel.Iterator.HeaderFooterEventStream._header_next()=Martel.Iterator.HeaderFooterEventStream-class.html#_header_next"><a title="Martel.Iterator.HeaderFooterEventStream._header_next" class="py-name" href="#" onclick="return doclink('link-47', '_header_next', 'link-47');">_header_next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">"record"</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-48" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-48', 'x', 'link-9');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-49" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-49', 'x', 'link-9');">x</a></tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">"record"</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt id="link-50" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-50', 'x', 'link-9');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Martel.Iterator.HeaderFooterEventStream._record_next()=Martel.Iterator.HeaderFooterEventStream-class.html#_record_next"><a title="Martel.Iterator.HeaderFooterEventStream._record_next" class="py-name" href="#" onclick="return doclink('link-51', '_record_next', 'link-51');">_record_next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-52" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-52', 'x', 'link-9');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-53" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-53', 'x', 'link-9');">x</a></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">"footer"</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">"footer"</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-54', 'x', 'link-9');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Method Martel.Iterator.HeaderFooterEventStream._footer_next()=Martel.Iterator.HeaderFooterEventStream-class.html#_footer_next"><a title="Martel.Iterator.HeaderFooterEventStream._footer_next" class="py-name" href="#" onclick="return doclink('link-55', '_footer_next', 'link-55');">_footer_next</a></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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">"end"</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-56" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-56', 'x', 'link-9');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-57" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-57', 'x', 'link-9');">x</a></tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">"end"</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt> <tt class="py-op">(</tt><tt class="py-string">"fatalError"</tt><tt class="py-op">,</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-58" 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-58', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Class Martel.Parser.ParserIncompleteException=Martel.Parser.ParserIncompleteException-class.html"><a title="Martel.Parser.ParserIncompleteException" class="py-name" href="#" onclick="return doclink('link-59', 'ParserIncompleteException', 'link-59');">ParserIncompleteException</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">]</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="L219"></a><tt class="py-lineno">219</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">"Should not get here"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt>
<a name="HeaderFooterEventStream._header_next"></a><div id="HeaderFooterEventStream._header_next-def"><a name="L221"></a><tt class="py-lineno">221</tt> <a class="py-toggle" href="#" id="HeaderFooterEventStream._header_next-toggle" onclick="return toggle('HeaderFooterEventStream._header_next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.HeaderFooterEventStream-class.html#_header_next">_header_next</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="HeaderFooterEventStream._header_next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HeaderFooterEventStream._header_next-expanded"><a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_header_reader</tt><tt class="py-op">(</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_args</tt><tt class="py-op">,</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-op">{</tt><tt class="py-string">"lookahead"</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt id="link-60" 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-60', 'text', 'link-27');">text</a></tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name" targets="Variable Bio.Entrez.SerialSet.errors=Bio.Entrez.SerialSet-module.html#errors"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-61', 'errors', 'link-61');">errors</a></tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name" targets="Function Martel.Iterator._get_next_text()=Martel.Iterator-module.html#_get_next_text"><a title="Martel.Iterator._get_next_text" class="py-name" href="#" onclick="return doclink('link-62', '_get_next_text', 'link-62');">_get_next_text</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Variable Bio.Affy.CelFile.remainder=Bio.Affy.CelFile-module.html#remainder,Variable Bio.LogisticRegression.remainder=Bio.LogisticRegression-module.html#remainder,Variable Bio.MarkovModel.remainder=Bio.MarkovModel-module.html#remainder,Variable Bio.MaxEntropy.remainder=Bio.MaxEntropy-module.html#remainder,Variable Bio.NaiveBayes.remainder=Bio.NaiveBayes-module.html#remainder,Variable Bio.Statistics.lowess.remainder=Bio.Statistics.lowess-module.html#remainder,Variable Bio.distance.remainder=Bio.distance-module.html#remainder,Variable Bio.kNN.remainder=Bio.kNN-module.html#remainder,Method Martel.RecordReader.CountLines.remainder()=Martel.RecordReader.CountLines-class.html#remainder,Method Martel.RecordReader.EndsWith.remainder()=Martel.RecordReader.EndsWith-class.html#remainder,Method Martel.RecordReader.Everything.remainder()=Martel.RecordReader.Everything-class.html#remainder,Method Martel.RecordReader.Nothing.remainder()=Martel.RecordReader.Nothing-class.html#remainder,Method Martel.RecordReader.RecordReader.remainder()=Martel.RecordReader.RecordReader-class.html#remainder,Method Martel.RecordReader.StartsWith.remainder()=Martel.RecordReader.StartsWith-class.html#remainder,Method Martel.RecordReader.Until.remainder()=Martel.RecordReader.Until-class.html#remainder"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-63', 'remainder', 'link-63');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-64" 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-64', 'text', 'link-27');">text</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-65" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-65', 'errors', 'link-61');">errors</a></tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt id="link-66" class="py-name"><a title="Martel.Iterator.StoreEvents" class="py-name" href="#" onclick="return doclink('link-66', 'StoreEvents', 'link-13');">StoreEvents</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">header_parser</tt><tt class="py-op">.</tt><tt id="link-67" 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-67', 'parseString', 'link-14');">parseString</a></tt><tt class="py-op">(</tt><tt id="link-68" 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-68', 'text', 'link-27');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">events</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="HeaderFooterEventStream._record_next"></a><div id="HeaderFooterEventStream._record_next-def"><a name="L238"></a><tt class="py-lineno">238</tt> <a class="py-toggle" href="#" id="HeaderFooterEventStream._record_next-toggle" onclick="return toggle('HeaderFooterEventStream._record_next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.HeaderFooterEventStream-class.html#_record_next">_record_next</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="HeaderFooterEventStream._record_next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HeaderFooterEventStream._record_next-expanded"><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_record_reader</tt><tt class="py-op">(</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_args</tt><tt class="py-op">,</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-op">{</tt><tt class="py-string">"lookahead"</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-keyword">else</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">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt id="link-69" 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-69', 'text', 'link-27');">text</a></tt><tt class="py-op">,</tt> <tt id="link-70" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-70', 'errors', 'link-61');">errors</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Martel.Iterator._get_next_text" class="py-name" href="#" onclick="return doclink('link-71', '_get_next_text', 'link-62');">_get_next_text</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-72" 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-72', 'text', 'link-27');">text</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-73', 'remainder', 'link-63');">remainder</a></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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-74" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-74', 'errors', 'link-61');">errors</a></tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt id="link-75" class="py-name"><a title="Martel.Iterator.StoreEvents" class="py-name" href="#" onclick="return doclink('link-75', 'StoreEvents', 'link-13');">StoreEvents</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">record_parser</tt><tt class="py-op">.</tt><tt id="link-76" 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-76', 'parseString', 'link-14');">parseString</a></tt><tt class="py-op">(</tt><tt id="link-77" 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-77', 'text', 'link-27');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">events</tt><tt class="py-op">.</tt><tt class="py-name">has_error</tt><tt class="py-op">:</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-comment"># Couldn't parse the record.</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-comment"># perhaps there's a footer here?</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># We'll need to try reading that</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-78', 'remainder', 'link-63');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt id="link-79" 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-79', 'text', 'link-27');">text</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-comment"># If no footer is possible, go on and pass</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># back the error as normal</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">events</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> </tt>
</div><a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="HeaderFooterEventStream._footer_next"></a><div id="HeaderFooterEventStream._footer_next-def"><a name="L273"></a><tt class="py-lineno">273</tt> <a class="py-toggle" href="#" id="HeaderFooterEventStream._footer_next-toggle" onclick="return toggle('HeaderFooterEventStream._footer_next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.HeaderFooterEventStream-class.html#_footer_next">_footer_next</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="HeaderFooterEventStream._footer_next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HeaderFooterEventStream._footer_next-expanded"><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">make_footer_reader</tt><tt class="py-op">(</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_args</tt><tt class="py-op">,</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-op">**</tt><tt class="py-op">{</tt><tt class="py-string">"lookahead"</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt id="link-80" 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-80', 'text', 'link-27');">text</a></tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-81', 'errors', 'link-61');">errors</a></tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="Martel.Iterator._get_next_text" class="py-name" href="#" onclick="return doclink('link-82', '_get_next_text', 'link-62');">_get_next_text</a></tt><tt class="py-op">(</tt><tt class="py-name">reader</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-83', 'remainder', 'link-63');">remainder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-84" 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-84', 'text', 'link-27');">text</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-85" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-85', 'errors', 'link-61');">errors</a></tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="Martel.Iterator.StoreEvents" class="py-name" href="#" onclick="return doclink('link-86', 'StoreEvents', 'link-13');">StoreEvents</a></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 class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</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">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">events</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">self</tt><tt class="py-op">.</tt><tt class="py-name">footer_parser</tt><tt class="py-op">.</tt><tt id="link-87" 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-87', 'parseString', 'link-14');">parseString</a></tt><tt class="py-op">(</tt><tt id="link-88" 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-88', 'text', 'link-27');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">events</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> </tt>
</div></div><a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </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>
<a name="IteratorHeaderFooter"></a><div id="IteratorHeaderFooter-def"><a name="L292"></a><tt class="py-lineno">292</tt> <a class="py-toggle" href="#" id="IteratorHeaderFooter-toggle" onclick="return toggle('IteratorHeaderFooter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.IteratorHeaderFooter-class.html">IteratorHeaderFooter</a><tt class="py-op">:</tt> </tt>
</div><div id="IteratorHeaderFooter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IteratorHeaderFooter-expanded"><a name="IteratorHeaderFooter.__init__"></a><div id="IteratorHeaderFooter.__init__-def"><a name="L293"></a><tt class="py-lineno">293</tt> <a class="py-toggle" href="#" id="IteratorHeaderFooter.__init__-toggle" onclick="return toggle('IteratorHeaderFooter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorHeaderFooter-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-param">header_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_header_reader</tt><tt class="py-op">,</tt> <tt class="py-param">header_args</tt><tt class="py-op">,</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-param">record_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_record_reader</tt><tt class="py-op">,</tt> <tt class="py-param">record_args</tt><tt class="py-op">,</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-param">footer_parser</tt><tt class="py-op">,</tt> <tt class="py-param">make_footer_reader</tt><tt class="py-op">,</tt> <tt class="py-param">footer_args</tt><tt class="py-op">,</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-param">marker_tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorHeaderFooter.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorHeaderFooter.__init__-expanded"><a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">header_parser</tt><tt class="py-op">,</tt> <tt class="py-name">make_header_reader</tt><tt class="py-op">,</tt> <tt class="py-name">header_args</tt><tt class="py-op">,</tt> \ </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-name">record_parser</tt><tt class="py-op">,</tt> <tt class="py-name">make_record_reader</tt><tt class="py-op">,</tt> <tt class="py-name">record_args</tt><tt class="py-op">,</tt> \ </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">footer_parser</tt><tt class="py-op">,</tt> <tt class="py-name">make_footer_reader</tt><tt class="py-op">,</tt> <tt class="py-name">footer_args</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">marker_tag</tt> </tt>
</div><a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="IteratorHeaderFooter.iterateString"></a><div id="IteratorHeaderFooter.iterateString-def"><a name="L304"></a><tt class="py-lineno">304</tt> <a class="py-toggle" href="#" id="IteratorHeaderFooter.iterateString-toggle" onclick="return toggle('IteratorHeaderFooter.iterateString');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorHeaderFooter-class.html#iterateString">iterateString</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorHeaderFooter.iterateString-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorHeaderFooter.iterateString-expanded"><a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-89', 'iterateFile', 'link-26');">iterateFile</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-15');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="IteratorHeaderFooter.iterateFile"></a><div id="IteratorHeaderFooter.iterateFile-def"><a name="L307"></a><tt class="py-lineno">307</tt> <a class="py-toggle" href="#" id="IteratorHeaderFooter.iterateFile-toggle" onclick="return toggle('IteratorHeaderFooter.iterateFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorHeaderFooter-class.html#iterateFile">iterateFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fileobj</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorHeaderFooter.iterateFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorHeaderFooter.iterateFile-expanded"><a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">fileobj</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-91" class="py-name"><a title="Martel.Iterator.Iterate" class="py-name" href="#" onclick="return doclink('link-91', 'Iterate', 'link-16');">Iterate</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-92" class="py-name" targets="Class Martel.Iterator.HeaderFooterEventStream=Martel.Iterator.HeaderFooterEventStream-class.html"><a title="Martel.Iterator.HeaderFooterEventStream" class="py-name" href="#" onclick="return doclink('link-92', 'HeaderFooterEventStream', 'link-92');">HeaderFooterEventStream</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">marker_tag</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div><a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="IteratorHeaderFooter.iterate"></a><div id="IteratorHeaderFooter.iterate-def"><a name="L312"></a><tt class="py-lineno">312</tt> <a class="py-toggle" href="#" id="IteratorHeaderFooter.iterate-toggle" onclick="return toggle('IteratorHeaderFooter.iterate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.IteratorHeaderFooter-class.html#iterate">iterate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IteratorHeaderFooter.iterate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IteratorHeaderFooter.iterate-expanded"><a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-docstring">"""parse using the URL or file handle"""</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt id="link-93" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-93', 'source', 'link-21');">source</a></tt> <tt class="py-op">=</tt> <tt class="py-name">saxutils</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-94', 'prepare_input_source', 'link-22');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-95', 'source', 'link-21');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-96', 'source', 'link-21');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-97" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-97', 'source', 'link-21');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Martel.IterParser.IterHeaderFooter.iterateFile
Martel.IterParser.IterRecords.iterateFile
Martel.Iterator.Iterator.iterateFile
Martel.Iterator.IteratorHeaderFooter.iterateFile
Martel.Iterator.IteratorRecords.iterateFile" class="py-name" href="#" onclick="return doclink('link-98', 'iterateFile', 'link-26');">iterateFile</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> </tt>
<a name="Iterate"></a><div id="Iterate-def"><a name="L319"></a><tt class="py-lineno">319</tt> <a class="py-toggle" href="#" id="Iterate-toggle" onclick="return toggle('Iterate');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.Iterator.Iterate-class.html">Iterate</a><tt class="py-op">:</tt> </tt>
</div><div id="Iterate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterate-expanded"><a name="Iterate.__init__"></a><div id="Iterate.__init__-def"><a name="L320"></a><tt class="py-lineno">320</tt> <a class="py-toggle" href="#" id="Iterate.__init__-toggle" onclick="return toggle('Iterate.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterate-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">parent</tt><tt class="py-op">,</tt> <tt class="py-param">event_stream</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterate.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterate.__init__-expanded"><a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cont_handler</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-99" class="py-name" targets="Module Martel.LAX=Martel.LAX-module.html,Class Martel.LAX.LAX=Martel.LAX.LAX-class.html"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-99', 'LAX', 'link-99');">LAX</a></tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">cont_handler</tt> <tt class="py-op">=</tt> <tt id="link-100" class="py-name"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-100', 'LAX', 'link-99');">LAX</a></tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Martel.LAX
Martel.LAX.LAX" class="py-name" href="#" onclick="return doclink('link-101', 'LAX', 'link-99');">LAX</a></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">self</tt><tt class="py-op">.</tt><tt class="py-name">event_stream</tt> <tt class="py-op">=</tt> <tt class="py-name">event_stream</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-102', 'tag', 'link-11');">tag</a></tt> <tt class="py-op">=</tt> <tt id="link-103" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-103', 'tag', 'link-11');">tag</a></tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">cont_handler</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_n</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt>
<a name="Iterate.next"></a><div id="Iterate.next-def"><a name="L334"></a><tt class="py-lineno">334</tt> <a class="py-toggle" href="#" id="Iterate.next-toggle" onclick="return toggle('Iterate.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterate-class.html#next">next</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="Iterate.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterate.next-expanded"><a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">events</tt><tt class="py-op">:</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">event_stream</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-104', 'next', 'link-28');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">events</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">events</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt id="link-105" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-105', 'i', 'link-105');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-comment"># Look for the start of the next record</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-106" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-106', 'i', 'link-105');">i</a></tt> <tt class="py-op">==</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">new_events</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">event_stream</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-107', 'next', 'link-28');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">new_events</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">events</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-108', 'extend', 'link-108');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">new_events</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">events</tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt id="link-109" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-109', 'name', 'link-109');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">events</tt><tt class="py-op">[</tt><tt id="link-110" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-110', 'i', 'link-105');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-111" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-111', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"error"</tt> <tt class="py-keyword">or</tt> <tt id="link-112" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-112', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"fatalError"</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-comment"># at this level the error is unrecoverable</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-113" 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-113', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-114" 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-114', 'ParserPositionException', 'link-114');">ParserPositionException</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">exc</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-115" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-115', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"startElement"</tt> <tt class="py-keyword">and</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-116', 'tag', 'link-11');">tag</a></tt><tt class="py-op">:</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cont_handler</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">cont_handler</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name" targets="Method Bio.EUtils.POM.ObjectParserHandler.startDocument()=Bio.EUtils.POM.ObjectParserHandler-class.html#startDocument,Method Bio.LocusLink._RecordConsumer.startDocument()=Bio.LocusLink._RecordConsumer-class.html#startDocument,Method Bio.Mindy.XPath.GrabXPathNodes.startDocument()=Bio.Mindy.XPath.GrabXPathNodes-class.html#startDocument,Method Bio.Saf._RecordConsumer.startDocument()=Bio.Saf._RecordConsumer-class.html#startDocument,Method Bio.StdHandler.ConvertHandler.startDocument()=Bio.StdHandler.ConvertHandler-class.html#startDocument,Method Martel.Dispatch.Dispatcher.startDocument()=Martel.Dispatch.Dispatcher-class.html#startDocument,Method Martel.Iterator.StoreEvents.startDocument()=Martel.Iterator.StoreEvents-class.html#startDocument,Method Martel.LAX.LAX.startDocument()=Martel.LAX.LAX-class.html#startDocument,Method Martel.test.support.CheckGood.startDocument()=Martel.test.support.CheckGood-class.html#startDocument,Method Martel.test.support.Dump.startDocument()=Martel.test.support.Dump-class.html#startDocument,Method Martel.test.test_attrs.GrabElements.startDocument()=Martel.test.test_attrs.GrabElements-class.html#startDocument,Method Martel.test.test_macros.Capture.startDocument()=Martel.test.test_macros.Capture-class.html#startDocument,Method Martel.test.test_optimize.GetErrorPos.startDocument()=Martel.test.test_optimize.GetErrorPos-class.html#startDocument"><a title="Bio.EUtils.POM.ObjectParserHandler.startDocument
Bio.LocusLink._RecordConsumer.startDocument
Bio.Mindy.XPath.GrabXPathNodes.startDocument
Bio.Saf._RecordConsumer.startDocument
Bio.StdHandler.ConvertHandler.startDocument
Martel.Dispatch.Dispatcher.startDocument
Martel.Iterator.StoreEvents.startDocument
Martel.LAX.LAX.startDocument
Martel.test.support.CheckGood.startDocument
Martel.test.support.Dump.startDocument
Martel.test.test_attrs.GrabElements.startDocument
Martel.test.test_macros.Capture.startDocument
Martel.test.test_optimize.GetErrorPos.startDocument" class="py-name" href="#" onclick="return doclink('link-117', 'startDocument', 'link-117');">startDocument</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-118" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-118', 'i', 'link-105');">i</a></tt> <tt class="py-op"><</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt id="link-119" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-119', 'name', 'link-109');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">events</tt><tt class="py-op">[</tt><tt id="link-120" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-120', 'i', 'link-105');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-121" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-121', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"characters"</tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-comment"># This is the most common case.</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Recall, args is not a tuple</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cont_handler</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Blast.NCBIXML._XMLparser.characters
Bio.EUtils.POM.ObjectParserHandler.characters
Bio.Entrez.Parser.DataHandler.characters
Bio.Mindy.XPath.GrabXPathNodes.characters
Bio.ParserSupport.EventGenerator.characters
Martel.Dispatch.Dispatcher.characters
Martel.LAX.LAX.characters
Martel.test.support.Dump.characters
Martel.test.test_delimiter.CatchFields.characters" class="py-name" href="#" onclick="return doclink('link-122', 'characters', 'link-1');">characters</a></tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> <tt class="py-op">+=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt id="link-123" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-123', 'i', 'link-105');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-124" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-124', 'i', 'link-105');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-125" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-125', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"error"</tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-comment"># in theory this is recoverable, so scan forward</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># until there's an endElement</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">exc</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-126" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-126', 'i', 'link-105');">i</a></tt> <tt class="py-op"><</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt id="link-127" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-127', 'name', 'link-109');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">events</tt><tt class="py-op">[</tt><tt id="link-128" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-128', 'i', 'link-105');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-129" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-129', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"endElement"</tt> <tt class="py-keyword">and</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-130', 'tag', 'link-11');">tag</a></tt><tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-131" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-131', 'i', 'link-105');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">exc</tt><tt class="py-op">,</tt> <tt id="link-132" 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-132', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-133', 'ParserPositionException', 'link-114');">ParserPositionException</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">exc</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">exc</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-134" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-134', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"characters"</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> <tt class="py-op">+=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt id="link-135" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-135', 'i', 'link-105');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-136', 'i', 'link-105');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-comment"># no end found, so not recoverable</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">exc</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-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-138', 'ParserPositionException', 'link-114');">ParserPositionException</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-name">exc</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">exc</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-139" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-139', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"fatalError"</tt><tt class="py-op">:</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-comment"># not recoverable</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-140" 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-140', 'Parser', 'link-0');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Martel.Parser.ParserPositionException" class="py-name" href="#" onclick="return doclink('link-141', 'ParserPositionException', 'link-114');">ParserPositionException</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-name">exc</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">cont_handler</tt><tt class="py-op">,</tt> <tt id="link-142" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-142', 'name', 'link-109');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-143" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-143', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"endElement"</tt> <tt class="py-keyword">and</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-144', 'tag', 'link-11');">tag</a></tt><tt class="py-op">:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt id="link-145" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-145', 'i', 'link-105');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-name">cont_handler</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name" targets="Method Bio.EUtils.POM.ObjectParserHandler.endDocument()=Bio.EUtils.POM.ObjectParserHandler-class.html#endDocument,Method Bio.ParserSupport.EventGenerator.endDocument()=Bio.ParserSupport.EventGenerator-class.html#endDocument,Method Martel.Dispatch.Dispatcher.endDocument()=Martel.Dispatch.Dispatcher-class.html#endDocument,Method Martel.Iterator.StoreEvents.endDocument()=Martel.Iterator.StoreEvents-class.html#endDocument,Method Martel.LAX.LAX.endDocument()=Martel.LAX.LAX-class.html#endDocument,Method Martel.test.support.CheckGood.endDocument()=Martel.test.support.CheckGood-class.html#endDocument,Method Martel.test.support.Dump.endDocument()=Martel.test.support.Dump-class.html#endDocument"><a title="Bio.EUtils.POM.ObjectParserHandler.endDocument
Bio.ParserSupport.EventGenerator.endDocument
Martel.Dispatch.Dispatcher.endDocument
Martel.Iterator.StoreEvents.endDocument
Martel.LAX.LAX.endDocument
Martel.test.support.CheckGood.endDocument
Martel.test.support.Dump.endDocument" class="py-name" href="#" onclick="return doclink('link-146', 'endDocument', 'link-146');">endDocument</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_n</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_n</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cont_handler</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt id="link-147" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-147', 'i', 'link-105');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-148" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-148', 'i', 'link-105');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-comment"># Got here without an endElement? Not supposed to happen!</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"no endElement(%s) and no errors?"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-149', 'tag', 'link-11');">tag</a></tt><tt class="py-op">)</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-150" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-150', 'name', 'link-109');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"characters"</tt><tt class="py-op">:</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_position</tt> <tt class="py-op">+=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-151', 'i', 'link-105');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-152" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-152', 'i', 'link-105');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-comment"># Went through the document and no more records were found</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">events</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> </tt>
<a name="Iterate.__getitem__"></a><div id="Iterate.__getitem__-def"><a name="L426"></a><tt class="py-lineno">426</tt> <a class="py-toggle" href="#" id="Iterate.__getitem__-toggle" onclick="return toggle('Iterate.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterate-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Iterate.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterate.__getitem__-expanded"><a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">n</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_n</tt><tt class="py-op">,</tt> <tt class="py-string">"forward iteration only"</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt id="link-153" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-153', 'x', 'link-9');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-154', 'next', 'link-28');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-155" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-155', 'x', 'link-9');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-156" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-156', 'x', 'link-9');">x</a></tt> </tt>
</div><a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> </tt>
<a name="Iterate.__iter__"></a><div id="Iterate.__iter__-def"><a name="L433"></a><tt class="py-lineno">433</tt> <a class="py-toggle" href="#" id="Iterate.__iter__-toggle" onclick="return toggle('Iterate.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.Iterator.Iterate-class.html#__iter__">__iter__</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="Iterate.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterate.__iter__-expanded"><a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-157', 'next', 'link-28');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> </tt><script type="text/javascript">
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