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        <a href="Martel-module.html">Package&nbsp;Martel</a> ::
        Module&nbsp;LAX
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<h1 class="epydoc">Source Code for <a href="Martel.LAX-module.html">Module Martel.LAX</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""A simple way to read lists of fields from flat XML records.</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">Many XML formats are very simple: all the fields are needed, there is</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">no tree hierarchy, all the text inside of the tags is used, and the</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">text is short (it can easily fit inside of memory).  SAX is pretty</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-docstring">good for this but it's still somewhat complicated to use.  DOM is</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-docstring">designed to handle tree structures so is a bit too much for a simple</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring">flat data structure.</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring">This module implements a new, simpler API, which I'll call LAX.  It</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">only works well when the elements are small and non-hierarchical.  LAX</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">has three callbacks.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring">  start() -- the first method called</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">  element(tag, attrs, text) -- called once for each element, after the</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">    element has been fully read.  (Ie, called when the endElement</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">    would be called.)  The 'tag' is the element name, the attrs is the</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">    attribute object that would be used in a startElement, and the</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring">    text is all the text between the two tags.  The text is the</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">    concatenation of all the characters() calls.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">  end() -- the last method called (unless there was an error)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">LAX.LAX is an content handler which converts the SAX events to</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring">LAX events.  Here is an example use:</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; from Martel import Word, Whitespace, Group, Integer, Rep1, AnyEol</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; format = Rep1(Group("line", Word("name") + Whitespace() +</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">  ...                             Integer("age")) + AnyEol())</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; parser = format.make_parser()</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt;</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; from Martel import LAX</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; class PrintFields(LAX.LAX):</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring">  ...     def element(self, tag, attrs, text):</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-docstring">  ...         print tag, "has", repr(text)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-docstring">  ...</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; parser.setContentHandler(PrintFields())</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; text = "Maggie 3\nPorter 1\n"</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; parser.parseString(text)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-docstring">  name has 'Maggie'</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">  age has '3'</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring">  line has 'Maggie 3'</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">  name has 'Porter'</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">  age has '1'</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">  line has 'Porter 1'</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt;</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">Callbacks take some getting used to.  Many people prefer an iterative</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">solution which returns all of the fields of a given record at one</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">time.  The default implementation of LAX.LAX helps this case.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-docstring">The 'start' method initializes a local variable named 'groups', which</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">is dictionary.  When the 'element' method is called, the information</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring">is added to groups; the key is the element name and the value is the</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-docstring">list of text strings.  It's a list because the same field name may</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-docstring">occur multiple times.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt class="py-docstring">If you need the element attributes as well as the name, use the</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-docstring">LAX.LAXAttrs class, which stores a list of 2-ples (text, attrs)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-docstring">instead of just the text.</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring">For examples:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; iterator = format.make_iterator("line")</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; for record in iterator.iterateString(text, LAX.LAX()):</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">  ...     print record.groups["name"][0], "is", record.groups["age"][0]</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">  ...</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">  Maggie is 3</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">  Porter is 1</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt;</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">If you only want a few fields, you can pass the list to constructor,</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">as in:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt; lax = LAX.LAX(["name", "sequence"])</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring">  &gt;&gt;&gt;</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> <tt class="py-keyword">import</tt> <tt class="py-name">handler</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-comment"># Used to simplify the check if </tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="_IsIn"></a><div id="_IsIn-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="_IsIn-toggle" onclick="return toggle('_IsIn');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.LAX._IsIn-class.html">_IsIn</a><tt class="py-op">:</tt> </tt>
</div><div id="_IsIn-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_IsIn-expanded"><a name="_IsIn.__contains__"></a><div id="_IsIn.__contains__-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="_IsIn.__contains__-toggle" onclick="return toggle('_IsIn.__contains__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX._IsIn-class.html#__contains__">__contains__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_IsIn.__contains__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_IsIn.__contains__-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div></div><a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"> </tt>
<a name="LAX"></a><div id="LAX-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="LAX-toggle" onclick="return toggle('LAX');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html">LAX</a><tt class="py-op">(</tt><tt class="py-base-class">handler</tt><tt class="py-op">.</tt><tt class="py-base-class">ContentHandler</tt><tt class="py-op">,</tt> <tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAX-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="LAX-expanded"><a name="LAX.__init__"></a><div id="LAX.__init__-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="LAX.__init__-toggle" onclick="return toggle('LAX.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-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">fields</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="LAX.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.__init__-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">        <tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">ContentHandler</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method 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Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-0', '__init__', 'link-0');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">        <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
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<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">(</tt><tt id="link-4" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-4', 'name', 'link-3');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"> </tt>
<a name="LAX.uses_tags"></a><div id="LAX.uses_tags-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="LAX.uses_tags-toggle" onclick="return toggle('LAX.uses_tags');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html#uses_tags">uses_tags</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="LAX.uses_tags-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.uses_tags-expanded"><a name="L104"></a><tt class="py-lineno">104</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">self</tt><tt class="py-op">.</tt><tt class="py-name">__fields</tt><tt class="py-op">,</tt> <tt id="link-5" class="py-name"><a title="Martel.LAX._IsIn" class="py-name" href="#" onclick="return doclink('link-5', '_IsIn', 'link-2');">_IsIn</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__fields</tt> </tt>
</div><a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">     </tt>
<a name="LAX.startDocument"></a><div id="LAX.startDocument-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="LAX.startDocument-toggle" onclick="return toggle('LAX.startDocument');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-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="LAX.startDocument-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.startDocument-expanded"><a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__capture</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__expect</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-name">self</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="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-6', 'start', 'link-6');">start</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">         </tt>
<a name="LAX.start"></a><div id="LAX.start-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="LAX.start-toggle" onclick="return toggle('LAX.start');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html#start">start</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="LAX.start-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.start-expanded"><a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Crystal.Crystal.clear()=Bio.Crystal.Crystal-class.html#clear,Method Bio.GenBank.NCBIDictionary.clear()=Bio.GenBank.NCBIDictionary-class.html#clear,Method Bio.Index._InMemoryIndex.clear()=Bio.Index._InMemoryIndex-class.html#clear,Method Bio.Prosite.ExPASyDictionary.clear()=Bio.Prosite.ExPASyDictionary-class.html#clear,Method Bio.Prosite.Prodoc.ExPASyDictionary.clear()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#clear,Method Bio.PubMed.Dictionary.clear()=Bio.PubMed.Dictionary-class.html#clear,Method Bio.SwissProt.SProt.ExPASyDictionary.clear()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#clear"><a title="Bio.Crystal.Crystal.clear
Bio.GenBank.NCBIDictionary.clear
Bio.Index._InMemoryIndex.clear
Bio.Prosite.ExPASyDictionary.clear
Bio.Prosite.Prodoc.ExPASyDictionary.clear
Bio.PubMed.Dictionary.clear
Bio.SwissProt.SProt.ExPASyDictionary.clear" class="py-name" href="#" onclick="return doclink('link-7', 'clear', 'link-7');">clear</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"> </tt>
<a name="LAX.startElement"></a><div id="LAX.startElement-def"><a name="L118"></a><tt class="py-lineno">118</tt> <a class="py-toggle" href="#" id="LAX.startElement-toggle" onclick="return toggle('LAX.startElement');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html#startElement">startElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAX.startElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.startElement-expanded"><a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-8" 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-8', 'tag', 'link-8');">tag</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__fields</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__capture</tt><tt class="py-op">.</tt><tt id="link-9" 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-9', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-10', 'tag', 'link-8');">tag</a></tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name" targets="Variable Martel.Time.attrs=Martel.Time-module.html#attrs"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-11', 'attrs', 'link-11');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__pos</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__expect</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-8');">tag</a></tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">             </tt>
<a name="LAX.characters"></a><div id="LAX.characters-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="LAX.characters-toggle" onclick="return toggle('LAX.characters');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html#characters">characters</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAX.characters-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.characters-expanded"><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">__pos</tt> <tt class="py-op">+=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-13" 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-13', 's', 'link-13');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">term</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__capture</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">term</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-15', 's', 'link-13');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">             </tt>
<a name="LAX.endElement"></a><div id="LAX.endElement-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="LAX.endElement-toggle" onclick="return toggle('LAX.endElement');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html#endElement">endElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAX.endElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.endElement-expanded"><a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-16" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-16', 'tag', 'link-8');">tag</a></tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__expect</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">            <tt class="py-name">cap</tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-17', 'attrs', 'link-11');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-name">text_items</tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-18', 'start', 'link-6');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__capture</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-19', 'pop', 'link-19');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Martel.LAX.LAX.element()=Martel.LAX.LAX-class.html#element,Method Martel.LAX.LAXAttrs.element()=Martel.LAX.LAXAttrs-class.html#element,Method Martel.LAX.LAXPositions.element()=Martel.LAX.LAXPositions-class.html#element"><a title="Martel.LAX.LAX.element
Martel.LAX.LAXAttrs.element
Martel.LAX.LAXPositions.element" class="py-name" href="#" onclick="return doclink('link-20', 'element', 'link-20');">element</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-21', 'tag', 'link-8');">tag</a></tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-22', 'attrs', 'link-11');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">text_items</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">                         <tt id="link-23" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-23', 'start', 'link-6');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__pos</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</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">__capture</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__expect</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__capture</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__expect</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"> </tt>
<a name="LAX.element"></a><div id="LAX.element-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="LAX.element-toggle" onclick="return toggle('LAX.element');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html#element">element</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">startpos</tt><tt class="py-op">,</tt> <tt class="py-param">endpos</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAX.element-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.element-expanded"><a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Crystal.Crystal.setdefault()=Bio.Crystal.Crystal-class.html#setdefault"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-24', 'setdefault', 'link-24');">setdefault</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-25', 'tag', 'link-8');">tag</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><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>
</div><a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">             </tt>
<a name="LAX.endDocument"></a><div id="LAX.endDocument-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="LAX.endDocument-toggle" onclick="return toggle('LAX.endDocument');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-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="LAX.endDocument-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.endDocument-expanded"><a name="L142"></a><tt class="py-lineno">142</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">__capture</tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">            <tt class="py-name">missing</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">term</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__capture</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">                <tt class="py-name">missing</tt><tt class="py-op">.</tt><tt id="link-28" 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-28', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">term</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Looking for endElements for %s"</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">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">missing</tt><tt class="py-op">,</tt> <tt class="py-string">","</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-29', 'end', 'link-29');">end</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line"> </tt>
<a name="LAX.end"></a><div id="LAX.end-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="LAX.end-toggle" onclick="return toggle('LAX.end');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAX-class.html#end">end</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="LAX.end-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAX.end-expanded"><a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-comment"># Also stores the attributes</tt> </tt>
<a name="LAXAttrs"></a><div id="LAXAttrs-def"><a name="L155"></a><tt class="py-lineno">155</tt> <a class="py-toggle" href="#" id="LAXAttrs-toggle" onclick="return toggle('LAXAttrs');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.LAX.LAXAttrs-class.html">LAXAttrs</a><tt class="py-op">(</tt><tt class="py-base-class">LAX</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAXAttrs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="LAXAttrs-expanded"><a name="LAXAttrs.element"></a><div id="LAXAttrs.element-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="LAXAttrs.element-toggle" onclick="return toggle('LAXAttrs.element');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAXAttrs-class.html#element">element</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">startpos</tt><tt class="py-op">,</tt> <tt class="py-param">endpos</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAXAttrs.element-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAXAttrs.element-expanded"><a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-30', 'setdefault', 'link-24');">setdefault</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-31', 'tag', 'link-8');">tag</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt id="link-33" 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-33', 'text', 'link-27');">text</a></tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-34', 'attrs', 'link-11');">attrs</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div></div><a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line"> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line"><tt class="py-comment"># Stores attributes and positions</tt> </tt>
<a name="ElementInfo"></a><div id="ElementInfo-def"><a name="L160"></a><tt class="py-lineno">160</tt> <a class="py-toggle" href="#" id="ElementInfo-toggle" onclick="return toggle('ElementInfo');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.LAX.ElementInfo-class.html">ElementInfo</a><tt class="py-op">:</tt> </tt>
</div><div id="ElementInfo-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ElementInfo-expanded"><a name="ElementInfo.__init__"></a><div id="ElementInfo.__init__-def"><a name="L161"></a><tt class="py-lineno">161</tt> <a class="py-toggle" href="#" id="ElementInfo.__init__-toggle" onclick="return toggle('ElementInfo.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.ElementInfo-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">text</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">,</tt> <tt class="py-param">startpos</tt><tt class="py-op">,</tt> <tt class="py-param">endpos</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ElementInfo.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ElementInfo.__init__-expanded"><a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" 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-35', 'text', 'link-27');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-36" 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-36', 'text', 'link-27');">text</a></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-37', 'attrs', 'link-11');">attrs</a></tt> <tt class="py-op">=</tt> <tt id="link-38" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-38', 'attrs', 'link-11');">attrs</a></tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">startpos</tt> <tt class="py-op">=</tt> <tt class="py-name">startpos</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">endpos</tt> <tt class="py-op">=</tt> <tt class="py-name">endpos</tt> </tt>
</div></div><a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"> </tt>
<a name="LAXPositions"></a><div id="LAXPositions-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="LAXPositions-toggle" onclick="return toggle('LAXPositions');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.LAX.LAXPositions-class.html">LAXPositions</a><tt class="py-op">(</tt><tt class="py-base-class">LAXAttrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAXPositions-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="LAXPositions-expanded"><a name="LAXPositions.element"></a><div id="LAXPositions.element-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="LAXPositions.element-toggle" onclick="return toggle('LAXPositions.element');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.LAX.LAXPositions-class.html#element">element</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">startpos</tt><tt class="py-op">,</tt> <tt class="py-param">endpos</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="LAXPositions.element-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="LAXPositions.element-expanded"><a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-39', 'setdefault', 'link-24');">setdefault</a></tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-40', 'tag', 'link-8');">tag</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-41" 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-41', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">            <tt id="link-42" class="py-name" targets="Class Martel.LAX.ElementInfo=Martel.LAX.ElementInfo-class.html"><a title="Martel.LAX.ElementInfo" class="py-name" href="#" onclick="return doclink('link-42', 'ElementInfo', 'link-42');">ElementInfo</a></tt><tt class="py-op">(</tt><tt id="link-43" 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-43', 'text', 'link-27');">text</a></tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-44', 'attrs', 'link-11');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-name">startpos</tt><tt class="py-op">,</tt> <tt class="py-name">endpos</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div></div><a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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