<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Entrez.Parser</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Entrez-module.html">Package Entrez</a> :: Module Parser </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Entrez.Parser-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.Entrez.Parser-module.html">Module Bio.Entrez.Parser</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 2008 by Michiel de Hoon. All rights reserved.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Parser for XML results returned by NCBI's Entrez Utilities. This</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">parser is used by the read() function in Bio.Entrez, and is not intended</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">be used directly.</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> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"># The question is how to represent an XML file as Python objects. Some</tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># XML files returned by NCBI look like lists, others look like dictionaries,</tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and others look like a mix of lists and dictionaries.</tt> </tt> <a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># My approach is to classify each possible element in the XML as a plain</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># string, an integer, a list, a dictionary, or a structure. The latter is a</tt> </tt> <a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># dictionary where the same key can occur multiple times; in Python, it is</tt> </tt> <a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># represented as a dictionary where that key occurs once, pointing to a list</tt> </tt> <a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># of values found in the XML file.</tt> </tt> <a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The parser then goes through the XML and creates the appropriate Python</tt> </tt> <a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># object for each element. The different levels encountered in the XML are</tt> </tt> <a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># preserved on the Python side. So a subelement of a subelement of an element</tt> </tt> <a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># is a value in a dictionary that is stored in a list which is a value in</tt> </tt> <a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># some other dictionary (or a value in a list which itself belongs to a list</tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># which is a value in a dictionary, and so on). Attributes encountered in </tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># the XML are stored as a dictionary in a member .attributes of each element,</tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and the tag name is saved in a member .tag.</tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># To decide which kind of Python object corresponds to each element in the</tt> </tt> <a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># XML, the parser analyzes the DTD referred at the top of (almost) every</tt> </tt> <a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># XML file returned by the Entrez Utilities. This is preferred over a hand-</tt> </tt> <a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># written solution, since the number of DTDs is rather large and their</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># contents may change over time. About half the code in this parser deals</tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># wih parsing the DTD, and the other half with the XML itself.</tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># One type of query (EFetch on the Journals database) returns an XML without</tt> </tt> <a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># an associated DTD. These files are handled using the hand-written</tt> </tt> <a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># SerialSet.py</tt> </tt> <a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> </tt> <a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt> </tt> <a name="L43"></a><tt class="py-lineno"> 43</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">parsers</tt> <tt class="py-keyword">import</tt> <tt class="py-name">expat</tt> </tt> <a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt> <a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"># The following four classes are used to add a member .attributes to integers,</tt> </tt> <a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># strings, lists, and dictionaries, respectively.</tt> </tt> <a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="IntegerElement"></a><div id="IntegerElement-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="IntegerElement-toggle" onclick="return toggle('IntegerElement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Entrez.Parser.IntegerElement-class.html">IntegerElement</a><tt class="py-op">(</tt><tt class="py-base-class">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">pass</tt> </tt> </div><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt> <a name="StringElement"></a><div id="StringElement-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="StringElement-toggle" onclick="return toggle('StringElement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Entrez.Parser.StringElement-class.html">StringElement</a><tt class="py-op">(</tt><tt class="py-base-class">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">pass</tt> </tt> </div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt> <a name="UnicodeElement"></a><div id="UnicodeElement-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="UnicodeElement-toggle" onclick="return toggle('UnicodeElement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Entrez.Parser.UnicodeElement-class.html">UnicodeElement</a><tt class="py-op">(</tt><tt class="py-base-class">unicode</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">pass</tt> </tt> </div><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt> <a name="ListElement"></a><div id="ListElement-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="ListElement-toggle" onclick="return toggle('ListElement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Entrez.Parser.ListElement-class.html">ListElement</a><tt class="py-op">(</tt><tt class="py-base-class">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">pass</tt> </tt> </div><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt> <a name="DictionaryElement"></a><div id="DictionaryElement-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="DictionaryElement-toggle" onclick="return toggle('DictionaryElement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DictionaryElement-class.html">DictionaryElement</a><tt class="py-op">(</tt><tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">pass</tt> </tt> </div><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-comment"># A StructureElement is like a dictionary, but some of its keys can have</tt> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># multiple values associated with it. These values are stored in a list</tt> </tt> <a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># under each key.</tt> </tt> <a name="StructureElement"></a><div id="StructureElement-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="StructureElement-toggle" onclick="return toggle('StructureElement');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Entrez.Parser.StructureElement-class.html">StructureElement</a><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="StructureElement-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StructureElement-expanded"><a name="StructureElement.__init__"></a><div id="StructureElement.__init__-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" 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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="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-1" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-1', 'key', 'link-1');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-2" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-2', 'keys', 'link-2');">keys</a></tt><tt class="py-op">:</tt> </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Chain.__setitem__()=Bio.Crystal.Chain-class.html#__setitem__,Method Bio.Crystal.Crystal.__setitem__()=Bio.Crystal.Crystal-class.html#__setitem__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__setitem__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__setitem__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__setitem__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__setitem__,Method Bio.EUtils.POM.ElementNode.__setitem__()=Bio.EUtils.POM.ElementNode-class.html#__setitem__,Method Bio.Entrez.Parser.StructureElement.__setitem__()=Bio.Entrez.Parser.StructureElement-class.html#__setitem__,Method Bio.GenBank.NCBIDictionary.__setitem__()=Bio.GenBank.NCBIDictionary-class.html#__setitem__,Method Bio.Index._InMemoryIndex.__setitem__()=Bio.Index._InMemoryIndex-class.html#__setitem__,Method Bio.PDB.Entity.DisorderedEntityWrapper.__setitem__()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__setitem__,Method Bio.PDB.Vector'.Vector.__setitem__()=Bio.PDB.Vector%27.Vector-class.html#__setitem__,Method Bio.Prosite.ExPASyDictionary.__setitem__()=Bio.Prosite.ExPASyDictionary-class.html#__setitem__,Method Bio.Prosite.Prodoc.ExPASyDictionary.__setitem__()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__setitem__,Method Bio.PubMed.Dictionary.__setitem__()=Bio.PubMed.Dictionary-class.html#__setitem__,Method Bio.Seq.MutableSeq.__setitem__()=Bio.Seq.MutableSeq-class.html#__setitem__,Method Bio.SwissProt.SProt.ExPASyDictionary.__setitem__()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#__setitem__,Method Martel.msre_parse.SubPattern.__setitem__()=Martel.msre_parse.SubPattern-class.html#__setitem__"><a title="Bio.Crystal.Chain.__setitem__ Bio.Crystal.Crystal.__setitem__ Bio.EUtils.MultiDict.OrderedMultiDict.__setitem__ Bio.EUtils.MultiDict.UnorderedMultiDict.__setitem__ Bio.EUtils.POM.ElementNode.__setitem__ Bio.Entrez.Parser.StructureElement.__setitem__ Bio.GenBank.NCBIDictionary.__setitem__ Bio.Index._InMemoryIndex.__setitem__ Bio.PDB.Entity.DisorderedEntityWrapper.__setitem__ Bio.PDB.Vector'.Vector.__setitem__ Bio.Prosite.ExPASyDictionary.__setitem__ Bio.Prosite.Prodoc.ExPASyDictionary.__setitem__ Bio.PubMed.Dictionary.__setitem__ Bio.Seq.MutableSeq.__setitem__ Bio.SwissProt.SProt.ExPASyDictionary.__setitem__ Martel.msre_parse.SubPattern.__setitem__" class="py-name" href="#" onclick="return doclink('link-3', '__setitem__', 'link-3');">__setitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-4', 'key', 'link-1');">key</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">listkeys</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-5', 'keys', 'link-2');">keys</a></tt> </tt> </div><a name="StructureElement.__setitem__"></a><div id="StructureElement.__setitem__-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="StructureElement.__setitem__-toggle" onclick="return toggle('StructureElement.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.StructureElement-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="StructureElement.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureElement.__setitem__-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-6" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-6', 'key', 'link-1');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">listkeys</tt><tt class="py-op">:</tt> </tt> <a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-7" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-7', 'key', 'link-1');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-8" 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-8', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-9', 'value', 'link-9');">value</a></tt><tt class="py-op">)</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Crystal.Chain.__setitem__ Bio.Crystal.Crystal.__setitem__ Bio.EUtils.MultiDict.OrderedMultiDict.__setitem__ Bio.EUtils.MultiDict.UnorderedMultiDict.__setitem__ Bio.EUtils.POM.ElementNode.__setitem__ Bio.Entrez.Parser.StructureElement.__setitem__ Bio.GenBank.NCBIDictionary.__setitem__ Bio.Index._InMemoryIndex.__setitem__ Bio.PDB.Entity.DisorderedEntityWrapper.__setitem__ Bio.PDB.Vector'.Vector.__setitem__ Bio.Prosite.ExPASyDictionary.__setitem__ Bio.Prosite.Prodoc.ExPASyDictionary.__setitem__ Bio.PubMed.Dictionary.__setitem__ Bio.Seq.MutableSeq.__setitem__ Bio.SwissProt.SProt.ExPASyDictionary.__setitem__ Martel.msre_parse.SubPattern.__setitem__" class="py-name" href="#" onclick="return doclink('link-10', '__setitem__', 'link-3');">__setitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-11', 'key', 'link-1');">key</a></tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-12', 'value', 'link-9');">value</a></tt><tt class="py-op">)</tt> </tt> </div></div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt> <a name="DataHandler"></a><div id="DataHandler-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="DataHandler-toggle" onclick="return toggle('DataHandler');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html">DataHandler</a><tt class="py-op">:</tt> </tt> </div><div id="DataHandler-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DataHandler-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt> <a name="DataHandler.__init__"></a><div id="DataHandler.__init__-def"><a name="L75"></a><tt class="py-lineno"> 75</tt> <a class="py-toggle" href="#" id="DataHandler.__init__-toggle" onclick="return toggle('DataHandler.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-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">dtd_dir</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.__init__-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">stack</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'errors', 'link-13');">errors</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Variable Bio.Entrez.SerialSet.integers=Bio.Entrez.SerialSet-module.html#integers"><a title="Bio.Entrez.SerialSet.integers" class="py-name" href="#" onclick="return doclink('link-14', 'integers', 'link-14');">integers</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <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 id="link-15" class="py-name" targets="Variable Bio.Entrez.SerialSet.strings=Bio.Entrez.SerialSet-module.html#strings"><a title="Bio.Entrez.SerialSet.strings" class="py-name" href="#" onclick="return doclink('link-15', 'strings', 'link-15');">strings</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</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 id="link-16" class="py-name" targets="Variable Bio.Entrez.SerialSet.lists=Bio.Entrez.SerialSet-module.html#lists"><a title="Bio.Entrez.SerialSet.lists" class="py-name" href="#" onclick="return doclink('link-16', 'lists', 'link-16');">lists</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Variable Bio.Entrez.SerialSet.dictionaries=Bio.Entrez.SerialSet-module.html#dictionaries"><a title="Bio.Entrez.SerialSet.dictionaries" class="py-name" href="#" onclick="return doclink('link-17', 'dictionaries', 'link-17');">dictionaries</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Variable Bio.Entrez.SerialSet.structures=Bio.Entrez.SerialSet-module.html#structures"><a title="Bio.Entrez.SerialSet.structures" class="py-name" href="#" onclick="return doclink('link-18', 'structures', 'link-18');">structures</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-19', 'items', 'link-19');">items</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <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">dtd_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">dtd_dir</tt> </tt> <a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">initialized</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name" targets="Variable Bio.EUtils.POM.False=Bio.EUtils.POM-module.html#False"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-20', 'False', 'link-20');">False</a></tt> </tt> </div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt> <a name="DataHandler.run"></a><div id="DataHandler.run-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="DataHandler.run-toggle" onclick="return toggle('DataHandler.run');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.run-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.run-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-docstring">"""Set up the parser and let it parse the XML results"""</tt> </tt> <a name="L89"></a><tt class="py-lineno"> 89</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">expat</tt><tt class="py-op">.</tt><tt class="py-name">ParserCreate</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L90"></a><tt class="py-lineno"> 90</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">SetParamEntityParsing</tt><tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">XML_PARAM_ENTITY_PARSING_ALWAYS</tt><tt class="py-op">)</tt> </tt> <a name="L91"></a><tt class="py-lineno"> 91</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">StartElementHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Blast.NCBIXML._XMLparser.startElement()=Bio.Blast.NCBIXML._XMLparser-class.html#startElement,Method Bio.EUtils.POM.ObjectParserHandler.startElement()=Bio.EUtils.POM.ObjectParserHandler-class.html#startElement,Method Bio.Entrez.Parser.DataHandler.startElement()=Bio.Entrez.Parser.DataHandler-class.html#startElement,Method Bio.Mindy.XPath.GrabXPathNodes.startElement()=Bio.Mindy.XPath.GrabXPathNodes-class.html#startElement,Method Bio.ParserSupport.EventGenerator.startElement()=Bio.ParserSupport.EventGenerator-class.html#startElement,Method Bio.StdHandler.ConvertHandler.startElement()=Bio.StdHandler.ConvertHandler-class.html#startElement,Method Martel.Dispatch.Dispatcher.startElement()=Martel.Dispatch.Dispatcher-class.html#startElement,Method Martel.Iterator.StoreEvents.startElement()=Martel.Iterator.StoreEvents-class.html#startElement,Method Martel.LAX.LAX.startElement()=Martel.LAX.LAX-class.html#startElement,Method Martel.test.support.Dump.startElement()=Martel.test.support.Dump-class.html#startElement,Method Martel.test.test_Parser.CountRecords.startElement()=Martel.test.test_Parser.CountRecords-class.html#startElement,Method Martel.test.test_attrs.GrabElements.startElement()=Martel.test.test_attrs.GrabElements-class.html#startElement,Method Martel.test.test_delimiter.CatchFields.startElement()=Martel.test.test_delimiter.CatchFields-class.html#startElement,Method Martel.test.test_macros.Capture.startElement()=Martel.test.test_macros.Capture-class.html#startElement"><a title="Bio.Blast.NCBIXML._XMLparser.startElement Bio.EUtils.POM.ObjectParserHandler.startElement Bio.Entrez.Parser.DataHandler.startElement Bio.Mindy.XPath.GrabXPathNodes.startElement Bio.ParserSupport.EventGenerator.startElement Bio.StdHandler.ConvertHandler.startElement Martel.Dispatch.Dispatcher.startElement Martel.Iterator.StoreEvents.startElement Martel.LAX.LAX.startElement Martel.test.support.Dump.startElement Martel.test.test_Parser.CountRecords.startElement Martel.test.test_attrs.GrabElements.startElement Martel.test.test_delimiter.CatchFields.startElement Martel.test.test_macros.Capture.startElement" class="py-name" href="#" onclick="return doclink('link-21', 'startElement', 'link-21');">startElement</a></tt> </tt> <a name="L92"></a><tt class="py-lineno"> 92</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">EndElementHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Blast.NCBIXML._XMLparser.endElement()=Bio.Blast.NCBIXML._XMLparser-class.html#endElement,Method Bio.EUtils.POM.ObjectParserHandler.endElement()=Bio.EUtils.POM.ObjectParserHandler-class.html#endElement,Method Bio.Entrez.Parser.DataHandler.endElement()=Bio.Entrez.Parser.DataHandler-class.html#endElement,Method Bio.Mindy.XPath.GrabXPathNodes.endElement()=Bio.Mindy.XPath.GrabXPathNodes-class.html#endElement,Method Bio.ParserSupport.EventGenerator.endElement()=Bio.ParserSupport.EventGenerator-class.html#endElement,Method Bio.StdHandler.ConvertHandler.endElement()=Bio.StdHandler.ConvertHandler-class.html#endElement,Method Bio.StdHandler.RecognizeHandler.endElement()=Bio.StdHandler.RecognizeHandler-class.html#endElement,Method Martel.Dispatch.Dispatcher.endElement()=Martel.Dispatch.Dispatcher-class.html#endElement,Method Martel.Iterator.StoreEvents.endElement()=Martel.Iterator.StoreEvents-class.html#endElement,Method Martel.LAX.LAX.endElement()=Martel.LAX.LAX-class.html#endElement,Method Martel.test.support.Dump.endElement()=Martel.test.support.Dump-class.html#endElement,Method Martel.test.test_delimiter.CatchFields.endElement()=Martel.test.test_delimiter.CatchFields-class.html#endElement,Method Martel.test.test_macros.Capture.endElement()=Martel.test.test_macros.Capture-class.html#endElement"><a title="Bio.Blast.NCBIXML._XMLparser.endElement Bio.EUtils.POM.ObjectParserHandler.endElement Bio.Entrez.Parser.DataHandler.endElement Bio.Mindy.XPath.GrabXPathNodes.endElement Bio.ParserSupport.EventGenerator.endElement Bio.StdHandler.ConvertHandler.endElement Bio.StdHandler.RecognizeHandler.endElement Martel.Dispatch.Dispatcher.endElement Martel.Iterator.StoreEvents.endElement Martel.LAX.LAX.endElement Martel.test.support.Dump.endElement Martel.test.test_delimiter.CatchFields.endElement Martel.test.test_macros.Capture.endElement" class="py-name" href="#" onclick="return doclink('link-22', 'endElement', 'link-22');">endElement</a></tt> </tt> <a name="L93"></a><tt class="py-lineno"> 93</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">CharacterDataHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" 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-23', 'characters', 'link-23');">characters</a></tt> </tt> <a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">ExternalEntityRefHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Entrez.Parser.DataHandler.external_entity_ref_handler()=Bio.Entrez.Parser.DataHandler-class.html#external_entity_ref_handler"><a title="Bio.Entrez.Parser.DataHandler.external_entity_ref_handler" class="py-name" href="#" onclick="return doclink('link-24', 'external_entity_ref_handler', 'link-24');">external_entity_ref_handler</a></tt> </tt> <a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">ParseFile</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-25', 'handle', 'link-25');">handle</a></tt><tt class="py-op">)</tt> </tt> <a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L97"></a><tt class="py-lineno"> 97</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">object</tt> </tt> </div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt> <a name="DataHandler.startElement"></a><div id="DataHandler.startElement-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="DataHandler.startElement-toggle" onclick="return toggle('DataHandler.startElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html#startElement">startElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.startElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.startElement-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">initialized</tt><tt class="py-op">:</tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-comment"># This XML file does not have a DTD; load its definitions here</tt> </tt> <a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># using the first element in the XML. As far as I know, this</tt> </tt> <a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># occurs only for EFetch results downloaded from the Journals</tt> </tt> <a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># database.</tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Entrez.Parser.DataHandler.load_definitions()=Bio.Entrez.Parser.DataHandler-class.html#load_definitions"><a title="Bio.Entrez.Parser.DataHandler.load_definitions" class="py-name" href="#" onclick="return doclink('link-26', 'load_definitions', 'link-26');">load_definitions</a></tt><tt class="py-op">(</tt><tt id="link-27" 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-27', 'name', 'link-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">content</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-28" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-28', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Entrez.SerialSet.lists" class="py-name" href="#" onclick="return doclink('link-29', 'lists', 'link-16');">lists</a></tt><tt class="py-op">:</tt> </tt> <a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">object</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name" targets="Class Bio.Entrez.Parser.ListElement=Bio.Entrez.Parser.ListElement-class.html"><a title="Bio.Entrez.Parser.ListElement" class="py-name" href="#" onclick="return doclink('link-30', 'ListElement', 'link-30');">ListElement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-31" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-31', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Entrez.SerialSet.dictionaries" class="py-name" href="#" onclick="return doclink('link-32', 'dictionaries', 'link-17');">dictionaries</a></tt><tt class="py-op">:</tt> </tt> <a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">object</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name" targets="Class Bio.Entrez.Parser.DictionaryElement=Bio.Entrez.Parser.DictionaryElement-class.html"><a title="Bio.Entrez.Parser.DictionaryElement" class="py-name" href="#" onclick="return doclink('link-33', 'DictionaryElement', 'link-33');">DictionaryElement</a></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-keyword">elif</tt> <tt id="link-34" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-34', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Entrez.SerialSet.structures" class="py-name" href="#" onclick="return doclink('link-35', 'structures', 'link-18');">structures</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">object</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name" targets="Class Bio.Entrez.Parser.StructureElement=Bio.Entrez.Parser.StructureElement-class.html"><a title="Bio.Entrez.Parser.StructureElement" class="py-name" href="#" onclick="return doclink('link-36', 'StructureElement', 'link-36');">StructureElement</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Entrez.SerialSet.structures" class="py-name" href="#" onclick="return doclink('link-37', 'structures', 'link-18');">structures</a></tt><tt class="py-op">[</tt><tt id="link-38" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-38', 'name', 'link-27');">name</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-39" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-39', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-40', 'items', 'link-19');">items</a></tt><tt class="py-op">:</tt> <tt class="py-comment"># Only appears in ESummary</tt> </tt> <a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-41', 'name', 'link-27');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-42" 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-42', 'attrs', 'link-42');">attrs</a></tt><tt class="py-op">[</tt><tt class="py-string">"Name"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># convert from Unicode</tt> </tt> <a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt id="link-43" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-43', 'attrs', 'link-42');">attrs</a></tt><tt class="py-op">[</tt><tt class="py-string">"Name"</tt><tt class="py-op">]</tt> </tt> <a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">itemtype</tt> <tt class="py-op">=</tt> <tt class="py-name">str</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-42');">attrs</a></tt><tt class="py-op">[</tt><tt class="py-string">"Type"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># convert from Unicode</tt> </tt> <a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt id="link-45" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-45', 'attrs', 'link-42');">attrs</a></tt><tt class="py-op">[</tt><tt class="py-string">"Type"</tt><tt class="py-op">]</tt> </tt> <a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">itemtype</tt><tt class="py-op">==</tt><tt class="py-string">"Structure"</tt><tt class="py-op">:</tt> </tt> <a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">object</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.Entrez.Parser.DictionaryElement" class="py-name" href="#" onclick="return doclink('link-46', 'DictionaryElement', 'link-33');">DictionaryElement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-47" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-47', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"ArticleIds"</tt><tt class="py-op">,</tt> <tt class="py-string">"History"</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">object</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.Entrez.Parser.StructureElement" class="py-name" href="#" onclick="return doclink('link-48', 'StructureElement', 'link-36');">StructureElement</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> <tt class="py-string">"medline"</tt><tt class="py-op">]</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">elif</tt> <tt class="py-name">itemtype</tt><tt class="py-op">==</tt><tt class="py-string">"List"</tt><tt class="py-op">:</tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">object</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.Entrez.Parser.ListElement" class="py-name" href="#" onclick="return doclink('link-49', 'ListElement', 'link-30');">ListElement</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-keyword">else</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">object</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name" targets="Class Bio.Entrez.Parser.StringElement=Bio.Entrez.Parser.StringElement-class.html"><a title="Bio.Entrez.Parser.StringElement" class="py-name" href="#" onclick="return doclink('link-50', 'StringElement', 'link-50');">StringElement</a></tt><tt class="py-op">(</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">object</tt><tt class="py-op">.</tt><tt class="py-name">itemname</tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-51', 'name', 'link-27');">name</a></tt> </tt> <a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">object</tt><tt class="py-op">.</tt><tt class="py-name">itemtype</tt> <tt class="py-op">=</tt> <tt class="py-name">itemtype</tt> </tt> <a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-52" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-52', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Entrez.SerialSet.strings" class="py-name" href="#" onclick="return doclink('link-53', 'strings', 'link-15');">strings</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-54', 'errors', 'link-13');">errors</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"><a title="Bio.Entrez.SerialSet.integers" class="py-name" href="#" onclick="return doclink('link-55', 'integers', 'link-14');">integers</a></tt><tt class="py-op">:</tt> </tt> <a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.attributes()=Bio.EUtils.POM.ElementNode-class.html#attributes"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-56', 'attributes', 'link-56');">attributes</a></tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-57', 'attrs', 'link-42');">attrs</a></tt> </tt> <a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">object</tt><tt class="py-op">!=</tt><tt class="py-string">""</tt><tt class="py-op">:</tt> </tt> <a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">object</tt><tt class="py-op">.</tt><tt id="link-58" 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-58', 'tag', 'link-58');">tag</a></tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-59', 'name', 'link-27');">name</a></tt> </tt> <a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-60" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-60', 'attrs', 'link-42');">attrs</a></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">object</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-61', 'attributes', 'link-56');">attributes</a></tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-62', 'attrs', 'link-42');">attrs</a></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">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack</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="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">current</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt> <a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">current</tt><tt class="py-op">.</tt><tt id="link-63" 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-63', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">object</tt><tt class="py-op">)</tt> </tt> <a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt> <a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">current</tt><tt class="py-op">[</tt><tt id="link-64" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-64', 'name', 'link-27');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">object</tt> </tt> <a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack</tt><tt class="py-op">.</tt><tt id="link-65" 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-65', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">object</tt><tt class="py-op">)</tt> </tt> </div><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt> <a name="DataHandler.endElement"></a><div id="DataHandler.endElement-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="DataHandler.endElement-toggle" onclick="return toggle('DataHandler.endElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html#endElement">endElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.endElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.endElement-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-66', 'value', 'link-9');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">content</tt> </tt> <a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-67" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-67', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-68', 'errors', 'link-13');">errors</a></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">if</tt> <tt id="link-69" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-69', 'value', 'link-9');">value</a></tt><tt class="py-op">==</tt><tt class="py-string">""</tt><tt class="py-op">:</tt> </tt> <a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-70', 'value', 'link-9');">value</a></tt><tt class="py-op">)</tt> </tt> <a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-71" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-71', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Entrez.SerialSet.integers" class="py-name" href="#" onclick="return doclink('link-72', 'integers', 'link-14');">integers</a></tt><tt class="py-op">:</tt> </tt> <a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-73', 'value', 'link-9');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name" targets="Class Bio.Entrez.Parser.IntegerElement=Bio.Entrez.Parser.IntegerElement-class.html"><a title="Bio.Entrez.Parser.IntegerElement" class="py-name" href="#" onclick="return doclink('link-74', 'IntegerElement', 'link-74');">IntegerElement</a></tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-75', 'value', 'link-9');">value</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-keyword">elif</tt> <tt id="link-76" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-76', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Entrez.SerialSet.strings" class="py-name" href="#" onclick="return doclink('link-77', 'strings', 'link-15');">strings</a></tt><tt class="py-op">:</tt> </tt> <a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-comment"># Convert Unicode strings to plain strings if possible</tt> </tt> <a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt id="link-78" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-78', 'value', 'link-9');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-79" class="py-name"><a title="Bio.Entrez.Parser.StringElement" class="py-name" href="#" onclick="return doclink('link-79', 'StringElement', 'link-50');">StringElement</a></tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-80', 'value', 'link-9');">value</a></tt><tt class="py-op">)</tt> </tt> <a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">UnicodeEncodeError</tt><tt class="py-op">:</tt> </tt> <a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt id="link-81" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-81', 'value', 'link-9');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name" targets="Class Bio.Entrez.Parser.UnicodeElement=Bio.Entrez.Parser.UnicodeElement-class.html"><a title="Bio.Entrez.Parser.UnicodeElement" class="py-name" href="#" onclick="return doclink('link-82', 'UnicodeElement', 'link-82');">UnicodeElement</a></tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-83', 'value', 'link-9');">value</a></tt><tt class="py-op">)</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-84" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-84', 'name', 'link-27');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-85', 'items', 'link-19');">items</a></tt><tt class="py-op">:</tt> </tt> <a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">object</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'pop', 'link-86');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">object</tt><tt class="py-op">.</tt><tt class="py-name">itemtype</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"List"</tt><tt class="py-op">,</tt> <tt class="py-string">"Structure"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">object</tt><tt class="py-op">.</tt><tt class="py-name">itemtype</tt><tt class="py-op">==</tt><tt class="py-string">"Integer"</tt><tt class="py-op">:</tt> </tt> <a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-87" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-87', 'value', 'link-9');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name"><a title="Bio.Entrez.Parser.IntegerElement" class="py-name" href="#" onclick="return doclink('link-88', 'IntegerElement', 'link-74');">IntegerElement</a></tt><tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-89', 'value', 'link-9');">value</a></tt><tt class="py-op">)</tt> </tt> <a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment"># Convert Unicode strings to plain strings if possible</tt> </tt> <a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-90" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-90', 'value', 'link-9');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-91" class="py-name"><a title="Bio.Entrez.Parser.StringElement" class="py-name" href="#" onclick="return doclink('link-91', 'StringElement', 'link-50');">StringElement</a></tt><tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-92', 'value', 'link-9');">value</a></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">except</tt> <tt class="py-name">UnicodeEncodeError</tt><tt class="py-op">:</tt> </tt> <a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt id="link-93" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-93', 'value', 'link-9');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-94" class="py-name"><a title="Bio.Entrez.Parser.UnicodeElement" class="py-name" href="#" onclick="return doclink('link-94', 'UnicodeElement', 'link-82');">UnicodeElement</a></tt><tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-95', 'value', 'link-9');">value</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-96" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-96', 'name', 'link-27');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">object</tt><tt class="py-op">.</tt><tt class="py-name">itemname</tt> </tt> <a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">object</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-97', 'pop', 'link-86');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt id="link-98" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-98', 'value', 'link-9');">value</a></tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-99', 'tag', 'link-58');">tag</a></tt> <tt class="py-op">=</tt> <tt id="link-100" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-100', 'name', 'link-27');">name</a></tt> </tt> <a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-101', 'attributes', 'link-56');">attributes</a></tt><tt class="py-op">:</tt> </tt> <a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-102" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-102', 'value', 'link-9');">value</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-103', 'attributes', 'link-56');">attributes</a></tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-104', 'attributes', 'link-56');">attributes</a></tt><tt class="py-op">)</tt> </tt> <a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-105', 'attributes', 'link-56');">attributes</a></tt> </tt> <a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">current</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">stack</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt> <a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">current</tt><tt class="py-op">.</tt><tt id="link-106" 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-106', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-107" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-107', 'value', 'link-9');">value</a></tt><tt class="py-op">)</tt> </tt> <a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt> <a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">current</tt><tt class="py-op">[</tt><tt id="link-108" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-108', 'name', 'link-27');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-109', 'value', 'link-9');">value</a></tt> </tt> </div><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt> <a name="DataHandler.characters"></a><div id="DataHandler.characters-def"><a name="L184"></a><tt class="py-lineno">184</tt> <a class="py-toggle" href="#" id="DataHandler.characters-toggle" onclick="return toggle('DataHandler.characters');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html#characters">characters</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">content</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.characters-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.characters-expanded"><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">content</tt> <tt class="py-op">+=</tt> <tt class="py-name">content</tt> </tt> </div><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt> <a name="DataHandler.elementDecl"></a><div id="DataHandler.elementDecl-def"><a name="L187"></a><tt class="py-lineno">187</tt> <a class="py-toggle" href="#" id="DataHandler.elementDecl-toggle" onclick="return toggle('DataHandler.elementDecl');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html#elementDecl">elementDecl</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.elementDecl-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.elementDecl-expanded"><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-docstring">"""This callback function is called for each element declaration:</tt> </tt> <a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> <!ELEMENT name (...)></tt> </tt> <a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> encountered in a DTD. The purpose of this function is to determine</tt> </tt> <a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> whether this element should be regarded as a string, integer, list</tt> </tt> <a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"> dictionary, structure, or error."""</tt> </tt> <a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-110" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-110', 'name', 'link-27');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">:</tt> </tt> <a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-111', 'errors', 'link-13');">errors</a></tt><tt class="py-op">.</tt><tt id="link-112" 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-112', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-113" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-113', 'name', 'link-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-114" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-114', 'name', 'link-27');">name</a></tt><tt class="py-op">==</tt><tt class="py-string">'Item'</tt> <tt class="py-keyword">and</tt> <tt class="py-name">model</tt><tt class="py-op">==</tt><tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_MIXED</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">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_REP</tt><tt class="py-op">,</tt> </tt> <a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_NAME</tt><tt class="py-op">,</tt> </tt> <a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_NONE</tt><tt class="py-op">,</tt> </tt> <a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-string">'Item'</tt><tt class="py-op">,</tt> </tt> <a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <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-op">)</tt> </tt> <a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-comment"># Special case. As far as I can tell, this only occurs in the</tt> </tt> <a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># eSummary DTD.</tt> </tt> <a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-115', 'items', 'link-19');">items</a></tt><tt class="py-op">.</tt><tt id="link-116" 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-116', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-117" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-117', 'name', 'link-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment"># First, remove ignorable parentheses around declarations</tt> </tt> <a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_SEQ</tt><tt class="py-op">,</tt> </tt> <a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_CHOICE</tt><tt class="py-op">)</tt> </tt> <a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-name">model</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_NONE</tt><tt class="py-op">,</tt> </tt> <a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_OPT</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">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">[</tt><tt class="py-number">3</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="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">model</tt> <tt class="py-op">=</tt> <tt class="py-name">model</tt><tt class="py-op">[</tt><tt class="py-number">3</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="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-comment"># PCDATA declarations correspond to strings</tt> </tt> <a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">model</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_MIXED</tt><tt class="py-op">,</tt> </tt> <a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_EMPTY</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.Entrez.SerialSet.strings" class="py-name" href="#" onclick="return doclink('link-118', 'strings', 'link-15');">strings</a></tt><tt class="py-op">.</tt><tt id="link-119" 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-119', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-120" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-120', 'name', 'link-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-comment"># List-type elements</tt> </tt> <a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_CHOICE</tt><tt class="py-op">,</tt> </tt> <a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CTYPE_SEQ</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> </tt> <a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">model</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_PLUS</tt><tt class="py-op">,</tt> </tt> <a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_REP</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.Entrez.SerialSet.lists" class="py-name" href="#" onclick="return doclink('link-121', 'lists', 'link-16');">lists</a></tt><tt class="py-op">.</tt><tt id="link-122" 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-122', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-123', 'name', 'link-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-comment"># This is the tricky case. Check which keys can occur multiple</tt> </tt> <a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># times. If only one key is possible, and it can occur multiple</tt> </tt> <a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># times, then this is a list. If more than one key is possible,</tt> </tt> <a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># but none of them can occur multiple times, then this is a</tt> </tt> <a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># dictionary. Otherwise, this is a structure.</tt> </tt> <a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># In 'single' and 'multiple', we keep track which keys can occur</tt> </tt> <a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># only once, and which can occur multiple times.</tt> </tt> <a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">single</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">multiple</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-comment"># The 'count' function is called recursively to make sure all the</tt> </tt> <a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># children in this model are counted. Error keys are ignored;</tt> </tt> <a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># they raise an exception in Python.</tt> </tt> <a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <tt class="py-def-name">count</tt><tt class="py-op">(</tt><tt class="py-param">model</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">quantifier</tt><tt class="py-op">,</tt> <tt id="link-124" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-124', 'name', 'link-27');">name</a></tt><tt class="py-op">,</tt> <tt id="link-125" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.children()=Bio.Pathway.Rep.Graph.Graph-class.html#children,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.children()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#children"><a title="Bio.Pathway.Rep.Graph.Graph.children Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-125', 'children', 'link-125');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-name">model</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="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-126" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-126', 'name', 'link-27');">name</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt> <a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">quantifier</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_PLUS</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">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_REP</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt id="link-127" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-127', 'children', 'link-125');">children</a></tt><tt class="py-op">:</tt> </tt> <a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">multiple</tt><tt class="py-op">.</tt><tt id="link-128" 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-128', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt id="link-129" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-129', 'children', 'link-125');">children</a></tt><tt class="py-op">:</tt> </tt> <a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt id="link-130" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count Bio.Seq.MutableSeq.count Bio.Seq.Seq.count Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-130', 'count', 'link-130');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt> <a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-131" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-131', 'name', 'link-27');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">:</tt> </tt> <a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">quantifier</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_NONE</tt><tt class="py-op">,</tt> </tt> <a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_OPT</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">single</tt><tt class="py-op">.</tt><tt id="link-132" 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-132', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-133" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-133', 'name', 'link-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">quantifier</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_PLUS</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">expat</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt class="py-name">XML_CQUANT_REP</tt><tt class="py-op">)</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">multiple</tt><tt class="py-op">.</tt><tt id="link-134" 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-134', 'append', 'link-8');">append</a></tt><tt class="py-op">(</tt><tt id="link-135" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-135', 'name', 'link-27');">name</a></tt><tt class="py-op">)</tt> </tt> </div><a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt id="link-136" class="py-name"><a title="Bio.Crystal.Chain.count Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count Bio.Seq.MutableSeq.count Bio.Seq.Seq.count Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-136', 'count', 'link-130');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">)</tt> </tt> <a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">single</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">multiple</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt> <a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Entrez.SerialSet.lists" class="py-name" href="#" onclick="return doclink('link-137', 'lists', 'link-16');">lists</a></tt><tt class="py-op">.</tt><tt id="link-138" 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-138', 'append', 'link-8');">append</a></tt><tt class="py-op">(</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-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">multiple</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="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Entrez.SerialSet.dictionaries" class="py-name" href="#" onclick="return doclink('link-140', 'dictionaries', 'link-17');">dictionaries</a></tt><tt class="py-op">.</tt><tt id="link-141" 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-141', 'append', 'link-8');">append</a></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-27');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.Entrez.SerialSet.structures" class="py-name" href="#" onclick="return doclink('link-143', 'structures', 'link-18');">structures</a></tt><tt class="py-op">.</tt><tt id="link-144" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-144', 'update', 'link-144');">update</a></tt><tt class="py-op">(</tt><tt class="py-op">{</tt><tt id="link-145" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-145', 'name', 'link-27');">name</a></tt><tt class="py-op">:</tt> <tt class="py-name">multiple</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt> </div><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt> <a name="DataHandler.external_entity_ref_handler"></a><div id="DataHandler.external_entity_ref_handler-def"><a name="L265"></a><tt class="py-lineno">265</tt> <a class="py-toggle" href="#" id="DataHandler.external_entity_ref_handler-toggle" onclick="return toggle('DataHandler.external_entity_ref_handler');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html#external_entity_ref_handler">external_entity_ref_handler</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">context</tt><tt class="py-op">,</tt> <tt class="py-param">base</tt><tt class="py-op">,</tt> <tt class="py-param">systemId</tt><tt class="py-op">,</tt> <tt class="py-param">publicId</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.external_entity_ref_handler-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.external_entity_ref_handler-expanded"><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-docstring">"""The purpose of this function is to load the DTD locally, instead</tt> </tt> <a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> of downloading it from the URL specified in the XML. Using the local</tt> </tt> <a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> DTD results in much faster parsing. If the DTD is not found locally,</tt> </tt> <a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-docstring"> we try to download it. In practice, this may fail though, if the XML</tt> </tt> <a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-docstring"> relies on many interrelated DTDs. If new DTDs appear, putting them in</tt> </tt> <a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"> Bio/Entrez/DTDs will allow the parser to see them."""</tt> </tt> <a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">initialized</tt> <tt class="py-op">=</tt> <tt id="link-146" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-146', 'True', 'link-146');">True</a></tt> </tt> <a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt id="link-147" class="py-name" targets="Method Bio.GFF.Feature.location()=Bio.GFF.Feature-class.html#location,Method Bio.GFF.FeatureAggregate.location()=Bio.GFF.FeatureAggregate-class.html#location,Method Bio.GenBank._FeatureConsumer.location()=Bio.GenBank._FeatureConsumer-class.html#location,Method Bio.GenBank._RecordConsumer.location()=Bio.GenBank._RecordConsumer-class.html#location,Variable Bio.expressions.genbank.location=Bio.expressions.genbank-module.html#location"><a title="Bio.GFF.Feature.location Bio.GFF.FeatureAggregate.location Bio.GenBank._FeatureConsumer.location Bio.GenBank._RecordConsumer.location Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-147', 'location', 'link-147');">location</a></tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-148', 'split', 'link-148');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">systemId</tt><tt class="py-op">)</tt> </tt> <a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dtd_dir</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt> <a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt id="link-149" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-149', 'handle', 'link-25');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-150" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-150', 'open', 'link-150');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt> <a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> </tt> <a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt><tt class="py-op">,</tt> <tt class="py-name">urllib</tt> </tt> <a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"DTD file %s not found in Biopython installation; trying to retrieve it from NCBI"</tt> <tt class="py-op">%</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt> <a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-151', 'handle', 'link-25');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">systemId</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">parser</tt> <tt class="py-op">=</tt> <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">ExternalEntityParserCreate</tt><tt class="py-op">(</tt><tt class="py-name">context</tt><tt class="py-op">)</tt> </tt> <a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">ElementDeclHandler</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name" targets="Method Bio.Entrez.Parser.DataHandler.elementDecl()=Bio.Entrez.Parser.DataHandler-class.html#elementDecl"><a title="Bio.Entrez.Parser.DataHandler.elementDecl" class="py-name" href="#" onclick="return doclink('link-152', 'elementDecl', 'link-152');">elementDecl</a></tt> </tt> <a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">ParseFile</tt><tt class="py-op">(</tt><tt id="link-153" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-153', 'handle', 'link-25');">handle</a></tt><tt class="py-op">)</tt> </tt> <a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt> </div><a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt> <a name="DataHandler.load_definitions"></a><div id="DataHandler.load_definitions-def"><a name="L286"></a><tt class="py-lineno">286</tt> <a class="py-toggle" href="#" id="DataHandler.load_definitions-toggle" onclick="return toggle('DataHandler.load_definitions');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Entrez.Parser.DataHandler-class.html#load_definitions">load_definitions</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="DataHandler.load_definitions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataHandler.load_definitions-expanded"><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-docstring">"""This function is only needed if the XML does not specify a DTD.</tt> </tt> <a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-docstring"> As far as I can tell, this only occurs for EFetch results from the</tt> </tt> <a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-docstring"> Journals database. Use a hand-written set of definitions instead."""</tt> </tt> <a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">initialized</tt> <tt class="py-op">=</tt> <tt id="link-154" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-154', 'True', 'link-146');">True</a></tt> </tt> <a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">filename</tt><tt class="py-op">==</tt><tt class="py-string">"SerialSet"</tt><tt class="py-op">:</tt> </tt> <a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-comment"># EFetch results from the Journals database</tt> </tt> <a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">import</tt> <tt id="link-155" class="py-name" targets="Module Bio.Entrez.SerialSet=Bio.Entrez.SerialSet-module.html"><a title="Bio.Entrez.SerialSet" class="py-name" href="#" onclick="return doclink('link-155', 'SerialSet', 'link-155');">SerialSet</a></tt> <tt class="py-keyword">as</tt> <tt class="py-name">module</tt> </tt> <a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt> <a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"No parser available for %s; skipping its elements"</tt> <tt class="py-op">%</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt> <a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-156', 'errors', 'link-13');">errors</a></tt><tt class="py-op">.</tt><tt id="link-157" 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-157', 'extend', 'link-157');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.Entrez.SerialSet.errors" class="py-name" href="#" onclick="return doclink('link-158', 'errors', 'link-13');">errors</a></tt><tt class="py-op">)</tt> </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 id="link-159" class="py-name"><a title="Bio.Entrez.SerialSet.integers" class="py-name" href="#" onclick="return doclink('link-159', 'integers', 'link-14');">integers</a></tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend Bio.SCOP.Raf.SeqMap.extend Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-160', 'extend', 'link-157');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.Entrez.SerialSet.integers" class="py-name" href="#" onclick="return doclink('link-161', 'integers', 'link-14');">integers</a></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">self</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Entrez.SerialSet.strings" class="py-name" href="#" onclick="return doclink('link-162', 'strings', 'link-15');">strings</a></tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend Bio.SCOP.Raf.SeqMap.extend Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-163', 'extend', 'link-157');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Entrez.SerialSet.strings" class="py-name" href="#" onclick="return doclink('link-164', 'strings', 'link-15');">strings</a></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">self</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.Entrez.SerialSet.lists" class="py-name" href="#" onclick="return doclink('link-165', 'lists', 'link-16');">lists</a></tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend Bio.SCOP.Raf.SeqMap.extend Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-166', 'extend', 'link-157');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.Entrez.SerialSet.lists" class="py-name" href="#" onclick="return doclink('link-167', 'lists', 'link-16');">lists</a></tt><tt class="py-op">)</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 id="link-168" class="py-name"><a title="Bio.Entrez.SerialSet.dictionaries" class="py-name" href="#" onclick="return doclink('link-168', 'dictionaries', 'link-17');">dictionaries</a></tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend Bio.SCOP.Raf.SeqMap.extend Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-169', 'extend', 'link-157');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.Entrez.SerialSet.dictionaries" class="py-name" href="#" onclick="return doclink('link-170', 'dictionaries', 'link-17');">dictionaries</a></tt><tt class="py-op">)</tt> </tt> <a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.Entrez.SerialSet.structures" class="py-name" href="#" onclick="return doclink('link-171', 'structures', 'link-18');">structures</a></tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-172', 'update', 'link-144');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="Bio.Entrez.SerialSet.structures" class="py-name" href="#" onclick="return doclink('link-173', 'structures', 'link-18');">structures</a></tt><tt class="py-op">)</tt> </tt> <a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-174', 'items', 'link-19');">items</a></tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend Bio.SCOP.Raf.SeqMap.extend Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-175', 'extend', 'link-157');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.Crystal.Crystal.items Bio.EUtils.MultiDict._BaseMultiDict.items Bio.Entrez.SerialSet.items Bio.GenBank.NCBIDictionary.items Bio.Mindy.BaseDB.DictLookup.items Bio.Prosite.ExPASyDictionary.items Bio.Prosite.Prodoc.ExPASyDictionary.items Bio.PubMed.Dictionary.items Bio.SwissProt.SProt.ExPASyDictionary.items Bio.config.Registry.Registry.items Bio.listfns.items BioSQL.BioSeqDatabase.BioSeqDatabase.items BioSQL.BioSeqDatabase.DBServer.items Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-176', 'items', 'link-19');">items</a></tt><tt class="py-op">)</tt> </tt> </div></div><a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help 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