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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.Mindy-module.html">Package&nbsp;Mindy</a> ::
        Module&nbsp;XPath
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<h1 class="epydoc">Source Code for <a href="Bio.Mindy.XPath-module.html">Module Bio.Mindy.XPath</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.Std=Bio.Std-module.html"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-1', 'Std', 'link-1');">Std</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment"># To help parse XPath queries</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-2" class="py-name" targets="Method Bio.KEGG.Compound.Record._name()=Bio.KEGG.Compound.Record-class.html#_name,Method Bio.KEGG.Enzyme.Record._name()=Bio.KEGG.Enzyme.Record-class.html#_name,Method Bio.MEME.Motif.Motif._name()=Bio.MEME.Motif.Motif-class.html#_name,Variable Bio.Mindy.XPath._name=Bio.Mindy.XPath-module.html#_name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-2', '_name', 'link-2');">_name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"[a-zA-Z_:][-a-zA-Z0-9._:]*"</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.Mindy.XPath._pat_tag_re=Bio.Mindy.XPath-module.html#_pat_tag_re"><a title="Bio.Mindy.XPath._pat_tag_re" class="py-name" href="#" onclick="return doclink('link-3', '_pat_tag_re', 'link-3');">_pat_tag_re</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-4', 'compile', 'link-4');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"""^//(%s)(\[@(%s)=("[^"]*"|'[^']*')\])?$"""</tt> <tt class="py-op">%</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line">                         <tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-5', '_name', 'link-2');">_name</a></tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-6', '_name', 'link-2');">_name</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line">                                                   <tt class="py-comment">#')  # emacs cruft</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"> </tt>
<a name="parse_simple_xpath"></a><div id="parse_simple_xpath-def"><a name="L13"></a><tt class="py-lineno"> 13</tt> <a class="py-toggle" href="#" id="parse_simple_xpath-toggle" onclick="return toggle('parse_simple_xpath');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath-module.html#parse_simple_xpath">parse_simple_xpath</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_simple_xpath-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_simple_xpath-expanded"><a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line">    <tt class="py-comment"># Only supports two formats</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"># //tag</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"># //tag[@attr="value"]</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.Mindy.XPath._pat_tag_re" class="py-name" href="#" onclick="return doclink('link-7', '_pat_tag_re', 'link-3');">_pat_tag_re</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-8', 'match', 'link-8');">match</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-9', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot yet understand the XPath expression: %r"</tt> <tt class="py-op">%</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">                        <tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-10', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">    <tt id="link-11" class="py-name" targets="Variable Martel.Time.tag=Martel.Time-module.html#tag"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-11', 'tag', 'link-11');">tag</a></tt> <tt class="py-op">=</tt>  <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-12', 'group', 'link-12');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-13', 'group', 'link-12');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">        <tt class="py-name">varname</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-14', 'group', 'link-12');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">        <tt class="py-name">varvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-15', 'group', 'link-12');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">        <tt class="py-name">node_matcher</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-16', 'tag', 'link-11');">tag</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">varname</tt><tt class="py-op">,</tt> <tt class="py-name">varvalue</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-name">node_matcher</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-17', 'tag', 'link-11');">tag</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">node_matcher</tt> </tt>
</div><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"> </tt>
<a name="xpath_index"></a><div id="xpath_index-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="xpath_index-toggle" onclick="return toggle('xpath_index');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath-module.html#xpath_index">xpath_index</a><tt class="py-op">(</tt><tt class="py-param">dbname</tt><tt class="py-op">,</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">                <tt class="py-param">filenames</tt><tt class="py-op">,</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">                <tt class="py-param">primary_namespace</tt><tt class="py-op">,</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">                <tt class="py-param">extract_info</tt><tt class="py-op">,</tt>  <tt class="py-comment"># pair of (data_value, xpath)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">                <tt class="py-param">format</tt> <tt class="py-op">=</tt> <tt class="py-string">"sequence"</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">                <tt class="py-param">record_tag</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-18', 'Std', 'link-1');">Std</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-19', 'record', 'link-19');">record</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-20', 'tag', 'link-11');">tag</a></tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">                <tt class="py-param">creator_factory</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">                <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="xpath_index-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="xpath_index-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">creator_factory</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt id="link-21" class="py-name" targets="Module Bio.Mindy.BerkeleyDB=Bio.Mindy.BerkeleyDB-module.html,Class Bio.Mindy.BerkeleyDB.BerkeleyDB=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html"><a title="Bio.Mindy.BerkeleyDB
Bio.Mindy.BerkeleyDB.BerkeleyDB" class="py-name" href="#" onclick="return doclink('link-21', 'BerkeleyDB', 'link-21');">BerkeleyDB</a></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">        <tt class="py-name">creator_factory</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.Mindy.BerkeleyDB
Bio.Mindy.BerkeleyDB.BerkeleyDB" class="py-name" href="#" onclick="return doclink('link-22', 'BerkeleyDB', 'link-21');">BerkeleyDB</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Function Bio.Mindy.BerkeleyDB.create()=Bio.Mindy.BerkeleyDB-module.html#create,Function Bio.Mindy.FlatDB.create()=Bio.Mindy.FlatDB-module.html#create"><a title="Bio.Mindy.BerkeleyDB.create
Bio.Mindy.FlatDB.create" class="py-name" href="#" onclick="return doclink('link-23', 'create', 'link-23');">create</a></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">     </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-name">data_names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-24" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-24', 'x', 'link-24');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-25" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-25', 'x', 'link-24');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">extract_info</tt><tt class="py-op">]</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">primary_namespace</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data_names</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">            <tt class="py-string">"No way to get the %r field needed for the primary (unique) id"</tt> <tt class="py-op">%</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-name">data_names</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-26', 'remove', 'link-26');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">prop</tt><tt class="py-op">,</tt> <tt class="py-name">xpath</tt> <tt class="py-keyword">in</tt> <tt class="py-name">extract_info</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">prop</tt> <tt class="py-op">==</tt> <tt class="py-name">primary_namespace</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">            <tt class="py-keyword">break</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Property %r has no xpath definition"</tt> <tt class="py-op">%</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">                        <tt class="py-op">(</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<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-name">creator</tt> <tt class="py-op">=</tt> <tt class="py-name">creator_factory</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt> <tt class="py-name">data_names</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-name">builder</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name" targets="Class Bio.Mindy.XPath.GrabXPathNodes=Bio.Mindy.XPath.GrabXPathNodes-class.html"><a title="Bio.Mindy.XPath.GrabXPathNodes" class="py-name" href="#" onclick="return doclink('link-27', 'GrabXPathNodes', 'link-27');">GrabXPathNodes</a></tt><tt class="py-op">(</tt><tt class="py-name">extract_info</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">filename</tt> <tt class="py-keyword">in</tt> <tt class="py-name">filenames</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">        <tt class="py-name">creator</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Function Bio.MarkovModel.load()=Bio.MarkovModel-module.html#load,Method Bio.Mindy.BaseDB.WriteDB.load()=Bio.Mindy.BaseDB.WriteDB-class.html#load,Function Bio.config._stanzaformat.load()=Bio.config._stanzaformat-module.html#load,Method BioSQL.BioSeqDatabase.BioSeqDatabase.load()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#load"><a title="Bio.MarkovModel.load
Bio.Mindy.BaseDB.WriteDB.load
Bio.config._stanzaformat.load
BioSQL.BioSeqDatabase.BioSeqDatabase.load" class="py-name" href="#" onclick="return doclink('link-28', 'load', 'link-28');">load</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">builder</tt> <tt class="py-op">=</tt> <tt class="py-name">builder</tt><tt class="py-op">,</tt> <tt class="py-name">record_tag</tt> <tt class="py-op">=</tt> <tt class="py-name">record_tag</tt><tt class="py-op">,</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">                     <tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Variable Bio.expressions.blast.ncbiblast.format=Bio.expressions.blast.ncbiblast-module.html#format,Variable Bio.expressions.blast.wublast.format=Bio.expressions.blast.wublast-module.html#format,Variable Bio.expressions.blocks.format=Bio.expressions.blocks-module.html#format,Variable Bio.expressions.embl.embl65.format=Bio.expressions.embl.embl65-module.html#format,Variable Bio.expressions.fasta.format=Bio.expressions.fasta-module.html#format,Variable Bio.expressions.genbank.format=Bio.expressions.genbank-module.html#format,Variable Bio.expressions.hmmpfam.format=Bio.expressions.hmmpfam-module.html#format,Variable Bio.expressions.swissprot.ipi.format=Bio.expressions.swissprot.ipi-module.html#format,Variable Bio.expressions.swissprot.speclist.format=Bio.expressions.swissprot.speclist-module.html#format,Variable Bio.expressions.swissprot.sprot38.format=Bio.expressions.swissprot.sprot38-module.html#format,Variable Bio.expressions.swissprot.sprot40.format=Bio.expressions.swissprot.sprot40-module.html#format,Variable Bio.expressions.transfac.format=Bio.expressions.transfac-module.html#format,Variable Martel.test.test_swissprot38.format=Martel.test.test_swissprot38-module.html#format,Variable Martel.test.testformats.swissprot38.format=Martel.test.testformats.swissprot38-module.html#format"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-29', 'format', 'link-29');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-name">creator</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-30', 'close', 'link-30');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"> </tt>
<a name="GrabXPathNodes"></a><div id="GrabXPathNodes-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="GrabXPathNodes-toggle" onclick="return toggle('GrabXPathNodes');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html">GrabXPathNodes</a><tt class="py-op">(</tt><tt class="py-base-class">xml</tt><tt class="py-op">.</tt><tt class="py-base-class">sax</tt><tt class="py-op">.</tt><tt class="py-base-class">ContentHandler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GrabXPathNodes-expanded"><a name="GrabXPathNodes.__init__"></a><div id="GrabXPathNodes.__init__-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.__init__-toggle" onclick="return toggle('GrabXPathNodes.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-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">extractinfo</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.__init__-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_fast_tags</tt> <tt class="py-op">=</tt> <tt class="py-name">_fast_tags</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-31" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.property=Bio.Encodings.IUPACEncoding-module.html#property"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-31', 'property', 'link-31');">property</a></tt><tt class="py-op">,</tt> <tt class="py-name">xpath</tt> <tt class="py-keyword">in</tt> <tt class="py-name">extractinfo</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">            <tt id="link-32" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-32', 'tag', 'link-11');">tag</a></tt><tt class="py-op">,</tt> <tt id="link-33" 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-33', 'attrs', 'link-33');">attrs</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name" targets="Function Bio.Mindy.XPath.parse_simple_xpath()=Bio.Mindy.XPath-module.html#parse_simple_xpath"><a title="Bio.Mindy.XPath.parse_simple_xpath" class="py-name" href="#" onclick="return doclink('link-34', 'parse_simple_xpath', 'link-34');">parse_simple_xpath</a></tt><tt class="py-op">(</tt><tt class="py-name">xpath</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">_fast_tags</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.Crystal.Crystal.setdefault()=Bio.Crystal.Crystal-class.html#setdefault"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-35', 'setdefault', 'link-35');">setdefault</a></tt><tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-36', 'tag', 'link-11');">tag</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-37" 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-37', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-38', 'attrs', 'link-33');">attrs</a></tt><tt class="py-op">,</tt> <tt id="link-39" class="py-name"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-39', 'property', 'link-31');">property</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt class="py-comment"># for doing the endElement in the correct order,</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># which is opposite to the input order</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_rev_tags</tt> <tt class="py-op">=</tt> <tt class="py-name">_rev_tags</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-40" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-40', 'v', 'link-40');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_fast_tags</tt><tt class="py-op">.</tt><tt id="link-41" 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-41', 'items', 'link-41');">items</a></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 id="link-42" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-42', 'v', 'link-40');">v</a></tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-43', 'v', 'link-40');">v</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 id="link-44" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-44', 'v', 'link-40');">v</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.GFF.easy.Location.reverse()=Bio.GFF.easy.Location-class.html#reverse,Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse,Function Bio.SeqUtils.reverse()=Bio.SeqUtils-module.html#reverse"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-45', 'reverse', 'link-45');">reverse</a></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 class="py-name">_rev_tags</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-46', 'v', 'link-40');">v</a></tt> </tt>
</div><a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"> </tt>
<a name="GrabXPathNodes.uses_tags"></a><div id="GrabXPathNodes.uses_tags-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.uses_tags-toggle" onclick="return toggle('GrabXPathNodes.uses_tags');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html#uses_tags">uses_tags</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.uses_tags-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.uses_tags-expanded"><a name="L82"></a><tt class="py-lineno"> 82</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">_fast_tags</tt><tt class="py-op">.</tt><tt id="link-47" 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-47', 'keys', 'link-47');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"> </tt>
<a name="GrabXPathNodes.startDocument"></a><div id="GrabXPathNodes.startDocument-def"><a name="L84"></a><tt class="py-lineno"> 84</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.startDocument-toggle" onclick="return toggle('GrabXPathNodes.startDocument');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html#startDocument">startDocument</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.startDocument-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.startDocument-expanded"><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">_text</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_capture</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">document</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">         </tt>
<a name="GrabXPathNodes.startElement"></a><div id="GrabXPathNodes.startElement-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.startElement-toggle" onclick="return toggle('GrabXPathNodes.startElement');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html#startElement">startElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.startElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.startElement-expanded"><a name="L90"></a><tt class="py-lineno"> 90</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">_fast_tags</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-48', 'has_key', 'link-48');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-49', 'tag', 'link-11');">tag</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">want_attrs</tt><tt class="py-op">,</tt> <tt class="py-name">prop</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_fast_tags</tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-50', 'tag', 'link-11');">tag</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">            <tt class="py-name">needed</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">want_attrs</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">                <tt class="py-name">needed</tt><tt class="py-op">.</tt><tt id="link-51" 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-51', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">prop</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-52" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-52', 'v', 'link-40');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">want_attrs</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-53" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-53', 'attrs', 'link-33');">attrs</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-54', 'has_key', 'link-48');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-55" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-55', 'attrs', 'link-33');">attrs</a></tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-56" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-56', 'v', 'link-40');">v</a></tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">                        <tt class="py-keyword">break</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">                    <tt class="py-name">needed</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">prop</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method Bio.Mindy.XPath.GrabXPathNodes.save_info()=Bio.Mindy.XPath.GrabXPathNodes-class.html#save_info"><a title="Bio.Mindy.XPath.GrabXPathNodes.save_info" class="py-name" href="#" onclick="return doclink('link-58', 'save_info', 'link-58');">save_info</a></tt><tt class="py-op">(</tt><tt class="py-name">needed</tt><tt class="py-op">)</tt> </tt>
</div><a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"> </tt>
<a name="GrabXPathNodes.characters"></a><div id="GrabXPathNodes.characters-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.characters-toggle" onclick="return toggle('GrabXPathNodes.characters');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html#characters">characters</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.characters-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.characters-expanded"><a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_capture</tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_text</tt> <tt class="py-op">+=</tt> <tt id="link-59" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-59', 's', 'link-9');">s</a></tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"> </tt>
<a name="GrabXPathNodes.save_info"></a><div id="GrabXPathNodes.save_info-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.save_info-toggle" onclick="return toggle('GrabXPathNodes.save_info');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html#save_info">save_info</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">needed</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.save_info-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.save_info-expanded"><a name="L110"></a><tt class="py-lineno">110</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">_capture</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_text</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_capture</tt><tt class="py-op">.</tt><tt id="link-60" 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-60', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-name">needed</tt><tt class="py-op">,</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">_text</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"> </tt>
<a name="GrabXPathNodes.get_info"></a><div id="GrabXPathNodes.get_info-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.get_info-toggle" onclick="return toggle('GrabXPathNodes.get_info');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html#get_info">get_info</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.get_info-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.get_info-expanded"><a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-name">needed</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_capture</tt><tt class="py-op">.</tt><tt id="link-61" 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-61', 'pop', 'link-61');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt id="link-62" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-62', 's', 'link-9');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_text</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-63" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-63', 's', 'link-9');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">needed</tt> </tt>
</div><a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"> </tt>
<a name="GrabXPathNodes.endElement"></a><div id="GrabXPathNodes.endElement-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="GrabXPathNodes.endElement-toggle" onclick="return toggle('GrabXPathNodes.endElement');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.XPath.GrabXPathNodes-class.html#endElement">endElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GrabXPathNodes.endElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="GrabXPathNodes.endElement-expanded"><a name="L120"></a><tt class="py-lineno">120</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">_rev_tags</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-64', 'has_key', 'link-48');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-65', 'tag', 'link-11');">tag</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt id="link-66" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-66', 'text', 'link-66');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">needed</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name" targets="Method Bio.Mindy.XPath.GrabXPathNodes.get_info()=Bio.Mindy.XPath.GrabXPathNodes-class.html#get_info"><a title="Bio.Mindy.XPath.GrabXPathNodes.get_info" class="py-name" href="#" onclick="return doclink('link-67', 'get_info', 'link-67');">get_info</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">need</tt> <tt class="py-keyword">in</tt> <tt class="py-name">needed</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">document</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-68', 'setdefault', 'link-35');">setdefault</a></tt><tt class="py-op">(</tt><tt class="py-name">need</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-69" 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-69', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-70', 'text', 'link-66');">text</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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