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<a href="Bio-module.html">Package Bio</a> ::
Module biblio
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<h1 class="epydoc">Source Code for <a href="Bio.biblio-module.html">Module Bio.biblio</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</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"># Copyright 2002 by Tiaan Wessels. All rights reserved.</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"># This code is part of the Biopython distribution and governed by its</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"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This file implements a SOAP interface into the Bibliographic database of</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">the European Bioinformatics Institute. It is a low-level interface and is</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">intended to be used by higher-level objects to build object representations</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">from data retrieved by this interface. This file needs a version of the</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">pywebsvcs package LATER than 0.97 available from www.sourceforge.net.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</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">"Bio.biblio is deprecated because it seems to be out of date, "</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-string">"and no one came forward saying they use this module. If you "</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-string">"use Bio.biblio, please join the biopython mailing list and "</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-string">"email us."</tt><tt class="py-op">,</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">SOAP</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-0', 'copy', 'link-0');">copy</a></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment">#SOAP.Config.debug = 1</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-name">SOAP</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.EUtils.Config=Bio.EUtils.Config-module.html"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-1', 'Config', 'link-1');">Config</a></tt><tt class="py-op">.</tt><tt class="py-name">BuildWithNoType</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-name">SOAP</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-2', 'Config', 'link-1');">Config</a></tt><tt class="py-op">.</tt><tt class="py-name">BuildWithNoNamespacePrefix</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<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 id="link-3" class="py-name" targets="Variable Bio.Std.namespace=Bio.Std-module.html#namespace,Variable Bio.biblio.namespace=Bio.biblio-module.html#namespace"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-3', 'namespace', 'link-3');">namespace</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'http://industry.ebi.ac.uk/openBQS'</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="Biblio"></a><div id="Biblio-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="Biblio-toggle" onclick="return toggle('Biblio');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html">Biblio</a><tt class="py-op">:</tt> </tt>
</div><div id="Biblio-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Biblio-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> this class provides low-level access to the EBI Bibliographics services exported</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> through SOAP. there exist an almost 1-to-1 mapping between the methods and the</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> RPC's available on the SOAP server.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="Biblio.__init__"></a><div id="Biblio.__init__-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="Biblio.__init__-toggle" onclick="return toggle('Biblio.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-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">serverurl</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.__init__-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">serverurl</tt> <tt class="py-op">=</tt> <tt class="py-name">serverurl</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-4', 'namespace', 'link-3');">namespace</a></tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-5', 'namespace', 'link-3');">namespace</a></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">server</tt> <tt class="py-op">=</tt> <tt class="py-name">SOAP</tt><tt class="py-op">.</tt><tt class="py-name">SOAPProxy</tt><tt class="py-op">(</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">serverurl</tt><tt class="py-op">,</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-6', 'namespace', 'link-3');">namespace</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-7', 'namespace', 'link-3');">namespace</a></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_count"></a><div id="Biblio.get_count-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="Biblio.get_count-toggle" onclick="return toggle('Biblio.get_count');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_count">get_count</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_count-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_count-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L50"></a><tt class="py-lineno"> 50</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">server</tt><tt class="py-op">.</tt><tt class="py-name">getBibRefCount</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">else</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">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">server</tt><tt class="py-op">.</tt><tt class="py-name">getBibRefCount</tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="Biblio.find"></a><div id="Biblio.find-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="Biblio.find-toggle" onclick="return toggle('Biblio.find');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#find">find</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">,</tt> <tt class="py-param">keywords</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">,</tt> <tt class="py-param">criteria</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.find-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.find-expanded"><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L56"></a><tt class="py-lineno"> 56</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">server</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-8', 'find', 'link-8');">find</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-9" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.keywords()=Bio.GenBank._FeatureConsumer-class.html#keywords,Method Bio.GenBank._RecordConsumer.keywords()=Bio.GenBank._RecordConsumer-class.html#keywords"><a title="Bio.GenBank._FeatureConsumer.keywords
Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-9', 'keywords', 'link-9');">keywords</a></tt><tt class="py-op">,</tt> <tt id="link-10" 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-10', 'attrs', 'link-10');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-name">criteria</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 class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</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">server</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-11', 'find', 'link-8');">find</a></tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt id="link-12" class="py-name"><a title="Bio.GenBank._FeatureConsumer.keywords
Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-12', 'keywords', 'link-9');">keywords</a></tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-13', 'attrs', 'link-10');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-name">criteria</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="Biblio.reset_retrieval"></a><div id="Biblio.reset_retrieval-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="Biblio.reset_retrieval-toggle" onclick="return toggle('Biblio.reset_retrieval');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#reset_retrieval">reset_retrieval</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.reset_retrieval-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.reset_retrieval-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id'</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">server</tt><tt class="py-op">.</tt><tt class="py-name">resetRetrieval</tt><tt class="py-op">(</tt><tt class="py-name">cid</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="Biblio.has_next"></a><div id="Biblio.has_next-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="Biblio.has_next-toggle" onclick="return toggle('Biblio.has_next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#has_next">has_next</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.has_next-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.has_next-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id'</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</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">server</tt><tt class="py-op">.</tt><tt class="py-name">hasNext</tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_next"></a><div id="Biblio.get_next-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="Biblio.get_next-toggle" onclick="return toggle('Biblio.get_next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_next">get_next</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_next-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_next-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id'</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</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">server</tt><tt class="py-op">.</tt><tt class="py-name">getNext</tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_more"></a><div id="Biblio.get_more-def"><a name="L75"></a><tt class="py-lineno"> 75</tt> <a class="py-toggle" href="#" id="Biblio.get_more-toggle" onclick="return toggle('Biblio.get_more');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_more">get_more</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">,</tt> <tt class="py-param">cnt</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_more-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_more-expanded"><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id'</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cnt</tt> <tt class="py-op"><=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'invalid count'</tt> <tt class="py-op">+</tt> <tt class="py-name">cnt</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</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">server</tt><tt class="py-op">.</tt><tt class="py-name">getMore</tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">,</tt> <tt class="py-name">cnt</tt><tt class="py-op">)</tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_all_ids"></a><div id="Biblio.get_all_ids-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="Biblio.get_all_ids-toggle" onclick="return toggle('Biblio.get_all_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_all_ids">get_all_ids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_all_ids-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_all_ids-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id (large result safeguard)'</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</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">server</tt><tt class="py-op">.</tt><tt class="py-name">getAllIDs</tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_all"></a><div id="Biblio.get_all-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="Biblio.get_all-toggle" onclick="return toggle('Biblio.get_all');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_all">get_all</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_all-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_all-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id (large result safeguard)'</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">server</tt><tt class="py-op">.</tt><tt class="py-name">getAllBibRefs</tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_by_id"></a><div id="Biblio.get_by_id-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="Biblio.get_by_id-toggle" onclick="return toggle('Biblio.get_by_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_by_id">get_by_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_by_id-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_by_id-expanded"><a name="L93"></a><tt class="py-lineno"> 93</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">server</tt><tt class="py-op">.</tt><tt class="py-name">getById</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-14', 'id', 'link-14');">id</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
<a name="Biblio.exists"></a><div id="Biblio.exists-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="Biblio.exists-toggle" onclick="return toggle('Biblio.exists');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#exists">exists</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.exists-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.exists-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id'</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</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">server</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.biblio.Biblio.exists()=Bio.biblio.Biblio-class.html#exists,Method Bio.biblio.BiblioCollection.exists()=Bio.biblio.BiblioCollection-class.html#exists"><a title="Bio.biblio.Biblio.exists
Bio.biblio.BiblioCollection.exists" class="py-name" href="#" onclick="return doclink('link-15', 'exists', 'link-15');">exists</a></tt><tt class="py-op">(</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="Biblio.destroy"></a><div id="Biblio.destroy-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="Biblio.destroy-toggle" onclick="return toggle('Biblio.destroy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#destroy">destroy</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.destroy-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.destroy-expanded"><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cid</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="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id'</tt> </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 class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.destroy()=Bio.EUtils.POM.ElementNode-class.html#destroy,Method Bio.EUtils.POM.IndentedText.destroy()=Bio.EUtils.POM.IndentedText-class.html#destroy,Method Bio.biblio.Biblio.destroy()=Bio.biblio.Biblio-class.html#destroy,Method Bio.biblio.BiblioCollection.destroy()=Bio.biblio.BiblioCollection-class.html#destroy"><a title="Bio.EUtils.POM.ElementNode.destroy
Bio.EUtils.POM.IndentedText.destroy
Bio.biblio.Biblio.destroy
Bio.biblio.BiblioCollection.destroy" class="py-name" href="#" onclick="return doclink('link-16', 'destroy', 'link-16');">destroy</a></tt><tt class="py-op">(</tt><tt class="py-name">cid</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="Biblio.get_vocabulary_names"></a><div id="Biblio.get_vocabulary_names-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="Biblio.get_vocabulary_names-toggle" onclick="return toggle('Biblio.get_vocabulary_names');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_vocabulary_names">get_vocabulary_names</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="Biblio.get_vocabulary_names-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_vocabulary_names-expanded"><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">server</tt><tt class="py-op">.</tt><tt class="py-name">getAllVocabularyNames</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_all_values"></a><div id="Biblio.get_all_values-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="Biblio.get_all_values-toggle" onclick="return toggle('Biblio.get_all_values');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_all_values">get_all_values</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">vocab</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_all_values-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_all_values-expanded"><a name="L109"></a><tt class="py-lineno">109</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">server</tt><tt class="py-op">.</tt><tt class="py-name">getAllValues</tt><tt class="py-op">(</tt><tt class="py-name">vocab</tt><tt class="py-op">)</tt> </tt>
</div><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="Biblio.get_entry_description"></a><div id="Biblio.get_entry_description-def"><a name="L111"></a><tt class="py-lineno">111</tt> <a class="py-toggle" href="#" id="Biblio.get_entry_description-toggle" onclick="return toggle('Biblio.get_entry_description');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#get_entry_description">get_entry_description</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">vocab</tt><tt class="py-op">,</tt> <tt class="py-param">entry</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.get_entry_description-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.get_entry_description-expanded"><a name="L112"></a><tt class="py-lineno">112</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">server</tt><tt class="py-op">.</tt><tt class="py-name">getEntryDescription</tt><tt class="py-op">(</tt><tt class="py-name">vocab</tt><tt class="py-op">,</tt> <tt class="py-name">entry</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="Biblio.contains"></a><div id="Biblio.contains-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="Biblio.contains-toggle" onclick="return toggle('Biblio.contains');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.Biblio-class.html#contains">contains</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">vocab</tt><tt class="py-op">,</tt> <tt class="py-param">entry</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Biblio.contains-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="Biblio.contains-expanded"><a name="L115"></a><tt class="py-lineno">115</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">server</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Alphabet.Alphabet.contains()=Bio.Alphabet.Alphabet-class.html#contains,Method Bio.Alphabet.AlphabetEncoder.contains()=Bio.Alphabet.AlphabetEncoder-class.html#contains,Method Bio.Alphabet.Gapped.contains()=Bio.Alphabet.Gapped-class.html#contains,Method Bio.Alphabet.HasStopCodon.contains()=Bio.Alphabet.HasStopCodon-class.html#contains,Method Bio.Pathway.Rep.HashSet.HashSet.contains()=Bio.Pathway.Rep.HashSet.HashSet-class.html#contains,Method Bio.biblio.Biblio.contains()=Bio.biblio.Biblio-class.html#contains"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-17', 'contains', 'link-17');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">vocab</tt><tt class="py-op">,</tt> <tt class="py-name">entry</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection"></a><div id="BiblioCollection-def"><a name="L118"></a><tt class="py-lineno">118</tt> <a class="py-toggle" href="#" id="BiblioCollection-toggle" onclick="return toggle('BiblioCollection');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html">BiblioCollection</a><tt class="py-op">:</tt> </tt>
</div><div id="BiblioCollection-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BiblioCollection-expanded"><a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> this class attempts to hide the concept of a collection id from users. each</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> find action's results are grouped in the server under a unique collection id.</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> this id could be used in subsequent calls to refine its content more by</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> entering more specific search criteria. it can also return a new collection</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> by using the subcollection method. each collection has its own current</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> collection id as returned by the SOAP server by using the lower level Biblio</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> class's services and it takes care of freeing this collection in the server</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> upon destruction.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.__init__"></a><div id="BiblioCollection.__init__-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="BiblioCollection.__init__-toggle" onclick="return toggle('BiblioCollection.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-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">biblio</tt><tt class="py-op">,</tt> <tt class="py-param">cid</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>
</div><div id="BiblioCollection.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.__init__-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Module Bio.biblio=Bio.biblio-module.html"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-18', 'biblio', 'link-18');">biblio</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-19', 'biblio', 'link-18');">biblio</a></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt> <tt class="py-op">=</tt> <tt class="py-name">cid</tt> </tt>
</div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.__del__"></a><div id="BiblioCollection.__del__-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="BiblioCollection.__del__-toggle" onclick="return toggle('BiblioCollection.__del__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#__del__">__del__</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="BiblioCollection.__del__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.__del__-expanded"><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.EUtils.POM.ElementNode.destroy
Bio.EUtils.POM.IndentedText.destroy
Bio.biblio.Biblio.destroy
Bio.biblio.BiblioCollection.destroy" class="py-name" href="#" onclick="return doclink('link-20', 'destroy', 'link-16');">destroy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.get_collection_id"></a><div id="BiblioCollection.get_collection_id-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="BiblioCollection.get_collection_id-toggle" onclick="return toggle('BiblioCollection.get_collection_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#get_collection_id">get_collection_id</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="BiblioCollection.get_collection_id-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.get_collection_id-expanded"><a name="L138"></a><tt class="py-lineno">138</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">cid</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="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'no collection id (use find)'</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt> </tt>
</div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.get_count"></a><div id="BiblioCollection.get_count-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="BiblioCollection.get_count-toggle" onclick="return toggle('BiblioCollection.get_count');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#get_count">get_count</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="BiblioCollection.get_count-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.get_count-expanded"><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-21', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.KDTree.CKDTree.KDTree.get_count()=Bio.KDTree.CKDTree.KDTree-class.html#get_count,Method Bio.biblio.Biblio.get_count()=Bio.biblio.Biblio-class.html#get_count,Method Bio.biblio.BiblioCollection.get_count()=Bio.biblio.BiblioCollection-class.html#get_count"><a title="Bio.KDTree.CKDTree.KDTree.get_count
Bio.biblio.Biblio.get_count
Bio.biblio.BiblioCollection.get_count" class="py-name" href="#" onclick="return doclink('link-22', 'get_count', 'link-22');">get_count</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.refine"></a><div id="BiblioCollection.refine-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="BiblioCollection.refine-toggle" onclick="return toggle('BiblioCollection.refine');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#refine">refine</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">keywords</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">,</tt> <tt class="py-param">criteria</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BiblioCollection.refine-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.refine-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">remembercid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-23', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-24', 'find', 'link-8');">find</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt><tt class="py-op">,</tt> <tt id="link-25" class="py-name"><a title="Bio.GenBank._FeatureConsumer.keywords
Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-25', 'keywords', 'link-9');">keywords</a></tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-26', 'attrs', 'link-10');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-name">criteria</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">remembercid</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="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-27', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.EUtils.POM.ElementNode.destroy
Bio.EUtils.POM.IndentedText.destroy
Bio.biblio.Biblio.destroy
Bio.biblio.BiblioCollection.destroy" class="py-name" href="#" onclick="return doclink('link-28', 'destroy', 'link-16');">destroy</a></tt><tt class="py-op">(</tt><tt class="py-name">remembercid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.subcollection"></a><div id="BiblioCollection.subcollection-def"><a name="L151"></a><tt class="py-lineno">151</tt> <a class="py-toggle" href="#" id="BiblioCollection.subcollection-toggle" onclick="return toggle('BiblioCollection.subcollection');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#subcollection">subcollection</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">keywords</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">,</tt> <tt class="py-param">criteria</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BiblioCollection.subcollection-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.subcollection-expanded"><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-29" class="py-name" targets="Class Bio.biblio.BiblioCollection=Bio.biblio.BiblioCollection-class.html"><a title="Bio.biblio.BiblioCollection" class="py-name" href="#" onclick="return doclink('link-29', 'BiblioCollection', 'link-29');">BiblioCollection</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-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-30', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-31', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-32', 'find', 'link-8');">find</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt><tt class="py-op">,</tt> <tt id="link-33" class="py-name"><a title="Bio.GenBank._FeatureConsumer.keywords
Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-33', 'keywords', 'link-9');">keywords</a></tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-34', 'attrs', 'link-10');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-name">criteria</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.get_all_ids"></a><div id="BiblioCollection.get_all_ids-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="BiblioCollection.get_all_ids-toggle" onclick="return toggle('BiblioCollection.get_all_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#get_all_ids">get_all_ids</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="BiblioCollection.get_all_ids-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.get_all_ids-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-35', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.biblio.Biblio.get_all_ids()=Bio.biblio.Biblio-class.html#get_all_ids,Method Bio.biblio.BiblioCollection.get_all_ids()=Bio.biblio.BiblioCollection-class.html#get_all_ids"><a title="Bio.biblio.Biblio.get_all_ids
Bio.biblio.BiblioCollection.get_all_ids" class="py-name" href="#" onclick="return doclink('link-36', 'get_all_ids', 'link-36');">get_all_ids</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.get_all"></a><div id="BiblioCollection.get_all-def"><a name="L159"></a><tt class="py-lineno">159</tt> <a class="py-toggle" href="#" id="BiblioCollection.get_all-toggle" onclick="return toggle('BiblioCollection.get_all');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#get_all">get_all</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="BiblioCollection.get_all-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.get_all-expanded"><a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-37', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.get_all()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#get_all,Method Bio.biblio.Biblio.get_all()=Bio.biblio.Biblio-class.html#get_all,Method Bio.biblio.BiblioCollection.get_all()=Bio.biblio.BiblioCollection-class.html#get_all"><a title="Bio.NeuralNetwork.Gene.Pattern.PatternRepository.get_all
Bio.biblio.Biblio.get_all
Bio.biblio.BiblioCollection.get_all" class="py-name" href="#" onclick="return doclink('link-38', 'get_all', 'link-38');">get_all</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.exists"></a><div id="BiblioCollection.exists-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="BiblioCollection.exists-toggle" onclick="return toggle('BiblioCollection.exists');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#exists">exists</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="BiblioCollection.exists-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.exists-expanded"><a name="L163"></a><tt class="py-lineno">163</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">cid</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="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-39', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.biblio.Biblio.exists
Bio.biblio.BiblioCollection.exists" class="py-name" href="#" onclick="return doclink('link-40', 'exists', 'link-15');">exists</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="BiblioCollection.destroy"></a><div id="BiblioCollection.destroy-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="BiblioCollection.destroy-toggle" onclick="return toggle('BiblioCollection.destroy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio.BiblioCollection-class.html#destroy">destroy</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="BiblioCollection.destroy-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="BiblioCollection.destroy-expanded"><a name="L168"></a><tt class="py-lineno">168</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">cid</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="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.biblio" class="py-name" href="#" onclick="return doclink('link-41', 'biblio', 'link-18');">biblio</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.EUtils.POM.ElementNode.destroy
Bio.EUtils.POM.IndentedText.destroy
Bio.biblio.Biblio.destroy
Bio.biblio.BiblioCollection.destroy" class="py-name" href="#" onclick="return doclink('link-42', 'destroy', 'link-16');">destroy</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cid</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="checkargv"></a><div id="checkargv-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="checkargv-toggle" onclick="return toggle('checkargv');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio-module.html#checkargv">checkargv</a><tt class="py-op">(</tt><tt class="py-param">idx</tt><tt class="py-op">,</tt> <tt class="py-param">msg</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="checkargv-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="checkargv-expanded"><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">idx</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-op">></tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">'argument expected at position %d for option %s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
</div><a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L176"></a><tt class="py-lineno">176</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.biblio-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> this function implements a command-line utility using the classes implemented</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> in this file above and serves as base-line access software to query the BQS.</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-comment"># the default server location at EBI</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">serverurl</tt> <tt class="py-op">=</tt> <tt class="py-string">'http://industry.ebi.ac.uk/soap/openBQS'</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment"># is help requested</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-43', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-h'</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"""</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-string">usage: biblio.py [options] [- [finds]]</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-string">where options may be:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-string"> -l <server URL> to change the server URL</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-string"> (the default URL is %s)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-string"> -g <citation ID> to get the XML version of a citation</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-string"> -c to obtain the size of a citation collection with each refinement</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-string"> -a to retrieve the citations in a collection instead of showing only</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-string"> their citation id's</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-string"> -f <prefix> to specify the location whereto dump citations (implies -a)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-string"> found in a collection</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-string"> -o get citations one-by-one i.e. each will end up in its own file if used</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-string"> in conjunction with -f</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-string"> -Vn to get the vocabulary names in the database</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-string"> -Vv <vocabulary> to get all antries for vocabulary</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-string"> -Vd <vocabulary> <entry> to get description for vocabulary entry</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-string"> -Ve <vocabulary> <entry> to determine whether vocabulary entry exist</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-string">and finds are any number of successive occurrences of the following:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-string"> -find <keyword> [-attr <attribute>]</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-string">where each new find occurrence refines the result of the previous</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-string">examples of using this script is:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-string"> biblio.py -l http://192.168.0.163:8123 -g 21322295</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-string"> biblio.py -g 21322295</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-string"> biblio.py -a - -find study -find gene</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-string"> biblio.py -f genestudies - -find study -find gene</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-string"> biblio.py -f brazma - -find brazma -attr author</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-string"> biblio.py -Vn</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-string"> biblio.py -Vv MEDLINE/Person/properties</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-string"> biblio.py -Vd MEDLINE/Person/properties LAST_NAME</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-string"> biblio.py -Ve MEDLINE/Person/properties LAST_NAME</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-string">"""</tt> <tt class="py-op">%</tt> <tt class="py-name">serverurl</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-comment"># make server. (see if different server URL specified with -l)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-44', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-l'</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt id="link-45" class="py-name" targets="Function Bio.biblio.checkargv()=Bio.biblio-module.html#checkargv"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-45', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-l'</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">serverurl</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">server</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name" targets="Class Bio.biblio.Biblio=Bio.biblio.Biblio-class.html"><a title="Bio.biblio.Biblio" class="py-name" href="#" onclick="return doclink('link-46', 'Biblio', 'link-46');">Biblio</a></tt><tt class="py-op">(</tt><tt class="py-name">serverurl</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-comment"># handle all the possible command-line options:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-comment"># get a citation by its id</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-47', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-g'</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-48', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-g'</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.biblio.Biblio.get_by_id()=Bio.biblio.Biblio-class.html#get_by_id"><a title="Bio.biblio.Biblio.get_by_id" class="py-name" href="#" onclick="return doclink('link-49', 'get_by_id', 'link-49');">get_by_id</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-comment"># size of citation collection</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">showsize</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-50', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-c'</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">except</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">pass</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'total number of citations ->'</tt><tt class="py-op">,</tt> <tt class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.KDTree.CKDTree.KDTree.get_count
Bio.biblio.Biblio.get_count
Bio.biblio.BiblioCollection.get_count" class="py-name" href="#" onclick="return doclink('link-51', 'get_count', 'link-22');">get_count</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">showsize</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-comment"># get all citations in collection</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-52" class="py-name" targets="Method Bio.EUtils.Mixins.PublicationFetchMixin.fetch()=Bio.EUtils.Mixins.PublicationFetchMixin-class.html#fetch"><a title="Bio.EUtils.Mixins.PublicationFetchMixin.fetch" class="py-name" href="#" onclick="return doclink('link-52', 'fetch', 'link-52');">fetch</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">try</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">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-53', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-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">except</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">pass</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 id="link-54" class="py-name"><a title="Bio.EUtils.Mixins.PublicationFetchMixin.fetch" class="py-name" href="#" onclick="return doclink('link-54', 'fetch', 'link-52');">fetch</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-comment"># dump to a file with prefix</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-55" class="py-name" targets="Variable Bio.DocSQL.Query.prefix=Bio.DocSQL.Query-class.html#prefix"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-55', 'prefix', 'link-55');">prefix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-56', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-f'</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-57', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-f'</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt id="link-58" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-58', 'prefix', 'link-55');">prefix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt id="link-59" class="py-name"><a title="Bio.EUtils.Mixins.PublicationFetchMixin.fetch" class="py-name" href="#" onclick="return doclink('link-59', 'fetch', 'link-52');">fetch</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-comment"># get individualy ?</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">indiv</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-60', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-o'</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt id="link-61" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-61', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-o'</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">indiv</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-comment"># get vocabulary names</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-62', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-Vn'</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt id="link-63" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-63', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-Vn'</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-name">vocab</tt> <tt class="py-op">=</tt> <tt class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.biblio.Biblio.get_vocabulary_names()=Bio.biblio.Biblio-class.html#get_vocabulary_names"><a title="Bio.biblio.Biblio.get_vocabulary_names" class="py-name" href="#" onclick="return doclink('link-64', 'get_vocabulary_names', 'link-64');">get_vocabulary_names</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</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">vocab</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="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'the vocabulary names are:'</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">else</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">print</tt> <tt class="py-string">'there is no names in the vocabulary.'</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-65" 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-65', 'v', 'link-65');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">vocab</tt><tt class="py-op">:</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-66" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-66', 'v', 'link-65');">v</a></tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-comment"># get entries for vocabulary name</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</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">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-67', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-Vv'</tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-68', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-Vv'</tt><tt class="py-op">)</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt id="link-69" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-69', 'values', 'link-69');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.biblio.Biblio.get_all_values()=Bio.biblio.Biblio-class.html#get_all_values"><a title="Bio.biblio.Biblio.get_all_values" class="py-name" href="#" onclick="return doclink('link-70', 'get_all_values', 'link-70');">get_all_values</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-71" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-71', 'values', 'link-69');">values</a></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="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'the vocabulary entries for %s are:'</tt> <tt class="py-op">%</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'there is no entries in the vocabulary %s.'</tt> <tt class="py-op">%</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-72" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-72', 'v', 'link-65');">v</a></tt> <tt class="py-keyword">in</tt> <tt id="link-73" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-73', 'values', 'link-69');">values</a></tt><tt class="py-op">:</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-74" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-74', 'v', 'link-65');">v</a></tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-comment"># get entry for vocabulary entry for name</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-75', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-Vd'</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-76', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-Vd name'</tt><tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt id="link-77" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-77', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">'-Vd entry'</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name" targets="Method Bio.biblio.Biblio.get_entry_description()=Bio.biblio.Biblio-class.html#get_entry_description"><a title="Bio.biblio.Biblio.get_entry_description" class="py-name" href="#" onclick="return doclink('link-78', 'get_entry_description', 'link-78');">get_entry_description</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-comment"># vocabulary entry for name exist ?</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-79', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-Ve'</tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt id="link-80" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-80', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-Ve name'</tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt id="link-81" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-81', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">'-Ve entry'</tt><tt class="py-op">)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-82', 'contains', 'link-17');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'entry %s::%s exists.'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'entry %s::%s doesn\'t exists.'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">idx</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="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-comment"># - separates find from rest so this is a Rubicon</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-83', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-'</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">idx</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-comment"># handle the find's (each successive find refines previous)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">collection</tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="Bio.biblio.BiblioCollection" class="py-name" href="#" onclick="return doclink('link-84', 'BiblioCollection', 'link-29');">BiblioCollection</a></tt><tt class="py-op">(</tt><tt class="py-name">server</tt><tt class="py-op">)</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt id="link-85" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-85', 'attrs', 'link-10');">attrs</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt id="link-86" 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-86', 'keys', 'link-86');">keys</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-name">idx</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-87', 'index', 'link-43');">index</a></tt><tt class="py-op">(</tt><tt class="py-string">'-find'</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt id="link-88" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-88', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'-find'</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt id="link-89" 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-89', 'keys', 'link-86');">keys</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</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">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'-attr'</tt><tt class="py-op">:</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt id="link-90" class="py-name"><a title="Bio.biblio.checkargv" class="py-name" href="#" onclick="return doclink('link-90', 'checkargv', 'link-45');">checkargv</a></tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-string">'-attr'</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt id="link-91" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-91', 'attrs', 'link-10');">attrs</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-92" class="py-name"><a title="Bio.EUtils.Mixins.PublicationFetchMixin.fetch" class="py-name" href="#" onclick="return doclink('link-92', 'fetch', 'link-52');">fetch</a></tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name" targets="Method Bio.biblio.BiblioCollection.refine()=Bio.biblio.BiblioCollection-class.html#refine"><a title="Bio.biblio.BiblioCollection.refine" class="py-name" href="#" onclick="return doclink('link-93', 'refine', 'link-93');">refine</a></tt><tt class="py-op">(</tt><tt id="link-94" 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-94', 'keys', 'link-86');">keys</a></tt><tt class="py-op">,</tt> <tt id="link-95" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-95', 'attrs', 'link-10');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'search with:'</tt><tt class="py-op">,</tt> <tt id="link-96" 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-96', 'keys', 'link-86');">keys</a></tt><tt class="py-op">,</tt> <tt id="link-97" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-97', 'attrs', 'link-10');">attrs</a></tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.biblio.BiblioCollection.refine" class="py-name" href="#" onclick="return doclink('link-98', 'refine', 'link-93');">refine</a></tt><tt class="py-op">(</tt><tt id="link-99" 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-99', 'keys', 'link-86');">keys</a></tt><tt class="py-op">,</tt> <tt id="link-100" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-100', 'attrs', 'link-10');">attrs</a></tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'collection ->'</tt><tt class="py-op">,</tt> <tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name" targets="Method Bio.biblio.BiblioCollection.get_collection_id()=Bio.biblio.BiblioCollection-class.html#get_collection_id"><a title="Bio.biblio.BiblioCollection.get_collection_id" class="py-name" href="#" onclick="return doclink('link-101', 'get_collection_id', 'link-101');">get_collection_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">showsize</tt><tt class="py-op">:</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'collection size is ->'</tt><tt class="py-op">,</tt> <tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="Bio.KDTree.CKDTree.KDTree.get_count
Bio.biblio.Biblio.get_count
Bio.biblio.BiblioCollection.get_count" class="py-name" href="#" onclick="return doclink('link-102', 'get_count', 'link-22');">get_count</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt id="link-103" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-103', 'ids', 'link-103');">ids</a></tt> <tt class="py-op">=</tt> <tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.biblio.Biblio.get_all_ids
Bio.biblio.BiblioCollection.get_all_ids" class="py-name" href="#" onclick="return doclink('link-104', 'get_all_ids', 'link-36');">get_all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-105" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-105', 'ids', 'link-103');">ids</a></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="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'citations in collection ->'</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'no citations in collection.'</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-106" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-106', 'id', 'link-14');">id</a></tt> <tt class="py-keyword">in</tt> <tt id="link-107" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-107', 'ids', 'link-103');">ids</a></tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-108" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-108', 'id', 'link-14');">id</a></tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-name">idx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-109" class="py-name"><a title="Bio.EUtils.Mixins.PublicationFetchMixin.fetch" class="py-name" href="#" onclick="return doclink('link-109', 'fetch', 'link-52');">fetch</a></tt><tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-110" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-110', 'prefix', 'link-55');">prefix</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">indiv</tt><tt class="py-op">:</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt id="link-111" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-111', 'ids', 'link-103');">ids</a></tt> <tt class="py-op">=</tt> <tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.biblio.Biblio.get_all_ids
Bio.biblio.BiblioCollection.get_all_ids" class="py-name" href="#" onclick="return doclink('link-112', 'get_all_ids', 'link-36');">get_all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-113" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-113', 'id', 'link-14');">id</a></tt> <tt class="py-keyword">in</tt> <tt id="link-114" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-114', 'ids', 'link-103');">ids</a></tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'saving %s ...'</tt> <tt class="py-op">%</tt> <tt id="link-115" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-115', 'id', 'link-14');">id</a></tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-name">fn</tt> <tt class="py-op">=</tt> <tt id="link-116" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-116', 'prefix', 'link-55');">prefix</a></tt> <tt class="py-op">+</tt> <tt class="py-string">'-'</tt> <tt class="py-op">+</tt> <tt id="link-117" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-117', 'id', 'link-14');">id</a></tt> <tt class="py-op">+</tt> <tt class="py-string">'.xml'</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-118" 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-118', 'open', 'link-118');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">fn</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'failed to open %s.'</tt> <tt class="py-op">%</tt> <tt class="py-name">fn</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-119', 'write', 'link-119');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">server</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="Bio.biblio.Biblio.get_by_id" class="py-name" href="#" onclick="return doclink('link-120', 'get_by_id', 'link-49');">get_by_id</a></tt><tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-121', 'id', 'link-14');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-122" 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-122', 'close', 'link-122');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">fn</tt> <tt class="py-op">=</tt> <tt id="link-123" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-123', 'prefix', 'link-55');">prefix</a></tt> <tt class="py-op">+</tt> <tt class="py-string">'.xml'</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-124" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-124', 'open', 'link-118');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">fn</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'failed to open %s.'</tt> <tt class="py-op">%</tt> <tt class="py-name">fn</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-125', 'write', 'link-119');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.NeuralNetwork.Gene.Pattern.PatternRepository.get_all
Bio.biblio.Biblio.get_all
Bio.biblio.BiblioCollection.get_all" class="py-name" href="#" onclick="return doclink('link-126', 'get_all', 'link-38');">get_all</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><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-127', 'close', 'link-122');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">collection</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.NeuralNetwork.Gene.Pattern.PatternRepository.get_all
Bio.biblio.Biblio.get_all
Bio.biblio.BiblioCollection.get_all" class="py-name" href="#" onclick="return doclink('link-128', 'get_all', 'link-38');">get_all</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt id="link-129" class="py-name" targets="Function Bio.EUtils.dtd2py.main()=Bio.EUtils.dtd2py-module.html#main,Function Bio.Mindy.main()=Bio.Mindy-module.html#main,Function Bio.Wise.dnal.main()=Bio.Wise.dnal-module.html#main,Function Bio.Wise.main()=Bio.Wise-module.html#main,Function Bio.Wise.psw.main()=Bio.Wise.psw-module.html#main,Function Bio.biblio.main()=Bio.biblio-module.html#main,Function Bio.expressions.blast.wublast.main()=Bio.expressions.blast.wublast-module.html#main,Function Martel.test.run_tests.main()=Martel.test.run_tests-module.html#main"><a title="Bio.EUtils.dtd2py.main
Bio.Mindy.main
Bio.Wise.dnal.main
Bio.Wise.main
Bio.Wise.psw.main
Bio.biblio.main
Bio.expressions.blast.wublast.main
Martel.test.run_tests.main" class="py-name" href="#" onclick="return doclink('link-129', 'main', 'link-129');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> </tt><script type="text/javascript">
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