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Module sourcegen
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<h1 class="epydoc">Source Code for <a href="Bio.EUtils.sourcegen-module.html">Module Bio.EUtils.sourcegen</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>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">This module can be used to generate python source code. It has an interface</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">similar to the "new" module.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></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>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.EUtils.sourcegen.BANGLINE=Bio.EUtils.sourcegen-module.html#BANGLINE"><a title="Bio.EUtils.sourcegen.BANGLINE" class="py-name" href="#" onclick="return doclink('link-0', 'BANGLINE', 'link-0');">BANGLINE</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"#!/usr/bin/env python\n"</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="_tuplestr"></a><div id="_tuplestr-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="_tuplestr-toggle" onclick="return toggle('_tuplestr');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#_tuplestr">_tuplestr</a><tt class="py-op">(</tt><tt class="py-param">tup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_tuplestr-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_tuplestr-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-1" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-1', 'map', 'link-1');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">tup</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">", "</tt><tt class="py-op">)</tt> </tt>
</div><a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"># These functions resembled the "new" module interface, but with different</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># names. This is the function interface. There are also generator object</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># interfaces below.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="genClass"></a><div id="genClass-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="genClass-toggle" onclick="return toggle('genClass');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#genClass">genClass</a><tt class="py-op">(</tt><tt class="py-param">klassname</tt><tt class="py-op">,</tt> <tt class="py-param">parents</tt><tt class="py-op">,</tt> <tt class="py-param">attribs</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">methods</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="genClass-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="genClass-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-docstring">"""genClass(name, parents, [attribs, [doc, [methods]]])</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> Return a string of Python source code defineing a class object.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> Where:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> name = class name (string)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> parents = tuple of parent class objects or strings.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> attribs = class-global attributes to define, contained in a dictionary.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> doc = a doc string (optional)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> methods = list of methods strings.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt id="link-2" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-2', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-3" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.parents()=Bio.Pathway.Rep.Graph.Graph-class.html#parents,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.parents()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#parents"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-3', 'parents', 'link-3');">parents</a></tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt id="link-4" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-4', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-5', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt> <tt class="py-string">"class %s(%s):"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">klassname</tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name" targets="Function Bio.EUtils.sourcegen._tuplestr()=Bio.EUtils.sourcegen-module.html#_tuplestr"><a title="Bio.EUtils.sourcegen._tuplestr" class="py-name" href="#" onclick="return doclink('link-6', '_tuplestr', 'link-6');">_tuplestr</a></tt><tt class="py-op">(</tt><tt id="link-7" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-7', 'parents', 'link-3');">parents</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-8', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-9', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt> <tt class="py-string">"class %s:"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">klassname</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">doc</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-10', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-11', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'\t"""%s"""'</tt> <tt class="py-op">%</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">attribs</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-12" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-12', 'key', 'link-12');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">attribs</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-13', 'items', 'link-13');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-14', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-15', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt> <tt class="py-string">"\t%s = %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-16', 'key', 'link-12');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">methods</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-17', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-18', 'extend', 'link-18');">extend</a></tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-19', 'map', 'link-1');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt id="link-20" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-20', 'list', 'link-20');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">methods</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</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-21" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-21', 's', 'link-2');">s</a></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="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-22', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-23', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\tpass"</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-24', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-25', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-26', 's', 'link-2');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="genFunc"></a><div id="genFunc-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="genFunc-toggle" onclick="return toggle('genFunc');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#genFunc">genFunc</a><tt class="py-op">(</tt><tt class="py-param">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">body</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">globals</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="genFunc-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="genFunc-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-27', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-28', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-29', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt> <tt class="py-string">"def %s(%s):"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">funcname</tt><tt class="py-op">,</tt> <tt id="link-30" class="py-name"><a title="Bio.EUtils.sourcegen._tuplestr" class="py-name" href="#" onclick="return doclink('link-30', '_tuplestr', 'link-6');">_tuplestr</a></tt><tt class="py-op">(</tt><tt class="py-name">params</tt><tt class="py-op">)</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">if</tt> <tt class="py-name">doc</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-31', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-32', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'\t"""%s"""'</tt> <tt class="py-op">%</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">globals</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-33', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-34', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\tglobal %s"</tt> <tt class="py-op">%</tt> <tt id="link-35" class="py-name"><a title="Bio.EUtils.sourcegen._tuplestr" class="py-name" href="#" onclick="return doclink('link-35', '_tuplestr', 'link-6');">_tuplestr</a></tt><tt class="py-op">(</tt><tt class="py-name">globals</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">body</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt id="link-36" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-36', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\tpass"</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 id="link-38" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-38', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-39', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">body</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt id="link-40" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-40', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-41', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-42', 's', 'link-2');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="genMethod"></a><div id="genMethod-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="genMethod-toggle" onclick="return toggle('genMethod');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#genMethod">genMethod</a><tt class="py-op">(</tt><tt class="py-param">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">body</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">globals</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="genMethod-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="genMethod-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-43', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-44', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-45', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt> <tt class="py-string">"def %s(self, %s):"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">funcname</tt><tt class="py-op">,</tt> <tt id="link-46" class="py-name"><a title="Bio.EUtils.sourcegen._tuplestr" class="py-name" href="#" onclick="return doclink('link-46', '_tuplestr', 'link-6');">_tuplestr</a></tt><tt class="py-op">(</tt><tt class="py-name">params</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">doc</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-47" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-47', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-48', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'\t"""%s"""'</tt> <tt class="py-op">%</tt> <tt class="py-name">doc</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">if</tt> <tt class="py-name">globals</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-49', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-50', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\tglobal %s"</tt> <tt class="py-op">%</tt> <tt id="link-51" class="py-name"><a title="Bio.EUtils.sourcegen._tuplestr" class="py-name" href="#" onclick="return doclink('link-51', '_tuplestr', 'link-6');">_tuplestr</a></tt><tt class="py-op">(</tt><tt class="py-name">globals</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">body</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-52', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-53', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\tpass"</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-54" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-54', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">body</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">str</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt id="link-55" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-55', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-56', 'extend', 'link-18');">extend</a></tt><tt class="py-op">(</tt> <tt id="link-57" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-57', 'map', 'link-1');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> <tt class="py-string">"\t%s"</tt><tt class="py-op">%</tt><tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-58', 'split', 'link-58');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">body</tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-59" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-59', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">body</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt id="link-60" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-60', 'list', 'link-20');">list</a></tt> <tt class="py-keyword">or</tt> <tt id="link-61" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-61', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">body</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">tuple</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt id="link-62" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-62', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-63', 'extend', 'link-18');">extend</a></tt><tt class="py-op">(</tt> <tt id="link-64" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-64', 'map', 'link-1');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> <tt class="py-string">"\t%s"</tt><tt class="py-op">%</tt><tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-name">body</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-string">"invalid type for body text"</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt id="link-65" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-65', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-66', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment"># insert a tab in the front of each line and return lines joined with newlines.</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-67', 'map', 'link-1');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> <tt class="py-string">"\t%s"</tt><tt class="py-op">%</tt><tt class="py-name">l</tt><tt class="py-op">,</tt> <tt id="link-68" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-68', 's', 'link-2');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="genComment"></a><div id="genComment-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="genComment-toggle" onclick="return toggle('genComment');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#genComment">genComment</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="genComment-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="genComment-expanded"><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-69', 'text', 'link-69');">text</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-70', 'split', 'link-58');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-71', 'map', 'link-1');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt> <tt class="py-string">"# %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-name">lines</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">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="genImport"></a><div id="genImport-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="genImport-toggle" onclick="return toggle('genImport');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#genImport">genImport</a><tt class="py-op">(</tt><tt class="py-param">module</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">indent</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="genImport-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="genImport-expanded"><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-72" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-72', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt id="link-73" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-73', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># a module type</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-74" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.obj=Bio.Encodings.IUPACEncoding-module.html#obj"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-74', 'obj', 'link-74');">obj</a></tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-75" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-75', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-76', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">tuple</tt> <tt class="py-keyword">or</tt> <tt id="link-77" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-77', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-78', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt id="link-79" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-79', 'list', 'link-20');">list</a></tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt id="link-80" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-80', 'obj', 'link-74');">obj</a></tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name"><a title="Bio.EUtils.sourcegen._tuplestr" class="py-name" href="#" onclick="return doclink('link-81', '_tuplestr', 'link-6');">_tuplestr</a></tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-82', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%sfrom %s import %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">*</tt><tt class="py-name">indent</tt><tt class="py-op">,</tt> <tt class="py-name">module</tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-83', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%simport %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">*</tt><tt class="py-name">indent</tt><tt class="py-op">,</tt> <tt class="py-name">module</tt><tt class="py-op">)</tt> </tt>
</div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"># a Python source producer object</tt> </tt>
<a name="SourceGen"></a><div id="SourceGen-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="SourceGen-toggle" onclick="return toggle('SourceGen');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html">SourceGen</a><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SourceGen-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-docstring">"""SourceGen(outfile, [bangline])</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring">An instance of this SourceGen class is a factory for generating python</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring">source code, by writing to a file object.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="SourceGen.__init__"></a><div id="SourceGen.__init__-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="SourceGen.__init__-toggle" onclick="return toggle('SourceGen.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-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">outfile</tt><tt class="py-op">,</tt> <tt class="py-param">bangline</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.__init__-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt class="py-name">outfile</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">bangline</tt> <tt class="py-op">=</tt> <tt class="py-name">bangline</tt> <tt class="py-keyword">or</tt> <tt id="link-84" class="py-name"><a title="Bio.EUtils.sourcegen.BANGLINE" class="py-name" href="#" onclick="return doclink('link-84', 'BANGLINE', 'link-0');">BANGLINE</a></tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-85" 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-85', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">bangline</tt><tt class="py-op">)</tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="SourceGen.genClass"></a><div id="SourceGen.genClass-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="SourceGen.genClass-toggle" onclick="return toggle('SourceGen.genClass');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#genClass">genClass</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">klassname</tt><tt class="py-op">,</tt> <tt class="py-param">parents</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">attribs</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">methods</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.genClass-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.genClass-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt> <tt id="link-87" class="py-name" targets="Method Bio.EUtils.sourcegen.SourceGen.genClass()=Bio.EUtils.sourcegen.SourceGen-class.html#genClass,Function Bio.EUtils.sourcegen.genClass()=Bio.EUtils.sourcegen-module.html#genClass"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-87', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-name">klassname</tt><tt class="py-op">,</tt> <tt id="link-88" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-88', 'parents', 'link-3');">parents</a></tt><tt class="py-op">,</tt> <tt class="py-name">attribs</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">,</tt> <tt class="py-name">methods</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="SourceGen.genFunc"></a><div id="SourceGen.genFunc-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="SourceGen.genFunc-toggle" onclick="return toggle('SourceGen.genFunc');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#genFunc">genFunc</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">attribs</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.genFunc-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.genFunc-expanded"><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-89" 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-89', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt> <tt id="link-90" class="py-name" targets="Method Bio.EUtils.sourcegen.SourceGen.genFunc()=Bio.EUtils.sourcegen.SourceGen-class.html#genFunc,Function Bio.EUtils.sourcegen.genFunc()=Bio.EUtils.sourcegen-module.html#genFunc"><a title="Bio.EUtils.sourcegen.SourceGen.genFunc
Bio.EUtils.sourcegen.genFunc" class="py-name" href="#" onclick="return doclink('link-90', 'genFunc', 'link-90');">genFunc</a></tt><tt class="py-op">(</tt><tt class="py-name">funcname</tt><tt class="py-op">,</tt> <tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-name">attribs</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="SourceGen.genMethod"></a><div id="SourceGen.genMethod-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="SourceGen.genMethod-toggle" onclick="return toggle('SourceGen.genMethod');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#genMethod">genMethod</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">body</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">globals</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.genMethod-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.genMethod-expanded"><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-91" 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-91', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt> <tt id="link-92" class="py-name" targets="Method Bio.EUtils.sourcegen.SourceGen.genMethod()=Bio.EUtils.sourcegen.SourceGen-class.html#genMethod,Function Bio.EUtils.sourcegen.genMethod()=Bio.EUtils.sourcegen-module.html#genMethod"><a title="Bio.EUtils.sourcegen.SourceGen.genMethod
Bio.EUtils.sourcegen.genMethod" class="py-name" href="#" onclick="return doclink('link-92', 'genMethod', 'link-92');">genMethod</a></tt><tt class="py-op">(</tt><tt class="py-name">funcname</tt><tt class="py-op">,</tt> <tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-name">body</tt><tt class="py-op">,</tt> <tt class="py-name">globals</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="SourceGen.genComment"></a><div id="SourceGen.genComment-def"><a name="L118"></a><tt class="py-lineno">118</tt> <a class="py-toggle" href="#" id="SourceGen.genComment-toggle" onclick="return toggle('SourceGen.genComment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#genComment">genComment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.genComment-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.genComment-expanded"><a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-93" 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-93', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt> <tt id="link-94" class="py-name" targets="Method Bio.EUtils.sourcegen.SourceGen.genComment()=Bio.EUtils.sourcegen.SourceGen-class.html#genComment,Function Bio.EUtils.sourcegen.genComment()=Bio.EUtils.sourcegen-module.html#genComment"><a title="Bio.EUtils.sourcegen.SourceGen.genComment
Bio.EUtils.sourcegen.genComment" class="py-name" href="#" onclick="return doclink('link-94', 'genComment', 'link-94');">genComment</a></tt><tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-95', 'text', 'link-69');">text</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="SourceGen.genImport"></a><div id="SourceGen.genImport-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="SourceGen.genImport-toggle" onclick="return toggle('SourceGen.genImport');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#genImport">genImport</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">module</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.genImport-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.genImport-expanded"><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-96" 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-96', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt> <tt id="link-97" class="py-name" targets="Method Bio.EUtils.sourcegen.SourceGen.genImport()=Bio.EUtils.sourcegen.SourceGen-class.html#genImport,Function Bio.EUtils.sourcegen.genImport()=Bio.EUtils.sourcegen-module.html#genImport"><a title="Bio.EUtils.sourcegen.SourceGen.genImport
Bio.EUtils.sourcegen.genImport" class="py-name" href="#" onclick="return doclink('link-97', 'genImport', 'link-97');">genImport</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">,</tt> <tt id="link-98" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-98', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
<a name="SourceGen.genBlank"></a><div id="SourceGen.genBlank-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="SourceGen.genBlank-toggle" onclick="return toggle('SourceGen.genBlank');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#genBlank">genBlank</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="SourceGen.genBlank-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.genBlank-expanded"><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-99" 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-99', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="SourceGen.write"></a><div id="SourceGen.write-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="SourceGen.write-toggle" onclick="return toggle('SourceGen.write');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#write">write</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.write-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.write-expanded"><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">.</tt><tt id="link-100" 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-100', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-101" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-101', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="SourceGen.writeln"></a><div id="SourceGen.writeln-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="SourceGen.writeln-toggle" onclick="return toggle('SourceGen.writeln');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceGen-class.html#writeln">writeln</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceGen.writeln-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceGen.writeln-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-102" 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-102', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt><tt id="link-103" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-103', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" 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-104', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-comment"># factory functions. </tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Returns a source generator ready to write to a file (or filename).</tt> </tt>
<a name="get_generator"></a><div id="get_generator-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="get_generator-toggle" onclick="return toggle('get_generator');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#get_generator">get_generator</a><tt class="py-op">(</tt><tt class="py-param">outfile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_generator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_generator-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-105" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-105', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">str</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt id="link-106" 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-106', 'open', 'link-106');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-107" class="py-name" targets="Class Bio.EUtils.sourcegen.SourceGen=Bio.EUtils.sourcegen.SourceGen-class.html"><a title="Bio.EUtils.sourcegen.SourceGen" class="py-name" href="#" onclick="return doclink('link-107', 'SourceGen', 'link-107');">SourceGen</a></tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt> </tt>
</div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"># return a SourceFile object.</tt> </tt>
<a name="get_sourcefile"></a><div id="get_sourcefile-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="get_sourcefile-toggle" onclick="return toggle('get_sourcefile');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen-module.html#get_sourcefile">get_sourcefile</a><tt class="py-op">(</tt><tt class="py-param">outfile</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">bangline</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_sourcefile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_sourcefile-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-108" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-108', 'type', 'link-54');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">str</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">outfile</tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-109', 'open', 'link-106');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-110" class="py-name" targets="Class Bio.EUtils.sourcegen.SourceFile=Bio.EUtils.sourcegen.SourceFile-class.html"><a title="Bio.EUtils.sourcegen.SourceFile" class="py-name" href="#" onclick="return doclink('link-110', 'SourceFile', 'link-110');">SourceFile</a></tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">,</tt> <tt class="py-name">bangline</tt><tt class="py-op">)</tt> </tt>
</div><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-comment"># object holder interface</tt> </tt>
<a name="FunctionHolder"></a><div id="FunctionHolder-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="FunctionHolder-toggle" onclick="return toggle('FunctionHolder');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.FunctionHolder-class.html">FunctionHolder</a><tt class="py-op">:</tt> </tt>
</div><div id="FunctionHolder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FunctionHolder-expanded"><a name="FunctionHolder.__init__"></a><div id="FunctionHolder.__init__-def"><a name="L151"></a><tt class="py-lineno">151</tt> <a class="py-toggle" href="#" id="FunctionHolder.__init__-toggle" onclick="return toggle('FunctionHolder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.FunctionHolder-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">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">attributes</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionHolder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="FunctionHolder.__init__-expanded"><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-111', 'name', 'link-111');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">funcname</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 class="py-name">params</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.attributes()=Bio.EUtils.POM.ElementNode-class.html#attributes"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-112', 'attributes', 'link-112');">attributes</a></tt> <tt class="py-op">=</tt> <tt id="link-113" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-113', 'attributes', 'link-112');">attributes</a></tt> <tt class="py-keyword">or</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-name">doc</tt> </tt>
</div><a name="FunctionHolder.__str__"></a><div id="FunctionHolder.__str__-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="FunctionHolder.__str__-toggle" onclick="return toggle('FunctionHolder.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.FunctionHolder-class.html#__str__">__str__</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="FunctionHolder.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="FunctionHolder.__str__-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-114" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genFunc
Bio.EUtils.sourcegen.genFunc" class="py-name" href="#" onclick="return doclink('link-114', 'genFunc', 'link-90');">genFunc</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-115', 'name', 'link-111');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-116', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
</div><a name="FunctionHolder.add_attribute"></a><div id="FunctionHolder.add_attribute-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="FunctionHolder.add_attribute-toggle" onclick="return toggle('FunctionHolder.add_attribute');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.FunctionHolder-class.html#add_attribute">add_attribute</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionHolder.add_attribute-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="FunctionHolder.add_attribute-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-117', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">[</tt><tt id="link-118" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-118', 'name', 'link-111');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-119" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-119', 'value', 'link-119');">value</a></tt> </tt>
</div><a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt id="link-120" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.set_attribute()=Bio.EUtils.POM.ElementNode-class.html#set_attribute"><a title="Bio.EUtils.POM.ElementNode.set_attribute" class="py-name" href="#" onclick="return doclink('link-120', 'set_attribute', 'link-120');">set_attribute</a></tt> <tt class="py-op">=</tt> <tt id="link-121" class="py-name" targets="Method Bio.EUtils.sourcegen.ClassHolder.add_attribute()=Bio.EUtils.sourcegen.ClassHolder-class.html#add_attribute,Method Bio.EUtils.sourcegen.FunctionHolder.add_attribute()=Bio.EUtils.sourcegen.FunctionHolder-class.html#add_attribute"><a title="Bio.EUtils.sourcegen.ClassHolder.add_attribute
Bio.EUtils.sourcegen.FunctionHolder.add_attribute" class="py-name" href="#" onclick="return doclink('link-121', 'add_attribute', 'link-121');">add_attribute</a></tt> </tt>
<a name="FunctionHolder.get_attribute"></a><div id="FunctionHolder.get_attribute-def"><a name="L161"></a><tt class="py-lineno">161</tt> <a class="py-toggle" href="#" id="FunctionHolder.get_attribute-toggle" onclick="return toggle('FunctionHolder.get_attribute');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.FunctionHolder-class.html#get_attribute">get_attribute</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionHolder.get_attribute-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="FunctionHolder.get_attribute-expanded"><a name="L162"></a><tt class="py-lineno">162</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-122" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-122', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">[</tt><tt id="link-123" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-123', 'name', 'link-111');">name</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="FunctionHolder.del_attribute"></a><div id="FunctionHolder.del_attribute-def"><a name="L163"></a><tt class="py-lineno">163</tt> <a class="py-toggle" href="#" id="FunctionHolder.del_attribute-toggle" onclick="return toggle('FunctionHolder.del_attribute');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.FunctionHolder-class.html#del_attribute">del_attribute</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionHolder.del_attribute-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="FunctionHolder.del_attribute-expanded"><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-124', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">[</tt><tt id="link-125" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-125', 'name', 'link-111');">name</a></tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="MethodHolder"></a><div id="MethodHolder-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="MethodHolder-toggle" onclick="return toggle('MethodHolder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.MethodHolder-class.html">MethodHolder</a><tt class="py-op">:</tt> </tt>
</div><div id="MethodHolder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MethodHolder-expanded"><a name="MethodHolder.__init__"></a><div id="MethodHolder.__init__-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="MethodHolder.__init__-toggle" onclick="return toggle('MethodHolder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.MethodHolder-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">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">body</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">globals</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MethodHolder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="MethodHolder.__init__-expanded"><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-126', 'name', 'link-111');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">funcname</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 class="py-name">params</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">body</tt> <tt class="py-op">=</tt> <tt class="py-name">body</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">globals</tt> <tt class="py-op">=</tt> <tt class="py-name">globals</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-name">doc</tt> </tt>
</div><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="MethodHolder.__str__"></a><div id="MethodHolder.__str__-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="MethodHolder.__str__-toggle" onclick="return toggle('MethodHolder.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.MethodHolder-class.html#__str__">__str__</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="MethodHolder.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="MethodHolder.__str__-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-127" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genMethod
Bio.EUtils.sourcegen.genMethod" class="py-name" href="#" onclick="return doclink('link-127', 'genMethod', 'link-92');">genMethod</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-128', 'name', 'link-111');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">body</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">globals</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="ClassHolder"></a><div id="ClassHolder-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="ClassHolder-toggle" onclick="return toggle('ClassHolder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.ClassHolder-class.html">ClassHolder</a><tt class="py-op">:</tt> </tt>
</div><div id="ClassHolder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ClassHolder-expanded"><a name="ClassHolder.__init__"></a><div id="ClassHolder.__init__-def"><a name="L180"></a><tt class="py-lineno">180</tt> <a class="py-toggle" href="#" id="ClassHolder.__init__-toggle" onclick="return toggle('ClassHolder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.ClassHolder-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">klassname</tt><tt class="py-op">,</tt> <tt class="py-param">parents</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">attributes</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">methods</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ClassHolder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ClassHolder.__init__-expanded"><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">classname</tt> <tt class="py-op">=</tt> <tt class="py-name">klassname</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-129', 'parents', 'link-3');">parents</a></tt> <tt class="py-op">=</tt> <tt id="link-130" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-130', 'parents', 'link-3');">parents</a></tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-131', 'attributes', 'link-112');">attributes</a></tt> <tt class="py-op">=</tt> <tt id="link-132" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-132', 'attributes', 'link-112');">attributes</a></tt> <tt class="py-keyword">or</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">methods</tt> <tt class="py-op">=</tt> <tt class="py-name">methods</tt> <tt class="py-keyword">or</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-name">doc</tt> </tt>
</div><a name="ClassHolder.__str__"></a><div id="ClassHolder.__str__-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="ClassHolder.__str__-toggle" onclick="return toggle('ClassHolder.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.ClassHolder-class.html#__str__">__str__</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="ClassHolder.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ClassHolder.__str__-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-133" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-133', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">classname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-134', 'parents', 'link-3');">parents</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-135', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">doc</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">methods</tt><tt class="py-op">)</tt> </tt>
</div><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt>
<a name="ClassHolder.add_method"></a><div id="ClassHolder.add_method-def"><a name="L189"></a><tt class="py-lineno">189</tt> <a class="py-toggle" href="#" id="ClassHolder.add_method-toggle" onclick="return toggle('ClassHolder.add_method');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.ClassHolder-class.html#add_method">add_method</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">body</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">globals</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ClassHolder.add_method-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ClassHolder.add_method-expanded"><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">mh</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name" targets="Class Bio.EUtils.sourcegen.MethodHolder=Bio.EUtils.sourcegen.MethodHolder-class.html"><a title="Bio.EUtils.sourcegen.MethodHolder" class="py-name" href="#" onclick="return doclink('link-136', 'MethodHolder', 'link-136');">MethodHolder</a></tt><tt class="py-op">(</tt><tt class="py-name">funcname</tt><tt class="py-op">,</tt> <tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-name">body</tt><tt class="py-op">,</tt> <tt class="py-name">globals</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">methods</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-137', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">mh</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mh</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="ClassHolder.add_attribute"></a><div id="ClassHolder.add_attribute-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="ClassHolder.add_attribute-toggle" onclick="return toggle('ClassHolder.add_attribute');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.ClassHolder-class.html#add_attribute">add_attribute</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ClassHolder.add_attribute-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ClassHolder.add_attribute-expanded"><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-138', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">[</tt><tt id="link-139" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-139', 'name', 'link-111');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-140" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-140', 'value', 'link-119');">value</a></tt> </tt>
</div><a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="Bio.EUtils.POM.ElementNode.set_attribute" class="py-name" href="#" onclick="return doclink('link-141', 'set_attribute', 'link-120');">set_attribute</a></tt> <tt class="py-op">=</tt> <tt id="link-142" class="py-name"><a title="Bio.EUtils.sourcegen.ClassHolder.add_attribute
Bio.EUtils.sourcegen.FunctionHolder.add_attribute" class="py-name" href="#" onclick="return doclink('link-142', 'add_attribute', 'link-121');">add_attribute</a></tt> </tt>
<a name="ClassHolder.get_attribute"></a><div id="ClassHolder.get_attribute-def"><a name="L197"></a><tt class="py-lineno">197</tt> <a class="py-toggle" href="#" id="ClassHolder.get_attribute-toggle" onclick="return toggle('ClassHolder.get_attribute');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.ClassHolder-class.html#get_attribute">get_attribute</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ClassHolder.get_attribute-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ClassHolder.get_attribute-expanded"><a name="L198"></a><tt class="py-lineno">198</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-143" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-143', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">[</tt><tt id="link-144" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-144', 'name', 'link-111');">name</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="ClassHolder.del_attribute"></a><div id="ClassHolder.del_attribute-def"><a name="L199"></a><tt class="py-lineno">199</tt> <a class="py-toggle" href="#" id="ClassHolder.del_attribute-toggle" onclick="return toggle('ClassHolder.del_attribute');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.ClassHolder-class.html#del_attribute">del_attribute</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ClassHolder.del_attribute-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ClassHolder.del_attribute-expanded"><a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-145', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">[</tt><tt id="link-146" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-146', 'name', 'link-111');">name</a></tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-comment"># this is only good for small file generation</tt> </tt>
<a name="SourceFile"></a><div id="SourceFile-def"><a name="L204"></a><tt class="py-lineno">204</tt> <a class="py-toggle" href="#" id="SourceFile-toggle" onclick="return toggle('SourceFile');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html">SourceFile</a><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SourceFile-expanded"><a name="SourceFile.__init__"></a><div id="SourceFile.__init__-def"><a name="L205"></a><tt class="py-lineno">205</tt> <a class="py-toggle" href="#" id="SourceFile.__init__-toggle" onclick="return toggle('SourceFile.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-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">fo</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">bangline</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.__init__-expanded"><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Writing to"</tt><tt class="py-op">,</tt> <tt class="py-name">fo</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fo</tt> <tt class="py-op">=</tt> <tt class="py-name">fo</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.elements()=Bio.Restriction.Restriction.RestrictionBatch-class.html#elements"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-147', 'elements', 'link-147');">elements</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">docstring</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">bangline</tt> <tt class="py-op">=</tt> <tt class="py-name">bangline</tt> <tt class="py-keyword">or</tt> <tt id="link-148" class="py-name"><a title="Bio.EUtils.sourcegen.BANGLINE" class="py-name" href="#" onclick="return doclink('link-148', 'BANGLINE', 'link-0');">BANGLINE</a></tt> </tt>
</div><a name="SourceFile.__str__"></a><div id="SourceFile.__str__-def"><a name="L211"></a><tt class="py-lineno">211</tt> <a class="py-toggle" href="#" id="SourceFile.__str__-toggle" onclick="return toggle('SourceFile.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#__str__">__str__</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="SourceFile.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.__str__-expanded"><a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt id="link-149" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-149', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">bangline</tt><tt class="py-op">]</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">docstring</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt id="link-150" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-150', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-151', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'"""\n%s\n"""\n\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">docstring</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt id="link-152" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-152', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-153', 'extend', 'link-18');">extend</a></tt><tt class="py-op">(</tt><tt id="link-154" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-154', 'map', 'link-1');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-155', 'elements', 'link-147');">elements</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-156', 's', 'link-2');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> </tt>
<a name="SourceFile.add_doc"></a><div id="SourceFile.add_doc-def"><a name="L218"></a><tt class="py-lineno">218</tt> <a class="py-toggle" href="#" id="SourceFile.add_doc-toggle" onclick="return toggle('SourceFile.add_doc');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#add_doc">add_doc</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">docstring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.add_doc-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.add_doc-expanded"><a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">docstring</tt> <tt class="py-op">=</tt> <tt class="py-name">docstring</tt> </tt>
</div><a name="SourceFile.add_comment"></a><div id="SourceFile.add_comment-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="SourceFile.add_comment-toggle" onclick="return toggle('SourceFile.add_comment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#add_comment">add_comment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.add_comment-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.add_comment-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-157', 'elements', 'link-147');">elements</a></tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-158', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt id="link-159" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genComment
Bio.EUtils.sourcegen.genComment" class="py-name" href="#" onclick="return doclink('link-159', 'genComment', 'link-94');">genComment</a></tt><tt class="py-op">(</tt><tt id="link-160" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-160', 'text', 'link-69');">text</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="SourceFile.add_import"></a><div id="SourceFile.add_import-def"><a name="L222"></a><tt class="py-lineno">222</tt> <a class="py-toggle" href="#" id="SourceFile.add_import-toggle" onclick="return toggle('SourceFile.add_import');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#add_import">add_import</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">module</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.add_import-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.add_import-expanded"><a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-161', 'elements', 'link-147');">elements</a></tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-162', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt id="link-163" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genImport
Bio.EUtils.sourcegen.genImport" class="py-name" href="#" onclick="return doclink('link-163', 'genImport', 'link-97');">genImport</a></tt><tt class="py-op">(</tt><tt class="py-name">module</tt><tt class="py-op">,</tt> <tt id="link-164" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-164', 'obj', 'link-74');">obj</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="SourceFile.add_blank"></a><div id="SourceFile.add_blank-def"><a name="L224"></a><tt class="py-lineno">224</tt> <a class="py-toggle" href="#" id="SourceFile.add_blank-toggle" onclick="return toggle('SourceFile.add_blank');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#add_blank">add_blank</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="SourceFile.add_blank-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.add_blank-expanded"><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-165', 'elements', 'link-147');">elements</a></tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-166', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="SourceFile.add_function"></a><div id="SourceFile.add_function-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="SourceFile.add_function-toggle" onclick="return toggle('SourceFile.add_function');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#add_function">add_function</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">funcname</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">attribs</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.add_function-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.add_function-expanded"><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">fh</tt> <tt class="py-op">=</tt> <tt id="link-167" class="py-name" targets="Class Bio.EUtils.sourcegen.FunctionHolder=Bio.EUtils.sourcegen.FunctionHolder-class.html"><a title="Bio.EUtils.sourcegen.FunctionHolder" class="py-name" href="#" onclick="return doclink('link-167', 'FunctionHolder', 'link-167');">FunctionHolder</a></tt><tt class="py-op">(</tt><tt class="py-name">funcname</tt><tt class="py-op">,</tt> <tt class="py-name">params</tt><tt class="py-op">,</tt> <tt class="py-name">attribs</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-168', 'elements', 'link-147');">elements</a></tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-169', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">fh</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">fh</tt> </tt>
</div><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> </tt>
<a name="SourceFile.add_class"></a><div id="SourceFile.add_class-def"><a name="L232"></a><tt class="py-lineno">232</tt> <a class="py-toggle" href="#" id="SourceFile.add_class-toggle" onclick="return toggle('SourceFile.add_class');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#add_class">add_class</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">klassname</tt><tt class="py-op">,</tt> <tt class="py-param">parents</tt><tt class="py-op">,</tt> <tt class="py-param">attributes</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">methods</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.add_class-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.add_class-expanded"><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">ch</tt> <tt class="py-op">=</tt> <tt id="link-170" class="py-name" targets="Class Bio.EUtils.sourcegen.ClassHolder=Bio.EUtils.sourcegen.ClassHolder-class.html"><a title="Bio.EUtils.sourcegen.ClassHolder" class="py-name" href="#" onclick="return doclink('link-170', 'ClassHolder', 'link-170');">ClassHolder</a></tt><tt class="py-op">(</tt><tt class="py-name">klassname</tt><tt class="py-op">,</tt> <tt id="link-171" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-171', 'parents', 'link-3');">parents</a></tt><tt class="py-op">,</tt> <tt id="link-172" class="py-name"><a title="Bio.EUtils.POM.ElementNode.attributes" class="py-name" href="#" onclick="return doclink('link-172', 'attributes', 'link-112');">attributes</a></tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">,</tt> <tt class="py-name">methods</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-173', 'elements', 'link-147');">elements</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-174', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ch</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ch</tt> </tt>
</div><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="SourceFile.append"></a><div id="SourceFile.append-def"><a name="L237"></a><tt class="py-lineno">237</tt> <a class="py-toggle" href="#" id="SourceFile.append-toggle" onclick="return toggle('SourceFile.append');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">holder</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.append-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.append-expanded"><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.elements" class="py-name" href="#" onclick="return doclink('link-175', 'elements', 'link-147');">elements</a></tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-176', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">holder</tt><tt class="py-op">)</tt> </tt>
</div><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="SourceFile.write"></a><div id="SourceFile.write-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="SourceFile.write-toggle" onclick="return toggle('SourceFile.write');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#write">write</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fo</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.write-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.write-expanded"><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">fo</tt> <tt class="py-op">=</tt> <tt class="py-name">fo</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fo</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">fo</tt><tt class="py-op">.</tt><tt id="link-177" 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-177', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="SourceFile.writefile"></a><div id="SourceFile.writefile-def"><a name="L243"></a><tt class="py-lineno">243</tt> <a class="py-toggle" href="#" id="SourceFile.writefile-toggle" onclick="return toggle('SourceFile.writefile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SourceFile-class.html#writefile">writefile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SourceFile.writefile-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SourceFile.writefile-expanded"><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">filename</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">filename</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">fo</tt> <tt class="py-op">=</tt> <tt id="link-178" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-178', 'open', 'link-106');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-179" 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-179', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">fo</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"SourceFile: no filename given to write to!"</tt> </tt>
</div></div><a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="L253"></a><tt class="py-lineno">253</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="SUBCLASS"></a><div id="SUBCLASS-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="SUBCLASS-toggle" onclick="return toggle('SUBCLASS');">-</a><tt class="py-line"> <tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.sourcegen.SUBCLASS-class.html">SUBCLASS</a><tt class="py-op">:</tt> </tt>
</div><div id="SUBCLASS-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="SUBCLASS-expanded"><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"generated classes"</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"-----------------"</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-180" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genComment
Bio.EUtils.sourcegen.genComment" class="py-name" href="#" onclick="return doclink('link-180', 'genComment', 'link-94');">genComment</a></tt><tt class="py-op">(</tt><tt id="link-181" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-181', '__doc__', 'link-181');">__doc__</a></tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-182" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-182', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-string">"test1"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</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">print</tt> <tt id="link-183" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-183', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-string">"test2"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"sub1"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-184" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-184', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-string">"test3"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"sub1"</tt><tt class="py-op">,</tt><tt class="py-string">"sub2"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-185" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-185', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-string">"test4"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">SUBCLASS</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-186" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-186', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-string">"test5"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"attr1"</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="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-187" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-187', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-string">"test6"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-string">"One docstring"</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-188" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genClass
Bio.EUtils.sourcegen.genClass" class="py-name" href="#" onclick="return doclink('link-188', 'genClass', 'link-87');">genClass</a></tt><tt class="py-op">(</tt><tt class="py-string">"test7"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"attr1"</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-string">"another docstring"</tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Holder classes"</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------------"</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-189" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genImport
Bio.EUtils.sourcegen.genImport" class="py-name" href="#" onclick="return doclink('link-189', 'genImport', 'link-97');">genImport</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">modules</tt><tt class="py-op">[</tt><tt class="py-name">__name__</tt><tt class="py-op">]</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">print</tt> <tt id="link-190" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genImport
Bio.EUtils.sourcegen.genImport" class="py-name" href="#" onclick="return doclink('link-190', 'genImport', 'link-97');">genImport</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-191" class="py-name"><a title="Bio.EUtils.sourcegen.SourceGen.genImport
Bio.EUtils.sourcegen.genImport" class="py-name" href="#" onclick="return doclink('link-191', 'genImport', 'link-97');">genImport</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-string">"open"</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">ch</tt> <tt class="py-op">=</tt> <tt id="link-192" class="py-name"><a title="Bio.EUtils.sourcegen.ClassHolder" class="py-name" href="#" onclick="return doclink('link-192', 'ClassHolder', 'link-170');">ClassHolder</a></tt><tt class="py-op">(</tt><tt class="py-string">"holdclass"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"sub1"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">ch</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------------"</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">ch</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name" targets="Method Bio.EUtils.sourcegen.ClassHolder.add_method()=Bio.EUtils.sourcegen.ClassHolder-class.html#add_method"><a title="Bio.EUtils.sourcegen.ClassHolder.add_method" class="py-name" href="#" onclick="return doclink('link-193', 'add_method', 'link-193');">add_method</a></tt><tt class="py-op">(</tt><tt class="py-string">"holdmethod1"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"param1"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">ch</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------------"</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">ch</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.EUtils.sourcegen.ClassHolder.add_method" class="py-name" href="#" onclick="return doclink('link-194', 'add_method', 'link-193');">add_method</a></tt><tt class="py-op">(</tt><tt class="py-string">"holdmethod2"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"hm2p1"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"print 'body code'"</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">=</tt><tt class="py-string">"Some docstring"</tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">ch</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------------"</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">ch</tt><tt class="py-op">.</tt><tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-string">"Documentation for holdclass."</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">ch</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------------"</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">sf</tt> <tt class="py-op">=</tt> <tt id="link-195" class="py-name"><a title="Bio.EUtils.sourcegen.SourceFile" class="py-name" href="#" onclick="return doclink('link-195', 'SourceFile', 'link-110');">SourceFile</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">sf</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name" targets="Method Bio.EUtils.sourcegen.SourceFile.add_doc()=Bio.EUtils.sourcegen.SourceFile-class.html#add_doc"><a title="Bio.EUtils.sourcegen.SourceFile.add_doc" class="py-name" href="#" onclick="return doclink('link-196', 'add_doc', 'link-196');">add_doc</a></tt><tt class="py-op">(</tt><tt class="py-string">"Testing the generator."</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">sf</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name" targets="Method Bio.EUtils.sourcegen.SourceFile.add_import()=Bio.EUtils.sourcegen.SourceFile-class.html#add_import"><a title="Bio.EUtils.sourcegen.SourceFile.add_import" class="py-name" href="#" onclick="return doclink('link-197', 'add_import', 'link-197');">add_import</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">sf</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-198', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ch</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">sf</tt><tt class="py-op">.</tt><tt id="link-199" 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-199', 'write', 'link-85');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdout</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </tt><script type="text/javascript">
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