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<h1 class="epydoc">Source Code for <a href="Bio.Pathway.Rep.MultiGraph-module.html">Module Bio.Pathway.Rep.MultiGraph</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Copyright 2001 by Tarjei Mikkelsen.  All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license.  Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment"># get set abstraction for graph representation</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Pathway=Bio.Pathway-module.html"><a title="Bio.Pathway" class="py-name" href="#" onclick="return doclink('link-1', 'Pathway', 'link-1');">Pathway</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.Pathway.Rep=Bio.Pathway.Rep-module.html,Function Martel.Rep()=Martel-module.html#Rep"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-2', 'Rep', 'link-2');">Rep</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Bio.Pathway.Rep.HashSet=Bio.Pathway.Rep.HashSet-module.html,Class Bio.Pathway.Rep.HashSet.HashSet=Bio.Pathway.Rep.HashSet.HashSet-class.html"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-3', 'HashSet', 'link-3');">HashSet</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph"></a><div id="MultiGraph-def"><a name="L9"></a><tt class="py-lineno">  9</tt> <a class="py-toggle" href="#" id="MultiGraph-toggle" onclick="return toggle('MultiGraph');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html">MultiGraph</a><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MultiGraph-expanded"><a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line">    <tt class="py-docstring">"""A directed multigraph abstraction with labeled edges."""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.__init__"></a><div id="MultiGraph.__init__-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="MultiGraph.__init__-toggle" onclick="return toggle('MultiGraph.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-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">nodes</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>
</div><div id="MultiGraph.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.__init__-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line">        <tt class="py-docstring">"""Initializes a new MultiGraph object."""</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt>    <tt class="py-comment"># maps parent -&gt; set of (child, label) pairs</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-4" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.nodes()=Bio.Pathway.Rep.Graph.Graph-class.html#nodes,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#nodes"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-4', 'nodes', 'link-4');">nodes</a></tt><tt class="py-op">:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-5', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt>         <tt class="py-comment"># maps label -&gt; set of (parent, child) pairs</tt> </tt>
</div><a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.__eq__"></a><div id="MultiGraph.__eq__-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="MultiGraph.__eq__-toggle" onclick="return toggle('MultiGraph.__eq__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__eq__">__eq__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">g</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.__eq__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.__eq__-expanded"><a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns true if g is equal to this graph."""</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name" targets="Module Bio.Pathway.Rep.MultiGraph=Bio.Pathway.Rep.MultiGraph-module.html,Class Bio.Pathway.Rep.MultiGraph.MultiGraph=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html"><a title="Bio.Pathway.Rep.MultiGraph
Bio.Pathway.Rep.MultiGraph.MultiGraph" class="py-name" href="#" onclick="return doclink('link-6', 'MultiGraph', 'link-6');">MultiGraph</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">               <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt> <tt class="py-op">==</tt> <tt class="py-name">g</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">               <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt> <tt class="py-op">==</tt> <tt class="py-name">g</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">)</tt> </tt>
</div><a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.__ne__"></a><div id="MultiGraph.__ne__-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="MultiGraph.__ne__-toggle" onclick="return toggle('MultiGraph.__ne__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__ne__">__ne__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">g</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.__ne__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.__ne__-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns true if g is not equal to this graph."""</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Crystal.Chain.__eq__()=Bio.Crystal.Chain-class.html#__eq__,Method Bio.Crystal.Hetero.__eq__()=Bio.Crystal.Hetero-class.html#__eq__,Method Bio.EUtils.Datatypes.CheckLinkSet.__eq__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__eq__,Method Bio.EUtils.Datatypes.DBIds.__eq__()=Bio.EUtils.Datatypes.DBIds-class.html#__eq__,Method Bio.EUtils.Datatypes.Date.__eq__()=Bio.EUtils.Datatypes.Date-class.html#__eq__,Method Bio.EUtils.Datatypes.IdCheck.__eq__()=Bio.EUtils.Datatypes.IdCheck-class.html#__eq__,Method Bio.EUtils.Datatypes.IdUrlSet.__eq__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__eq__,Method Bio.EUtils.Datatypes.Link.__eq__()=Bio.EUtils.Datatypes.Link-class.html#__eq__,Method Bio.EUtils.Datatypes.LinkSetDb.__eq__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__eq__,Method Bio.EUtils.Datatypes.LinksLinkSet.__eq__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__eq__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__eq__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__eq__,Method Bio.EUtils.Datatypes.ObjUrl.__eq__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__eq__,Method Bio.EUtils.Datatypes.Problem.__eq__()=Bio.EUtils.Datatypes.Problem-class.html#__eq__,Method Bio.EUtils.Datatypes.Provider.__eq__()=Bio.EUtils.Datatypes.Provider-class.html#__eq__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__eq__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__eq__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__eq__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__eq__,Method Bio.LocusLink.web_parse.Token.__eq__()=Bio.LocusLink.web_parse.Token-class.html#__eq__,Method Bio.Pathway.Reaction.__eq__()=Bio.Pathway.Reaction-class.html#__eq__,Method Bio.Pathway.Rep.Graph.Graph.__eq__()=Bio.Pathway.Rep.Graph.Graph-class.html#__eq__,Method Bio.Pathway.Rep.HashSet.HashSet.__eq__()=Bio.Pathway.Rep.HashSet.HashSet-class.html#__eq__,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.__eq__()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__eq__,Method Bio.Restriction.Restriction.FormattedSeq.__eq__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__eq__,Method Bio.Restriction.Restriction.RestrictionType.__eq__()=Bio.Restriction.Restriction.RestrictionType-class.html#__eq__"><a title="Bio.Crystal.Chain.__eq__
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Bio.Restriction.Restriction.RestrictionType.__eq__" class="py-name" href="#" onclick="return doclink('link-7', '__eq__', 'link-7');">__eq__</a></tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">)</tt> </tt>
</div><a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.__repr__"></a><div id="MultiGraph.__repr__-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="MultiGraph.__repr__-toggle" onclick="return toggle('MultiGraph.__repr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__repr__">__repr__</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="MultiGraph.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.__repr__-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns an unique string representation of this graph."""</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt id="link-8" 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-8', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"&lt;MultiGraph: "</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">        <tt id="link-9" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
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Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-9', 'keys', 'link-9');">keys</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Crystal.Crystal.keys
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Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-10', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt id="link-11" class="py-name"><a title="Bio.Crystal.Crystal.keys
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Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-11', 'keys', 'link-9');">keys</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-12', 'sort', 'link-12');">sort</a></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">for</tt> <tt id="link-13" 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-13', 'key', 'link-13');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-14" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-14', 'keys', 'link-9');">keys</a></tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">            <tt id="link-15" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-15', 'values', 'link-15');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</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-13');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'list', 'link-17');">list</a></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 id="link-18" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-18', 'values', 'link-15');">values</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-19', 'sort', 'link-12');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">            <tt id="link-20" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-20', 's', 'link-8');">s</a></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-8');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"("</tt> <tt class="py-op">+</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-22', 'key', 'link-13');">key</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">": "</tt> <tt class="py-op">+</tt> <tt class="py-string">","</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-23" 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-23', 'map', 'link-23');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">,</tt> <tt id="link-24" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-24', 'values', 'link-15');">values</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">")"</tt>  </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-25" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-25', 's', 'link-8');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"&gt;"</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.__str__"></a><div id="MultiGraph.__str__-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="MultiGraph.__str__-toggle" onclick="return toggle('MultiGraph.__str__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-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="MultiGraph.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.__str__-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a concise string description of this graph."""</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">        <tt class="py-name">nodenum</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-26', 'keys', 'link-9');">keys</a></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-name">edgenum</tt> <tt class="py-op">=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-27" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-27', 'x', 'link-27');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt> <tt id="link-28" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-28', 'x', 'link-27');">x</a></tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">                         <tt id="link-29" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-29', 'map', 'link-23');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-30', 'values', 'link-15');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">        <tt class="py-name">labelnum</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-31', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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-string">"&lt;MultiGraph: "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">               <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">nodenum</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" node(s), "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">               <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">edgenum</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" edge(s), "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">               <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">labelnum</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" unique label(s)&gt;"</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.add_node"></a><div id="MultiGraph.add_node-def"><a name="L51"></a><tt class="py-lineno"> 51</tt> <a class="py-toggle" href="#" id="MultiGraph.add_node-toggle" onclick="return toggle('MultiGraph.add_node');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#add_node">add_node</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.add_node-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.add_node-expanded"><a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt class="py-docstring">"""Adds a node to this graph."""</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-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-32', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.node()=Bio.EUtils.POM.ElementNode-class.html#node,Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-33', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt id="link-34" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-34', 'node', 'link-33');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-35', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.add_edge"></a><div id="MultiGraph.add_edge-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="MultiGraph.add_edge-toggle" onclick="return toggle('MultiGraph.add_edge');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#add_edge">add_edge</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">to</tt><tt class="py-op">,</tt> <tt class="py-param">label</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="MultiGraph.add_edge-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.add_edge-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">        <tt class="py-docstring">"""Adds an edge to this graph."""</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-36', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-37" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-37', 'source', 'link-37');">source</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</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">"Unknown &lt;from&gt; node: "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-38', 'source', 'link-37');">source</a></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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-39', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">to</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</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">"Unknown &lt;to&gt; node: "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">to</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">        <tt class="py-name">edge</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">to</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt id="link-40" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-40', 'source', 'link-37');">source</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-41', 'add', 'link-41');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">edge</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-42', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">label</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">[</tt><tt class="py-name">label</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-43', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">[</tt><tt class="py-name">label</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-44', 'add', 'link-41');">add</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-45', 'source', 'link-37');">source</a></tt><tt class="py-op">,</tt><tt class="py-name">to</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.child_edges"></a><div id="MultiGraph.child_edges-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <a class="py-toggle" href="#" id="MultiGraph.child_edges-toggle" onclick="return toggle('MultiGraph.child_edges');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#child_edges">child_edges</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.child_edges-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.child_edges-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a list of (child, label) pairs for parent."""</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-46', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown &lt;parent&gt; node: "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt class="py-name">parent</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-47', 'list', 'link-17');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.children"></a><div id="MultiGraph.children-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="MultiGraph.children-toggle" onclick="return toggle('MultiGraph.children');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#children">children</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.children-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.children-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a list of unique children for parent."""</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">        <tt id="link-48" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-48', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-49', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-50', 'x', 'link-27');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-51" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-51', 'x', 'link-27');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.child_edges()=Bio.Pathway.Rep.Graph.Graph-class.html#child_edges,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.child_edges()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#child_edges"><a title="Bio.Pathway.Rep.Graph.Graph.child_edges
Bio.Pathway.Rep.MultiGraph.MultiGraph.child_edges" class="py-name" href="#" onclick="return doclink('link-52', 'child_edges', 'link-52');">child_edges</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-53" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-53', 's', 'link-8');">s</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-54', 'list', 'link-17');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.edges"></a><div id="MultiGraph.edges-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="MultiGraph.edges-toggle" onclick="return toggle('MultiGraph.edges');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#edges">edges</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">label</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.edges-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.edges-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a list of all the edges with this label."""</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-55', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown label: "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">[</tt><tt class="py-name">label</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-56', 'list', 'link-17');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.labels"></a><div id="MultiGraph.labels-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="MultiGraph.labels-toggle" onclick="return toggle('MultiGraph.labels');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#labels">labels</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="MultiGraph.labels-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.labels-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a list of all the edge labels in this graph."""</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-57', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.nodes"></a><div id="MultiGraph.nodes-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="MultiGraph.nodes-toggle" onclick="return toggle('MultiGraph.nodes');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#nodes">nodes</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="MultiGraph.nodes-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.nodes-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a list of the nodes in this graph."""</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-58', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.parent_edges"></a><div id="MultiGraph.parent_edges-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="MultiGraph.parent_edges-toggle" onclick="return toggle('MultiGraph.parent_edges');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#parent_edges">parent_edges</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">child</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.parent_edges-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.parent_edges-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a list of (parent, label) pairs for child."""</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-59', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown &lt;child&gt; node: "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt id="link-60" 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-60', 'parents', 'link-60');">parents</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">parent</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-61', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">            <tt id="link-62" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.children()=Bio.Pathway.Rep.Graph.Graph-class.html#children,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.children()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#children"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-62', 'children', 'link-62');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt class="py-name">parent</tt><tt class="py-op">]</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-63" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-63', 'x', 'link-27');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-64" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-64', 'children', 'link-62');">children</a></tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-65', 'list', 'link-17');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-66" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-66', 'x', 'link-27');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-name">child</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">                    <tt id="link-67" 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-67', 'parents', 'link-60');">parents</a></tt><tt class="py-op">.</tt><tt id="link-68" 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-68', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt id="link-69" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-69', 'x', 'link-27');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-70" 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-70', 'parents', 'link-60');">parents</a></tt> </tt>
</div><a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.parents"></a><div id="MultiGraph.parents-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="MultiGraph.parents-toggle" onclick="return toggle('MultiGraph.parents');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#parents">parents</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">child</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.parents-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.parents-expanded"><a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns a list of unique parents for child."""</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">        <tt id="link-71" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-71', 's', 'link-8');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-72', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-73" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-73', 'x', 'link-27');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-74" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-74', 'x', 'link-27');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.parent_edges()=Bio.Pathway.Rep.Graph.Graph-class.html#parent_edges,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.parent_edges()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#parent_edges"><a title="Bio.Pathway.Rep.Graph.Graph.parent_edges
Bio.Pathway.Rep.MultiGraph.MultiGraph.parent_edges" class="py-name" href="#" onclick="return doclink('link-75', 'parent_edges', 'link-75');">parent_edges</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-76" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-76', 's', 'link-8');">s</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-77', 'list', 'link-17');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.remove_node"></a><div id="MultiGraph.remove_node-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="MultiGraph.remove_node-toggle" onclick="return toggle('MultiGraph.remove_node');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#remove_node">remove_node</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.remove_node-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.remove_node-expanded"><a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">        <tt class="py-docstring">"""Removes node and all edges connected to it."""</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-78', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-79', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown node: "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-80', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">        <tt class="py-comment"># remove node (and all out-edges) from adjacency list</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt id="link-81" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-81', 'node', 'link-33');">node</a></tt><tt class="py-op">]</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-comment"># remove all in-edges from adjacency list</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-82', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-83', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt id="link-84" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-84', 'filter', 'link-84');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-85" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-85', 'x', 'link-27');">x</a></tt><tt class="py-op">,</tt><tt id="link-86" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-86', 'node', 'link-33');">node</a></tt><tt class="py-op">=</tt><tt id="link-87" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-87', 'node', 'link-33');">node</a></tt><tt class="py-op">:</tt> <tt id="link-88" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-88', 'x', 'link-27');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt id="link-89" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-89', 'node', 'link-33');">node</a></tt><tt class="py-op">,</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">                                                      <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__adjacency_list</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-90', 'list', 'link-17');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">        <tt class="py-comment"># remove all refering pairs in label map</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt class="py-name">label</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-91', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">            <tt class="py-name">lm</tt> <tt class="py-op">=</tt> <tt id="link-92" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-92', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-93', 'filter', 'link-84');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-94" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-94', 'x', 'link-27');">x</a></tt><tt class="py-op">,</tt><tt id="link-95" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-95', 'node', 'link-33');">node</a></tt><tt class="py-op">=</tt><tt id="link-96" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-96', 'node', 'link-33');">node</a></tt><tt class="py-op">:</tt> \ </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">                                <tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-97', 'x', 'link-27');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt id="link-98" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-98', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt id="link-99" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-99', 'x', 'link-27');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt id="link-100" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-100', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">                                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">[</tt><tt class="py-name">label</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-101', 'list', 'link-17');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">            <tt class="py-comment"># remove the entry completely if the label is now unused</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-name">lm</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.empty()=Bio.Pathway.Rep.HashSet.HashSet-class.html#empty,Variable Bio.formatdefs.sequence.empty=Bio.formatdefs.sequence-module.html#empty,Module Bio.writers.SeqRecord.empty=Bio.writers.SeqRecord.empty-module.html"><a title="Bio.Pathway.Rep.HashSet.HashSet.empty
Bio.formatdefs.sequence.empty
Bio.writers.SeqRecord.empty" class="py-name" href="#" onclick="return doclink('link-102', 'empty', 'link-102');">empty</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">                <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">[</tt><tt class="py-name">label</tt><tt class="py-op">]</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__label_map</tt><tt class="py-op">[</tt><tt class="py-name">label</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lm</tt> </tt>
</div><a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"> </tt>
<a name="MultiGraph.remove_edge"></a><div id="MultiGraph.remove_edge-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="MultiGraph.remove_edge-toggle" onclick="return toggle('MultiGraph.remove_edge');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#remove_edge">remove_edge</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">,</tt> <tt class="py-param">child</tt><tt class="py-op">,</tt> <tt class="py-param">label</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiGraph.remove_edge-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiGraph.remove_edge-expanded"><a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">        <tt class="py-docstring">"""Removes edge. -- NOT IMPLEMENTED"""</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">        <tt class="py-comment"># hm , this is a multigraph - how should this be implemented?</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"remove_edge is not yet implemented"</tt> </tt>
</div></div><a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-comment"># auxilliary graph functions</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="df_search"></a><div id="df_search-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="df_search-toggle" onclick="return toggle('df_search');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph-module.html#df_search">df_search</a><tt class="py-op">(</tt><tt class="py-param">graph</tt><tt class="py-op">,</tt> <tt class="py-param">root</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="df_search-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="df_search-expanded"><a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">    <tt class="py-docstring">"""Depth first search of g.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a list of all nodes that can be reached from the root node</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-docstring">    in depth-first order.</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"><tt class="py-docstring">    If root is not given, the search will be rooted at an arbitrary node.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">    <tt class="py-name">seen</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">    <tt id="link-103" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-103', 'search', 'link-103');">search</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-104', 'nodes', 'link-4');">nodes</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-105" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-105', 'search', 'link-103');">search</a></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">root</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">        <tt class="py-name">root</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-106', 'nodes', 'link-4');">nodes</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">    <tt class="py-name">seen</tt><tt class="py-op">[</tt><tt class="py-name">root</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">    <tt id="link-107" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-107', 'search', 'link-103');">search</a></tt><tt class="py-op">.</tt><tt id="link-108" 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-108', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">root</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">current</tt> <tt class="py-op">=</tt> <tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-109', 'children', 'link-62');">children</a></tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">        <tt id="link-110" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-110', 'node', 'link-33');">node</a></tt> <tt class="py-op">=</tt> <tt class="py-name">current</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-name">current</tt> <tt class="py-op">=</tt> <tt class="py-name">current</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="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">seen</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-111', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-112" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-112', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">            <tt id="link-113" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-113', 'search', 'link-103');">search</a></tt><tt class="py-op">.</tt><tt id="link-114" 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-114', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt id="link-115" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-115', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">            <tt class="py-name">seen</tt><tt class="py-op">[</tt><tt id="link-116" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-116', 'node', 'link-33');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">            <tt class="py-name">current</tt> <tt class="py-op">=</tt> <tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-117', 'children', 'link-62');">children</a></tt><tt class="py-op">(</tt><tt id="link-118" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-118', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">current</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-119" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-119', 'search', 'link-103');">search</a></tt>    </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"> </tt>
<a name="bf_search"></a><div id="bf_search-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="bf_search-toggle" onclick="return toggle('bf_search');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Rep.MultiGraph-module.html#bf_search">bf_search</a><tt class="py-op">(</tt><tt class="py-param">graph</tt><tt class="py-op">,</tt> <tt class="py-param">root</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="bf_search-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bf_search-expanded"><a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">    <tt class="py-docstring">"""Breadth first search of g.</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a list of all nodes that can be reached from the root node</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-docstring">    in breadth-first order.</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-docstring">    If root is not given, the search will be rooted at an arbitrary node.</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">    <tt class="py-name">seen</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">    <tt id="link-120" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-120', 'search', 'link-103');">search</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-121', 'nodes', 'link-4');">nodes</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-122" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-122', 'search', 'link-103');">search</a></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">root</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">        <tt class="py-name">root</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-123', 'nodes', 'link-4');">nodes</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">    <tt class="py-name">seen</tt><tt class="py-op">[</tt><tt class="py-name">root</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">    <tt id="link-124" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-124', 'search', 'link-103');">search</a></tt><tt class="py-op">.</tt><tt id="link-125" 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-125', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">    <tt class="py-name">current</tt> <tt class="py-op">=</tt> <tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-126', 'children', 'link-62');">children</a></tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt id="link-127" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-127', 'node', 'link-33');">node</a></tt> <tt class="py-op">=</tt> <tt class="py-name">current</tt><tt class="py-op">[</tt><tt class="py-number">0</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">current</tt> <tt class="py-op">=</tt> <tt class="py-name">current</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="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">seen</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-128', 'has_key', 'link-32');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-129" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-129', 'node', 'link-33');">node</a></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 id="link-130" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-130', 'search', 'link-103');">search</a></tt><tt class="py-op">.</tt><tt id="link-131" 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-131', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt id="link-132" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-132', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">            <tt class="py-name">seen</tt><tt class="py-op">[</tt><tt id="link-133" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-133', 'node', 'link-33');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">            <tt class="py-name">current</tt><tt class="py-op">.</tt><tt id="link-134" 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-134', 'extend', 'link-134');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-135', 'children', 'link-62');">children</a></tt><tt class="py-op">(</tt><tt id="link-136" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-136', 'node', 'link-33');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-137" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-137', 'search', 'link-103');">search</a></tt> </tt>
</div><a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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