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<h1 class="epydoc">Source Code for <a href="Bio.Nexus.Nodes-module.html">Module Bio.Nexus.Nodes</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 2005-2008 by Frank Kauff & Cymon J. Cox. 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 class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Nodes.py</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Provides functionality of a linked list.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Each node has one (or none) predecessor, and an arbitrary number of successors.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Nodes can store arbitrary data in a NodeData class.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Subclassed by Nexus.Trees to store phylogenetic trees.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bug reports to Frank Kauff (fkauff@biologie.uni-kl.de)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="ChainException"></a><div id="ChainException-def"><a name="L17"></a><tt class="py-lineno"> 17</tt> <a class="py-toggle" href="#" id="ChainException-toggle" onclick="return toggle('ChainException');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.ChainException-class.html">ChainException</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChainException-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ChainException-expanded"><a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="NodeException"></a><div id="NodeException-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="NodeException-toggle" onclick="return toggle('NodeException');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.NodeException-class.html">NodeException</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NodeException-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NodeException-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="Chain"></a><div id="Chain-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="Chain-toggle" onclick="return toggle('Chain');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html">Chain</a><tt class="py-op">:</tt> </tt>
</div><div id="Chain-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Chain-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-docstring">"""Stores a list of nodes that are linked together."""</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="Chain.__init__"></a><div id="Chain.__init__-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="Chain.__init__-toggle" onclick="return toggle('Chain.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#__init__">__init__</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="Chain.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.__init__-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-docstring">"""Initiates a node chain: (self)."""</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-0', 'id', 'link-0');">id</a></tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="Chain._get_id"></a><div id="Chain._get_id-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="Chain._get_id-toggle" onclick="return toggle('Chain._get_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#_get_id">_get_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Chain._get_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain._get_id-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a new id for a node in the chain."""</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-1', 'id', 'link-0');">id</a></tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-2', 'id', 'link-0');">id</a></tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="Chain.all_ids"></a><div id="Chain.all_ids-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="Chain.all_ids-toggle" onclick="return toggle('Chain.all_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#all_ids">all_ids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Chain.all_ids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.all_ids-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a list of all node ids."""</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</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">chain</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-3', 'keys', 'link-3');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
<a name="Chain.add"></a><div id="Chain.add-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="Chain.add-toggle" onclick="return toggle('Chain.add');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#add">add</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-param">prev</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="Chain.add-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.add-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-docstring">"""Attaches node to another: (self, node, prev)."""</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">prev</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">prev</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-4" class="py-name" targets="Class Bio.Nexus.Nodes.ChainException=Bio.Nexus.Nodes.ChainException-class.html"><a title="Bio.Nexus.Nodes.ChainException" class="py-name" href="#" onclick="return doclink('link-4', 'ChainException', 'link-4');">ChainException</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknow predecessor: '</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-5" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-5', 'id', 'link-0');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Nexus.Nodes.Chain._get_id()=Bio.Nexus.Nodes.Chain-class.html#_get_id"><a title="Bio.Nexus.Nodes.Chain._get_id" class="py-name" href="#" onclick="return doclink('link-6', '_get_id', 'link-6');">_get_id</a></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 id="link-7" 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-7', 'node', 'link-7');">node</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Nexus.Nodes.Node.set_id()=Bio.Nexus.Nodes.Node-class.html#set_id"><a title="Bio.Nexus.Nodes.Node.set_id" class="py-name" href="#" onclick="return doclink('link-8', 'set_id', 'link-8');">set_id</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-9', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-10', 'node', 'link-7');">node</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.Nexus.Nodes.Node.set_prev()=Bio.Nexus.Nodes.Node-class.html#set_prev"><a title="Bio.Nexus.Nodes.Node.set_prev" class="py-name" href="#" onclick="return doclink('link-11', 'set_prev', 'link-11');">set_prev</a></tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">prev</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">prev</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.Nexus.Nodes.Node.add_succ()=Bio.Nexus.Nodes.Node-class.html#add_succ"><a title="Bio.Nexus.Nodes.Node.add_succ" class="py-name" href="#" onclick="return doclink('link-12', 'add_succ', 'link-12');">add_succ</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-13', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-14" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-14', 'id', 'link-0');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-15" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-15', 'node', 'link-7');">node</a></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-16" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-16', 'id', 'link-0');">id</a></tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="Chain.collapse"></a><div id="Chain.collapse-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="Chain.collapse-toggle" onclick="return toggle('Chain.collapse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#collapse">collapse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Chain.collapse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.collapse-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-docstring">"""Deletes node from chain and relinks successors to predecessor: collapse(self, id)."""</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-17" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-17', 'id', 'link-0');">id</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-18" class="py-name"><a title="Bio.Nexus.Nodes.ChainException" class="py-name" href="#" onclick="return doclink('link-18', 'ChainException', 'link-4');">ChainException</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown ID: '</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-19', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">prev_id</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-20" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-20', 'id', 'link-0');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Nexus.Nodes.Node.get_prev()=Bio.Nexus.Nodes.Node-class.html#get_prev"><a title="Bio.Nexus.Nodes.Node.get_prev" class="py-name" href="#" onclick="return doclink('link-21', 'get_prev', 'link-21');">get_prev</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">prev_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Nexus.Nodes.Node.remove_succ()=Bio.Nexus.Nodes.Node-class.html#remove_succ"><a title="Bio.Nexus.Nodes.Node.remove_succ" class="py-name" href="#" onclick="return doclink('link-22', 'remove_succ', 'link-22');">remove_succ</a></tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-23', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">succ_ids</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-24" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-24', 'id', 'link-0');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.Nexus.Nodes.Node.get_succ()=Bio.Nexus.Nodes.Node-class.html#get_succ"><a title="Bio.Nexus.Nodes.Node.get_succ" class="py-name" href="#" onclick="return doclink('link-25', 'get_succ', 'link-25');">get_succ</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-26" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-26', 'i', 'link-26');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">succ_ids</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-26');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Nexus.Nodes.Node.set_prev" class="py-name" href="#" onclick="return doclink('link-28', 'set_prev', 'link-11');">set_prev</a></tt><tt class="py-op">(</tt><tt class="py-name">prev_id</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">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">prev_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Nexus.Nodes.Node.add_succ" class="py-name" href="#" onclick="return doclink('link-29', 'add_succ', 'link-12');">add_succ</a></tt><tt class="py-op">(</tt><tt class="py-name">succ_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-30" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-30', 'node', 'link-7');">node</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-31" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-31', 'id', 'link-0');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.kill()=Bio.Nexus.Nodes.Chain-class.html#kill"><a title="Bio.Nexus.Nodes.Chain.kill" class="py-name" href="#" onclick="return doclink('link-32', 'kill', 'link-32');">kill</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-33', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">return</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-7');">node</a></tt> </tt>
</div><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="Chain.kill"></a><div id="Chain.kill-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="Chain.kill-toggle" onclick="return toggle('Chain.kill');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#kill">kill</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Chain.kill-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.kill-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-docstring">"""Kills a node from chain without caring to what it is connected: kill(self,id)."""</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-35" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-35', 'id', 'link-0');">id</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-36" class="py-name"><a title="Bio.Nexus.Nodes.ChainException" class="py-name" href="#" onclick="return doclink('link-36', 'ChainException', 'link-4');">ChainException</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown ID: '</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-37', 'id', 'link-0');">id</a></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">else</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">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-38" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-38', 'id', 'link-0');">id</a></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="Chain.unlink"></a><div id="Chain.unlink-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="Chain.unlink-toggle" onclick="return toggle('Chain.unlink');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#unlink">unlink</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Chain.unlink-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.unlink-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-docstring">"""Disconnects node from his predecessor: unlink(self,id)."""</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-39" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-39', 'id', 'link-0');">id</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-40" class="py-name"><a title="Bio.Nexus.Nodes.ChainException" class="py-name" href="#" onclick="return doclink('link-40', 'ChainException', 'link-4');">ChainException</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown ID: '</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-41', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">prev_id</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-42', 'id', 'link-0');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">prev_id</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">prev_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-43', 'pop', 'link-43');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">prev_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-44', 'index', 'link-44');">index</a></tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-45', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-46" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-46', 'id', 'link-0');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt><tt class="py-op">=</tt><tt class="py-name">None</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">prev_id</tt> </tt>
</div><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="Chain.link"></a><div id="Chain.link-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="Chain.link-toggle" onclick="return toggle('Chain.link');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#link">link</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-op">:</tt> </tt>
</div><div id="Chain.link-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.link-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-docstring">"""Connects son to parent: link(self,son,parent)."""</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">child</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-47" class="py-name"><a title="Bio.Nexus.Nodes.ChainException" class="py-name" href="#" onclick="return doclink('link-47', 'ChainException', 'link-4');">ChainException</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown ID: '</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 class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">parent</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-48" class="py-name"><a title="Bio.Nexus.Nodes.ChainException" class="py-name" href="#" onclick="return doclink('link-48', 'ChainException', 'link-4');">ChainException</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown ID: '</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 class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.unlink()=Bio.Nexus.Nodes.Chain-class.html#unlink"><a title="Bio.Nexus.Nodes.Chain.unlink" class="py-name" href="#" onclick="return doclink('link-49', 'unlink', 'link-49');">unlink</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</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-name">succ</tt><tt class="py-op">.</tt><tt id="link-50" 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-50', 'append', 'link-50');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">child</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.Nexus.Nodes.Node.set_prev" class="py-name" href="#" onclick="return doclink('link-51', 'set_prev', 'link-11');">set_prev</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
</div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="Chain.is_parent_of"></a><div id="Chain.is_parent_of-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="Chain.is_parent_of-toggle" onclick="return toggle('Chain.is_parent_of');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#is_parent_of">is_parent_of</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">grandchild</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Chain.is_parent_of-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.is_parent_of-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-docstring">"""Check if grandchild is a subnode of parent: is_parent_of(self,parent,grandchild)."""</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">grandchild</tt><tt class="py-op">==</tt><tt class="py-name">parent</tt> <tt class="py-keyword">or</tt> <tt class="py-name">grandchild</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</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-52" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_succ" class="py-name" href="#" onclick="return doclink('link-52', 'get_succ', 'link-25');">get_succ</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 class="py-keyword">return</tt> <tt id="link-53" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-53', 'True', 'link-53');">True</a></tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">sn</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</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-54" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_succ" class="py-name" href="#" onclick="return doclink('link-54', 'get_succ', 'link-25');">get_succ</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.is_parent_of()=Bio.Nexus.Nodes.Chain-class.html#is_parent_of"><a title="Bio.Nexus.Nodes.Chain.is_parent_of" class="py-name" href="#" onclick="return doclink('link-55', 'is_parent_of', 'link-55');">is_parent_of</a></tt><tt class="py-op">(</tt><tt class="py-name">sn</tt><tt class="py-op">,</tt><tt class="py-name">grandchild</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-56" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-56', 'True', 'link-53');">True</a></tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-57" class="py-name" targets="Variable Bio.EUtils.POM.False=Bio.EUtils.POM-module.html#False"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-57', 'False', 'link-57');">False</a></tt> </tt>
</div><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="Chain.trace"></a><div id="Chain.trace-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="Chain.trace-toggle" onclick="return toggle('Chain.trace');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Chain-class.html#trace">trace</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">start</tt><tt class="py-op">,</tt><tt class="py-param">finish</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Chain.trace-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Chain.trace-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a list of all node_ids between two nodes (excluding start, including end): trace(start,end)."""</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-58" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-58', 'start', 'link-58');">start</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt> <tt class="py-keyword">or</tt> <tt class="py-name">finish</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-59" class="py-name" targets="Class Bio.Nexus.Nodes.NodeException=Bio.Nexus.Nodes.NodeException-class.html"><a title="Bio.Nexus.Nodes.NodeException" class="py-name" href="#" onclick="return doclink('link-59', 'NodeException', 'link-59');">NodeException</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown node.'</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Nexus.Nodes.Chain.is_parent_of" class="py-name" href="#" onclick="return doclink('link-60', 'is_parent_of', 'link-55');">is_parent_of</a></tt><tt class="py-op">(</tt><tt id="link-61" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-61', 'start', 'link-58');">start</a></tt><tt class="py-op">,</tt><tt class="py-name">finish</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-62" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-62', 'start', 'link-58');">start</a></tt><tt class="py-op">==</tt><tt class="py-name">finish</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">return</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">for</tt> <tt class="py-name">sn</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt id="link-63" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-63', 'start', 'link-58');">start</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_succ" class="py-name" href="#" onclick="return doclink('link-64', 'get_succ', 'link-25');">get_succ</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Nexus.Nodes.Chain.is_parent_of" class="py-name" href="#" onclick="return doclink('link-65', 'is_parent_of', 'link-55');">is_parent_of</a></tt><tt class="py-op">(</tt><tt class="py-name">sn</tt><tt class="py-op">,</tt><tt class="py-name">finish</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">sn</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.trace()=Bio.Nexus.Nodes.Chain-class.html#trace"><a title="Bio.Nexus.Nodes.Chain.trace" class="py-name" href="#" onclick="return doclink('link-66', 'trace', 'link-66');">trace</a></tt><tt class="py-op">(</tt><tt class="py-name">sn</tt><tt class="py-op">,</tt><tt class="py-name">finish</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="Node"></a><div id="Node-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="Node-toggle" onclick="return toggle('Node');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html">Node</a><tt class="py-op">:</tt> </tt>
</div><div id="Node-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Node-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-docstring">"""A single node."""</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="Node.__init__"></a><div id="Node.__init__-def"><a name="L120"></a><tt class="py-lineno">120</tt> <a class="py-toggle" href="#" id="Node.__init__-toggle" onclick="return toggle('Node.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-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">data</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="Node.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.__init__-expanded"><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-docstring">"""Represents a node with one predecessor and multiple successors: (self, data=None)."""</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-67', 'id', 'link-0');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-68', 'data', 'link-68');">data</a></tt><tt class="py-op">=</tt><tt id="link-69" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-69', 'data', 'link-68');">data</a></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">prev</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="Node.set_id"></a><div id="Node.set_id-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="Node.set_id-toggle" onclick="return toggle('Node.set_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#set_id">set_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Node.set_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.set_id-expanded"><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-docstring">"""Sets the id of a node, if not set yet: (self,id)."""</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-70', 'id', 'link-0');">id</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-71" class="py-name"><a title="Bio.Nexus.Nodes.NodeException" class="py-name" href="#" onclick="return doclink('link-71', 'NodeException', 'link-59');">NodeException</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Node id cannot be changed.'</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-72', 'id', 'link-0');">id</a></tt><tt class="py-op">=</tt><tt id="link-73" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-73', 'id', 'link-0');">id</a></tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="Node.get_id"></a><div id="Node.get_id-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="Node.get_id-toggle" onclick="return toggle('Node.get_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#get_id">get_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Node.get_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.get_id-expanded"><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the node's id: (self)."""</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-74', 'id', 'link-0');">id</a></tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="Node.get_succ"></a><div id="Node.get_succ-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="Node.get_succ-toggle" onclick="return toggle('Node.get_succ');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#get_succ">get_succ</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="Node.get_succ-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.get_succ-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a list of the node's successors: (self)."""</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</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">succ</tt> </tt>
</div><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="Node.get_prev"></a><div id="Node.get_prev-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="Node.get_prev-toggle" onclick="return toggle('Node.get_prev');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#get_prev">get_prev</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="Node.get_prev-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.get_prev-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the id of the node's predecessor: (self)."""</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="Node.add_succ"></a><div id="Node.add_succ-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="Node.add_succ-toggle" onclick="return toggle('Node.add_succ');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#add_succ">add_succ</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Node.add_succ-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.add_succ-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-docstring">"""Adds a node id to the node's successors: (self,id)."""</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-75', 'id', 'link-0');">id</a></tt><tt class="py-op">,</tt><tt id="link-76" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-76', 'type', 'link-76');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">.</tt><tt id="link-77" 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-77', 'extend', 'link-77');">extend</a></tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-78', 'id', 'link-0');">id</a></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">else</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">.</tt><tt id="link-79" 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-79', 'append', 'link-50');">append</a></tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-80', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="Node.remove_succ"></a><div id="Node.remove_succ-def"><a name="L152"></a><tt class="py-lineno">152</tt> <a class="py-toggle" href="#" id="Node.remove_succ-toggle" onclick="return toggle('Node.remove_succ');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#remove_succ">remove_succ</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Node.remove_succ-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.remove_succ-expanded"><a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-docstring">"""Removes a node id from the node's successors: (self,id)."""</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-81', 'remove', 'link-81');">remove</a></tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-82', 'id', 'link-0');">id</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="Node.set_succ"></a><div id="Node.set_succ-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="Node.set_succ-toggle" onclick="return toggle('Node.set_succ');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#set_succ">set_succ</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">new_succ</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Node.set_succ-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.set_succ-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-docstring">"""Sets the node's successors: (self,new_succ)."""</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">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">new_succ</tt><tt class="py-op">,</tt><tt id="link-83" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-83', 'type', 'link-76');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-84" class="py-name"><a title="Bio.Nexus.Nodes.NodeException" class="py-name" href="#" onclick="return doclink('link-84', 'NodeException', 'link-59');">NodeException</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Node successor must be of list type.'</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">=</tt><tt class="py-name">new_succ</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="Node.set_prev"></a><div id="Node.set_prev-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="Node.set_prev-toggle" onclick="return toggle('Node.set_prev');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#set_prev">set_prev</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Node.set_prev-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.set_prev-expanded"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-docstring">"""Sets the node's predecessor: (self,id)."""</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt><tt class="py-op">=</tt><tt id="link-85" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-85', 'id', 'link-0');">id</a></tt> </tt>
</div><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="Node.get_data"></a><div id="Node.get_data-def"><a name="L166"></a><tt class="py-lineno">166</tt> <a class="py-toggle" href="#" id="Node.get_data-toggle" onclick="return toggle('Node.get_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#get_data">get_data</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="Node.get_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.get_data-expanded"><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a node's data: (self)."""</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-86', 'data', 'link-68');">data</a></tt> </tt>
</div><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="Node.set_data"></a><div id="Node.set_data-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="Node.set_data-toggle" onclick="return toggle('Node.set_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Nodes.Node-class.html#set_data">set_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Node.set_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.set_data-expanded"><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-docstring">"""Sets a node's data: (self,data)."""</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-87', 'data', 'link-68');">data</a></tt><tt class="py-op">=</tt><tt id="link-88" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-88', 'data', 'link-68');">data</a></tt> </tt>
</div></div><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt><script type="text/javascript">
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