<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Bio.Nexus.Trees</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Nexus-module.html">Package Nexus</a> ::
Module Trees
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.Nexus.Trees-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Nexus.Trees-module.html">Module Bio.Nexus.Trees</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Trees.py </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">#</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"># Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.</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"># This code is part of the Biopython distribution and governed by its</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"># license. Please see the LICENSE file that should have been included</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"># as part of this package.</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">#</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"># Tree class handles phylogenetic trees. Provides a set of methods to read and write newick-format tree</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"># descriptions, get information about trees (monphyly of taxon sets, congruence between trees, common ancestors,...)</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"># and to manipulate trees (reroot trees, split terminal nodes).</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 welcome: 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="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">random</tt><tt class="py-op">,</tt> <tt class="py-name">sets</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.Nexus.Nodes=Bio.Nexus.Nodes-module.html"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-0', 'Nodes', 'link-0');">Nodes</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable Bio.Nexus.Trees.PRECISION_BRANCHLENGTH=Bio.Nexus.Trees-module.html#PRECISION_BRANCHLENGTH"><a title="Bio.Nexus.Trees.PRECISION_BRANCHLENGTH" class="py-name" href="#" onclick="return doclink('link-1', 'PRECISION_BRANCHLENGTH', 'link-1');">PRECISION_BRANCHLENGTH</a></tt><tt class="py-op">=</tt><tt class="py-number">6</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Bio.Nexus.Trees.PRECISION_SUPPORT=Bio.Nexus.Trees-module.html#PRECISION_SUPPORT"><a title="Bio.Nexus.Trees.PRECISION_SUPPORT" class="py-name" href="#" onclick="return doclink('link-2', 'PRECISION_SUPPORT', 'link-2');">PRECISION_SUPPORT</a></tt><tt class="py-op">=</tt><tt class="py-number">6</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="TreeError"></a><div id="TreeError-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="TreeError-toggle" onclick="return toggle('TreeError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Nexus.Trees.TreeError-class.html">TreeError</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="NodeData"></a><div id="NodeData-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="NodeData-toggle" onclick="return toggle('NodeData');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Nexus.Trees.NodeData-class.html">NodeData</a><tt class="py-op">:</tt> </tt>
</div><div id="NodeData-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NodeData-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-docstring">"""Stores tree-relevant data associated with nodes (e.g. branches or otus)."""</tt> </tt>
<a name="NodeData.__init__"></a><div id="NodeData.__init__-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="NodeData.__init__-toggle" onclick="return toggle('NodeData.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.NodeData-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">taxon</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">branchlength</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt><tt class="py-param">support</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="NodeData.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NodeData.__init__-expanded"><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">taxon</tt><tt class="py-op">=</tt><tt class="py-name">taxon</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 class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">branchlength</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Martel.test.support=Martel.test.support-module.html"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-3', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt id="link-4" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-4', 'support', 'link-3');">support</a></tt> </tt>
</div></div><a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="Tree"></a><div id="Tree-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="Tree-toggle" onclick="return toggle('Tree');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html">Tree</a><tt class="py-op">(</tt><tt class="py-base-class">Nodes</tt><tt class="py-op">.</tt><tt class="py-base-class">Chain</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Tree-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-docstring">"""Represents a tree using a chain of nodes with on predecessor (=ancestor)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> and multiple successors (=subclades).</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-comment"># A newick tree is parsed into nested list and then converted to a node list in two stages</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># mostly due to historical reasons. This could be done in one swoop). Note: parentheses ( ) and</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># colon : are not allowed in taxon names. This is against NEXUS standard, but makes life much</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># easier when parsing trees.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-comment">## NOTE: Tree should store its data class in something like self.dataclass=data,</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## so that nodes that are generated have easy access to the data class</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## Some routines use automatically NodeData, this needs to be more concise</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="Tree.__init__"></a><div id="Tree.__init__-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="Tree.__init__-toggle" onclick="return toggle('Tree.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-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">tree</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">weight</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt><tt class="py-param">rooted</tt><tt class="py-op">=</tt><tt id="link-5" 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-5', 'False', 'link-5');">False</a></tt><tt class="py-op">,</tt><tt class="py-param">name</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">=</tt><tt id="link-6" class="py-name" targets="Class Bio.Nexus.Trees.NodeData=Bio.Nexus.Trees.NodeData-class.html"><a title="Bio.Nexus.Trees.NodeData" class="py-name" href="#" onclick="return doclink('link-6', 'NodeData', 'link-6');">NodeData</a></tt><tt class="py-op">,</tt><tt class="py-param">values_are_support</tt><tt class="py-op">=</tt><tt id="link-7" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-7', 'False', 'link-5');">False</a></tt><tt class="py-op">,</tt><tt class="py-param">max_support</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.__init__-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-docstring">"""Ntree(self,tree)."""</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-8', 'Nodes', 'link-0');">Nodes</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Class Bio.Crystal.Chain=Bio.Crystal.Chain-class.html,Class Bio.Nexus.Nodes.Chain=Bio.Nexus.Nodes.Chain-class.html,Module Bio.PDB.Chain=Bio.PDB.Chain-module.html,Class Bio.PDB.Chain.Chain=Bio.PDB.Chain.Chain-class.html"><a title="Bio.Crystal.Chain
Bio.Nexus.Nodes.Chain
Bio.PDB.Chain
Bio.PDB.Chain.Chain" class="py-name" href="#" onclick="return doclink('link-9', 'Chain', 'link-9');">Chain</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.CDD.Iterator.__init__()=Bio.CDD.Iterator-class.html#__init__,Method Bio.CDD.Record.Record.__init__()=Bio.CDD.Record.Record-class.html#__init__,Method Bio.CDD.RecordParser.__init__()=Bio.CDD.RecordParser-class.html#__init__,Method Bio.CDD._RecordConsumer.__init__()=Bio.CDD._RecordConsumer-class.html#__init__,Method Bio.CDD._Scanner.__init__()=Bio.CDD._Scanner-class.html#__init__,Method Bio.Clustalw.ClustalAlignment.__init__()=Bio.Clustalw.ClustalAlignment-class.html#__init__,Method Bio.Clustalw.MultipleAlignCL.__init__()=Bio.Clustalw.MultipleAlignCL-class.html#__init__,Method Bio.Cluster.DataFile.__init__()=Bio.Cluster.DataFile-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method Bio.Compass.Iterator.__init__()=Bio.Compass.Iterator-class.html#__init__,Method Bio.Compass.Record.__init__()=Bio.Compass.Record-class.html#__init__,Method Bio.Compass.RecordParser.__init__()=Bio.Compass.RecordParser-class.html#__init__,Method Bio.Compass._Consumer.__init__()=Bio.Compass._Consumer-class.html#__init__,Method Bio.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.CrystalError.__init__()=Bio.Crystal.CrystalError-class.html#__init__,Method Bio.Crystal.Error.__init__()=Bio.Crystal.Error-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.DBXRef.DBXRef.__init__()=Bio.DBXRef.DBXRef-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousCodonTable.__init__()=Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__init__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__init__,Method Bio.Data.CodonTable.CodonTable.__init__()=Bio.Data.CodonTable.CodonTable-class.html#__init__,Method Bio.Data.CodonTable.NCBICodonTable.__init__()=Bio.Data.CodonTable.NCBICodonTable-class.html#__init__,Method Bio.Decode.DecodeParser.__init__()=Bio.Decode.DecodeParser-class.html#__init__,Method Bio.Decode.DecodeScanner.__init__()=Bio.Decode.DecodeScanner-class.html#__init__,Method Bio.Decode.Float.__init__()=Bio.Decode.Float-class.html#__init__,Method Bio.Decode.Function.__init__()=Bio.Decode.Function-class.html#__init__,Method Bio.Decode.FunctionCall.__init__()=Bio.Decode.FunctionCall-class.html#__init__,Method Bio.Decode.FunctionCallChain.__init__()=Bio.Decode.FunctionCallChain-class.html#__init__,Method Bio.Decode.FunctionName.__init__()=Bio.Decode.FunctionName-class.html#__init__,Method Bio.Decode.Integer.__init__()=Bio.Decode.Integer-class.html#__init__,Method Bio.Decode.String.__init__()=Bio.Decode.String-class.html#__init__,Method Bio.Decode.Token.__init__()=Bio.Decode.Token-class.html#__init__,Method Bio.Decode.ValueToken.__init__()=Bio.Decode.ValueToken-class.html#__init__,Method Bio.DocSQL.Create.__init__()=Bio.DocSQL.Create-class.html#__init__,Method Bio.DocSQL.Insert.__init__()=Bio.DocSQL.Insert-class.html#__init__,Method Bio.DocSQL.IterationCursor.__init__()=Bio.DocSQL.IterationCursor-class.html#__init__,Method Bio.DocSQL.Query.__init__()=Bio.DocSQL.Query-class.html#__init__,Method Bio.DocSQL.QueryAll.__init__()=Bio.DocSQL.QueryAll-class.html#__init__,Method Bio.DocSQL.QueryGeneric.__init__()=Bio.DocSQL.QueryGeneric-class.html#__init__,Method Bio.DocSQL.QueryRow.__init__()=Bio.DocSQL.QueryRow-class.html#__init__,Method Bio.DocSQL.QuerySingle.__init__()=Bio.DocSQL.QuerySingle-class.html#__init__,Method Bio.ECell.ECellError.__init__()=Bio.ECell.ECellError-class.html#__init__,Method Bio.ECell.Error.__init__()=Bio.ECell.Error-class.html#__init__,Method Bio.ECell.Iterator.__init__()=Bio.ECell.Iterator-class.html#__init__,Method Bio.ECell.Record.Record.__init__()=Bio.ECell.Record.Record-class.html#__init__,Method Bio.ECell.RecordParser.__init__()=Bio.ECell.RecordParser-class.html#__init__,Method Bio.ECell._RecordConsumer.__init__()=Bio.ECell._RecordConsumer-class.html#__init__,Method Bio.ECell._Scanner.__init__()=Bio.ECell._Scanner-class.html#__init__,Method Bio.EUtils.Config.DatabaseInfo.__init__()=Bio.EUtils.Config.DatabaseInfo-class.html#__init__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsClient.__init__()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsLookup.__init__()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#__init__,Method Bio.EUtils.Datatypes.BinaryOp.__init__()=Bio.EUtils.Datatypes.BinaryOp-class.html#__init__,Method Bio.EUtils.Datatypes.CheckLinkSet.__init__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.DBIds.__init__()=Bio.EUtils.Datatypes.DBIds-class.html#__init__,Method Bio.EUtils.Datatypes.Date.__init__()=Bio.EUtils.Datatypes.Date-class.html#__init__,Method Bio.EUtils.Datatypes.DateRange.__init__()=Bio.EUtils.Datatypes.DateRange-class.html#__init__,Method Bio.EUtils.Datatypes.EUtilsSearchError.__init__()=Bio.EUtils.Datatypes.EUtilsSearchError-class.html#__init__,Method Bio.EUtils.Datatypes.IdCheck.__init__()=Bio.EUtils.Datatypes.IdCheck-class.html#__init__,Method Bio.EUtils.Datatypes.IdUrlSet.__init__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__init__,Method Bio.EUtils.Datatypes.Link.__init__()=Bio.EUtils.Datatypes.Link-class.html#__init__,Method Bio.EUtils.Datatypes.LinkSetDb.__init__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__init__,Method Bio.EUtils.Datatypes.LinksLinkSet.__init__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__init__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.ObjUrl.__init__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__init__,Method Bio.EUtils.Datatypes.PostResult.__init__()=Bio.EUtils.Datatypes.PostResult-class.html#__init__,Method Bio.EUtils.Datatypes.Problem.__init__()=Bio.EUtils.Datatypes.Problem-class.html#__init__,Method Bio.EUtils.Datatypes.Provider.__init__()=Bio.EUtils.Datatypes.Provider-class.html#__init__,Method Bio.EUtils.Datatypes.Range.__init__()=Bio.EUtils.Datatypes.Range-class.html#__init__,Method Bio.EUtils.Datatypes.SearchResult.__init__()=Bio.EUtils.Datatypes.SearchResult-class.html#__init__,Method Bio.EUtils.Datatypes.Summary.__init__()=Bio.EUtils.Datatypes.Summary-class.html#__init__,Method Bio.EUtils.Datatypes.Term.__init__()=Bio.EUtils.Datatypes.Term-class.html#__init__,Method Bio.EUtils.Datatypes.WithinNDays.__init__()=Bio.EUtils.Datatypes.WithinNDays-class.html#__init__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryClient.__init__()=Bio.EUtils.HistoryClient.HistoryClient-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryCookie.__init__()=Bio.EUtils.HistoryClient.HistoryCookie-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryLookup.__init__()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryRecord.__init__()=Bio.EUtils.HistoryClient.HistoryRecord-class.html#__init__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__init__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__init__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__init__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__init__,Method Bio.EUtils.POM.Comment.__init__()=Bio.EUtils.POM.Comment-class.html#__init__,Method Bio.EUtils.POM.ContentModel.__init__()=Bio.EUtils.POM.ContentModel-class.html#__init__,Method Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__()=Bio.EUtils.POM.DTDConsumerForSourceGeneration-class.html#__init__,Method Bio.EUtils.POM.ElementNode.__init__()=Bio.EUtils.POM.ElementNode-class.html#__init__,Method Bio.EUtils.POM.IndentedText.__init__()=Bio.EUtils.POM.IndentedText-class.html#__init__,Method Bio.EUtils.POM.ObjectParserHandler.__init__()=Bio.EUtils.POM.ObjectParserHandler-class.html#__init__,Method Bio.EUtils.POM.POMDocument.__init__()=Bio.EUtils.POM.POMDocument-class.html#__init__,Method Bio.EUtils.POM.XMLAttribute.__init__()=Bio.EUtils.POM.XMLAttribute-class.html#__init__,Method Bio.EUtils.POM._ContentModelGenerator.__init__()=Bio.EUtils.POM._ContentModelGenerator-class.html#__init__,Method Bio.EUtils.ReseekFile.ReseekFile.__init__()=Bio.EUtils.ReseekFile.ReseekFile-class.html#__init__,Method Bio.EUtils.ThinClient.ThinClient.__init__()=Bio.EUtils.ThinClient.ThinClient-class.html#__init__,Method Bio.EUtils.parse.UsePOMParser.__init__()=Bio.EUtils.parse.UsePOMParser-class.html#__init__,Method Bio.EUtils.sourcegen.ClassHolder.__init__()=Bio.EUtils.sourcegen.ClassHolder-class.html#__init__,Method Bio.EUtils.sourcegen.FunctionHolder.__init__()=Bio.EUtils.sourcegen.FunctionHolder-class.html#__init__,Method Bio.EUtils.sourcegen.MethodHolder.__init__()=Bio.EUtils.sourcegen.MethodHolder-class.html#__init__,Method Bio.EUtils.sourcegen.SourceFile.__init__()=Bio.EUtils.sourcegen.SourceFile-class.html#__init__,Method Bio.EUtils.sourcegen.SourceGen.__init__()=Bio.EUtils.sourcegen.SourceGen-class.html#__init__,Method Bio.Emboss.Applications.EConsenseCommandline.__init__()=Bio.Emboss.Applications.EConsenseCommandline-class.html#__init__,Method Bio.Emboss.Applications.EInvertedCommandline.__init__()=Bio.Emboss.Applications.EInvertedCommandline-class.html#__init__,Method Bio.Emboss.Applications.ENeighborCommandline.__init__()=Bio.Emboss.Applications.ENeighborCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtDistCommandline.__init__()=Bio.Emboss.Applications.EProtDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtParsCommandline.__init__()=Bio.Emboss.Applications.EProtParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.ESeqBootCommandline.__init__()=Bio.Emboss.Applications.ESeqBootCommandline-class.html#__init__,Method Bio.Emboss.Applications.ETandemCommandline.__init__()=Bio.Emboss.Applications.ETandemCommandline-class.html#__init__,Method Bio.Emboss.Applications.Est2GenomeCommandline.__init__()=Bio.Emboss.Applications.Est2GenomeCommandline-class.html#__init__,Method Bio.Emboss.Applications.FuzznucCommandline.__init__()=Bio.Emboss.Applications.FuzznucCommandline-class.html#__init__,Method Bio.Emboss.Applications.PalindromeCommandline.__init__()=Bio.Emboss.Applications.PalindromeCommandline-class.html#__init__,Method Bio.Emboss.Applications.Primer3Commandline.__init__()=Bio.Emboss.Applications.Primer3Commandline-class.html#__init__,Method Bio.Emboss.Applications.PrimerSearchCommandline.__init__()=Bio.Emboss.Applications.PrimerSearchCommandline-class.html#__init__,Method Bio.Emboss.Applications.TranalignCommandline.__init__()=Bio.Emboss.Applications.TranalignCommandline-class.html#__init__,Method Bio.Emboss.Applications.WaterCommandline.__init__()=Bio.Emboss.Applications.WaterCommandline-class.html#__init__,Method Bio.Emboss.Primer.Primer3Parser.__init__()=Bio.Emboss.Primer.Primer3Parser-class.html#__init__,Method Bio.Emboss.Primer.Primer3Primers.__init__()=Bio.Emboss.Primer.Primer3Primers-class.html#__init__,Method Bio.Emboss.Primer.Primer3Record.__init__()=Bio.Emboss.Primer.Primer3Record-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchAmplifier.__init__()=Bio.Emboss.Primer.PrimerSearchAmplifier-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchInputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchInputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchParser.__init__()=Bio.Emboss.Primer.PrimerSearchParser-class.html#__init__,Method Bio.Emboss.Primer._Primer3RecordConsumer.__init__()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#__init__,Method Bio.Emboss.Primer._Primer3Scanner.__init__()=Bio.Emboss.Primer._Primer3Scanner-class.html#__init__,Method Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#__init__,Method Bio.Emboss.Primer._PrimerSearchScanner.__init__()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#__init__,Method Bio.Entrez.Parser.DataHandler.__init__()=Bio.Entrez.Parser.DataHandler-class.html#__init__,Method Bio.Entrez.Parser.StructureElement.__init__()=Bio.Entrez.Parser.StructureElement-class.html#__init__,Method Bio.Enzyme.DataRecord.__init__()=Bio.Enzyme.DataRecord-class.html#__init__,Method Bio.Enzyme.EnzymeRecord.__init__()=Bio.Enzyme.EnzymeRecord-class.html#__init__,Method Bio.Enzyme.Iterator.__init__()=Bio.Enzyme.Iterator-class.html#__init__,Method Bio.Enzyme.RecordParser.__init__()=Bio.Enzyme.RecordParser-class.html#__init__,Method Bio.Enzyme._RecordConsumer.__init__()=Bio.Enzyme._RecordConsumer-class.html#__init__,Method Bio.FSSP.FSSPAlignDict.__init__()=Bio.FSSP.FSSPAlignDict-class.html#__init__,Method Bio.FSSP.FSSPAlignRec.__init__()=Bio.FSSP.FSSPAlignRec-class.html#__init__,Method Bio.FSSP.FSSPHeader.__init__()=Bio.FSSP.FSSPHeader-class.html#__init__,Method Bio.FSSP.FSSPSumRec.__init__()=Bio.FSSP.FSSPSumRec-class.html#__init__,Method Bio.FSSP.FSSPTools.FSSPMultAlign.__init__()=Bio.FSSP.FSSPTools.FSSPMultAlign-class.html#__init__,Method Bio.FSSP.PosAlign.__init__()=Bio.FSSP.PosAlign-class.html#__init__,Method Bio.FSSP.fssp_rec.fff_rec.__init__()=Bio.FSSP.fssp_rec.fff_rec-class.html#__init__,Method Bio.Fasta.FastaAlign.FastaAlignment.__init__()=Bio.Fasta.FastaAlign.FastaAlignment-class.html#__init__,Method Bio.Fasta.Iterator.__init__()=Bio.Fasta.Iterator-class.html#__init__,Method Bio.Fasta.Record.__init__()=Bio.Fasta.Record-class.html#__init__,Method Bio.Fasta.RecordParser.__init__()=Bio.Fasta.RecordParser-class.html#__init__,Method Bio.Fasta.SequenceParser.__init__()=Bio.Fasta.SequenceParser-class.html#__init__,Method Bio.File.SGMLHandle.__init__()=Bio.File.SGMLHandle-class.html#__init__,Method Bio.File.SGMLStripper.MyParser.__init__()=Bio.File.SGMLStripper.MyParser-class.html#__init__,Method Bio.File.SGMLStripper.__init__()=Bio.File.SGMLStripper-class.html#__init__,Method Bio.File.UndoHandle.__init__()=Bio.File.UndoHandle-class.html#__init__,Method Bio.FilteredReader.FilteredReader.__init__()=Bio.FilteredReader.FilteredReader-class.html#__init__,Method Bio.GA.Crossover.General.SafeFitnessCrossover.__init__()=Bio.GA.Crossover.General.SafeFitnessCrossover-class.html#__init__,Method Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__()=Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover-class.html#__init__,Method Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__()=Bio.GA.Crossover.GeneralPoint.InterleaveCrossover-class.html#__init__,Method Bio.GA.Crossover.Point.SinglePointCrossover.__init__()=Bio.GA.Crossover.Point.SinglePointCrossover-class.html#__init__,Method Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__()=Bio.GA.Crossover.TwoPoint.TwoPointCrossover-class.html#__init__,Method Bio.GA.Crossover.Uniform.UniformCrossover.__init__()=Bio.GA.Crossover.Uniform.UniformCrossover-class.html#__init__,Method Bio.GA.Evolver.GenerationEvolver.__init__()=Bio.GA.Evolver.GenerationEvolver-class.html#__init__,Method Bio.GA.Evolver.SteadyStateEvolver.__init__()=Bio.GA.Evolver.SteadyStateEvolver-class.html#__init__,Method Bio.GA.Mutation.General.SafeFitnessMutation.__init__()=Bio.GA.Mutation.General.SafeFitnessMutation-class.html#__init__,Method Bio.GA.Mutation.Simple.ConversionMutation.__init__()=Bio.GA.Mutation.Simple.ConversionMutation-class.html#__init__,Method Bio.GA.Mutation.Simple.SinglePositionMutation.__init__()=Bio.GA.Mutation.Simple.SinglePositionMutation-class.html#__init__,Method Bio.GA.Organism.Organism.__init__()=Bio.GA.Organism.Organism-class.html#__init__,Method Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__()=Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html#__init__,Method Bio.GA.Selection.Abstract.AbstractSelection.__init__()=Bio.GA.Selection.Abstract.AbstractSelection-class.html#__init__,Method Bio.GA.Selection.Diversity.DiversitySelection.__init__()=Bio.GA.Selection.Diversity.DiversitySelection-class.html#__init__,Method Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__()=Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html#__init__,Method Bio.GA.Selection.Tournament.TournamentSelection.__init__()=Bio.GA.Selection.Tournament.TournamentSelection-class.html#__init__,Method Bio.GFF.Connection.__init__()=Bio.GFF.Connection-class.html#__init__,Method Bio.GFF.Feature.__init__()=Bio.GFF.Feature-class.html#__init__,Method Bio.GFF.FeatureAggregate.__init__()=Bio.GFF.FeatureAggregate-class.html#__init__,Method Bio.GFF.FeatureQuery.__init__()=Bio.GFF.FeatureQuery-class.html#__init__,Method Bio.GFF.FeatureQueryRow.__init__()=Bio.GFF.FeatureQueryRow-class.html#__init__,Method Bio.GFF.GenericTools.ArgsParser.__init__()=Bio.GFF.GenericTools.ArgsParser-class.html#__init__,Method Bio.GFF.GenericTools.Surrogate.__init__()=Bio.GFF.GenericTools.Surrogate-class.html#__init__,Method Bio.GFF.GenericTools.TempFile.__init__()=Bio.GFF.GenericTools.TempFile-class.html#__init__,Method Bio.GFF.RetrieveSeqname.__init__()=Bio.GFF.RetrieveSeqname-class.html#__init__,Method Bio.GFF.Segment.__init__()=Bio.GFF.Segment-class.html#__init__,Method Bio.GFF.easy.FeatureDict.__init__()=Bio.GFF.easy.FeatureDict-class.html#__init__,Method Bio.GFF.easy.Location.__init__()=Bio.GFF.easy.Location-class.html#__init__,Method Bio.GFF.easy.LocationFromCoords.__init__()=Bio.GFF.easy.LocationFromCoords-class.html#__init__,Method Bio.GFF.easy.LocationFromString.__init__()=Bio.GFF.easy.LocationFromString-class.html#__init__,Method Bio.GFF.easy.LocationJoin.__init__()=Bio.GFF.easy.LocationJoin-class.html#__init__,Method Bio.GenBank.FeatureParser.__init__()=Bio.GenBank.FeatureParser-class.html#__init__,Method Bio.GenBank.Iterator.__init__()=Bio.GenBank.Iterator-class.html#__init__,Method Bio.GenBank.LocationParser.AbsoluteLocation.__init__()=Bio.GenBank.LocationParser.AbsoluteLocation-class.html#__init__,Method Bio.GenBank.LocationParser.Between.__init__()=Bio.GenBank.LocationParser.Between-class.html#__init__,Method Bio.GenBank.LocationParser.FeatureName.__init__()=Bio.GenBank.LocationParser.FeatureName-class.html#__init__,Method Bio.GenBank.LocationParser.Function.__init__()=Bio.GenBank.LocationParser.Function-class.html#__init__,Method Bio.GenBank.LocationParser.HighBound.__init__()=Bio.GenBank.LocationParser.HighBound-class.html#__init__,Method Bio.GenBank.LocationParser.Integer.__init__()=Bio.GenBank.LocationParser.Integer-class.html#__init__,Method Bio.GenBank.LocationParser.LocationParser.__init__()=Bio.GenBank.LocationParser.LocationParser-class.html#__init__,Method Bio.GenBank.LocationParser.LocationScanner.__init__()=Bio.GenBank.LocationParser.LocationScanner-class.html#__init__,Method Bio.GenBank.LocationParser.LowBound.__init__()=Bio.GenBank.LocationParser.LowBound-class.html#__init__,Method Bio.GenBank.LocationParser.Path.__init__()=Bio.GenBank.LocationParser.Path-class.html#__init__,Method Bio.GenBank.LocationParser.Range.__init__()=Bio.GenBank.LocationParser.Range-class.html#__init__,Method Bio.GenBank.LocationParser.Symbol.__init__()=Bio.GenBank.LocationParser.Symbol-class.html#__init__,Method Bio.GenBank.LocationParser.Token.__init__()=Bio.GenBank.LocationParser.Token-class.html#__init__,Method Bio.GenBank.LocationParser.TwoBound.__init__()=Bio.GenBank.LocationParser.TwoBound-class.html#__init__,Method Bio.GenBank.NCBIDictionary.__init__()=Bio.GenBank.NCBIDictionary-class.html#__init__,Method Bio.GenBank.Record.Feature.__init__()=Bio.GenBank.Record.Feature-class.html#__init__,Method Bio.GenBank.Record.Qualifier.__init__()=Bio.GenBank.Record.Qualifier-class.html#__init__,Method Bio.GenBank.Record.Record.__init__()=Bio.GenBank.Record.Record-class.html#__init__,Method Bio.GenBank.Record.Reference.__init__()=Bio.GenBank.Record.Reference-class.html#__init__,Method Bio.GenBank.RecordParser.__init__()=Bio.GenBank.RecordParser-class.html#__init__,Method Bio.GenBank.Scanner.InsdcScanner.__init__()=Bio.GenBank.Scanner.InsdcScanner-class.html#__init__,Method Bio.GenBank._BaseGenBankConsumer.__init__()=Bio.GenBank._BaseGenBankConsumer-class.html#__init__,Method Bio.GenBank._FeatureConsumer.__init__()=Bio.GenBank._FeatureConsumer-class.html#__init__,Method Bio.GenBank._RecordConsumer.__init__()=Bio.GenBank._RecordConsumer-class.html#__init__,Method Bio.GenBank.utils.FeatureValueCleaner.__init__()=Bio.GenBank.utils.FeatureValueCleaner-class.html#__init__,Method Bio.Geo.Record.Record.__init__()=Bio.Geo.Record.Record-class.html#__init__,Method Bio.Gobase.Dictionary.__init__()=Bio.Gobase.Dictionary-class.html#__init__,Method Bio.Gobase.GeneRecord.__init__()=Bio.Gobase.GeneRecord-class.html#__init__,Method Bio.Gobase.Iterator.__init__()=Bio.Gobase.Iterator-class.html#__init__,Method Bio.Gobase.ProteinRecord.__init__()=Bio.Gobase.ProteinRecord-class.html#__init__,Method Bio.Gobase.Record.__init__()=Bio.Gobase.Record-class.html#__init__,Method Bio.Gobase.RecordParser.__init__()=Bio.Gobase.RecordParser-class.html#__init__,Method Bio.Gobase.SequenceRecord.__init__()=Bio.Gobase.SequenceRecord-class.html#__init__,Method Bio.Gobase._RecordConsumer.__init__()=Bio.Gobase._RecordConsumer-class.html#__init__,Method Bio.Graphics.BasicChromosome.Chromosome.__init__()=Bio.Graphics.BasicChromosome.Chromosome-class.html#__init__,Method Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__()=Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html#__init__,Method Bio.Graphics.BasicChromosome.Organism.__init__()=Bio.Graphics.BasicChromosome.Organism-class.html#__init__,Method Bio.Graphics.BasicChromosome.TelomereSegment.__init__()=Bio.Graphics.BasicChromosome.TelomereSegment-class.html#__init__,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#__init__,Method Bio.Graphics.Comparative.ComparativeScatterPlot.__init__()=Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#__init__,Method Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__()=Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#__init__,Method Bio.Graphics.Distribution.BarChartDistribution.__init__()=Bio.Graphics.Distribution.BarChartDistribution-class.html#__init__,Method Bio.Graphics.Distribution.DistributionPage.__init__()=Bio.Graphics.Distribution.DistributionPage-class.html#__init__,Method Bio.Graphics.Distribution.LineDistribution.__init__()=Bio.Graphics.Distribution.LineDistribution-class.html#__init__,Method Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#__init__,Method Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.LogDPAlgorithms-class.html#__init__,Method Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#__init__,Method Bio.HMM.MarkovModel.HiddenMarkovModel.__init__()=Bio.HMM.MarkovModel.HiddenMarkovModel-class.html#__init__,Method Bio.HMM.MarkovModel.MarkovModelBuilder.__init__()=Bio.HMM.MarkovModel.MarkovModelBuilder-class.html#__init__,Method Bio.HMM.Trainer.AbstractTrainer.__init__()=Bio.HMM.Trainer.AbstractTrainer-class.html#__init__,Method Bio.HMM.Trainer.BaumWelchTrainer.__init__()=Bio.HMM.Trainer.BaumWelchTrainer-class.html#__init__,Method Bio.HMM.Trainer.KnownStateTrainer.__init__()=Bio.HMM.Trainer.KnownStateTrainer-class.html#__init__,Method Bio.HMM.Trainer.TrainingSequence.__init__()=Bio.HMM.Trainer.TrainingSequence-class.html#__init__,Method Bio.HotRand.HotCache.__init__()=Bio.HotRand.HotCache-class.html#__init__,Method Bio.HotRand.HotRandom.__init__()=Bio.HotRand.HotRandom-class.html#__init__,Method Bio.Index._InMemoryIndex.__init__()=Bio.Index._InMemoryIndex-class.html#__init__,Method Bio.Index._ShelveIndex.__init__()=Bio.Index._ShelveIndex-class.html#__init__,Method Bio.IntelliGenetics.IntelliGeneticsReader.__init__()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#__init__,Method Bio.IntelliGenetics.Iterator.__init__()=Bio.IntelliGenetics.Iterator-class.html#__init__,Method Bio.IntelliGenetics.Record.Record.__init__()=Bio.IntelliGenetics.Record.Record-class.html#__init__,Method Bio.IntelliGenetics.RecordParser.__init__()=Bio.IntelliGenetics.RecordParser-class.html#__init__,Method Bio.IntelliGenetics._RecordConsumer.__init__()=Bio.IntelliGenetics._RecordConsumer-class.html#__init__,Method Bio.IntelliGenetics._Scanner.__init__()=Bio.IntelliGenetics._Scanner-class.html#__init__,Method Bio.KDTree.CKDTree.KDTree.__init__()=Bio.KDTree.CKDTree.KDTree-class.html#__init__,Method Bio.KDTree.CKDTree.KDTreePtr.__init__()=Bio.KDTree.CKDTree.KDTreePtr-class.html#__init__,Method Bio.KDTree.KDTree.KDTree.__init__()=Bio.KDTree.KDTree.KDTree-class.html#__init__,Method Bio.KEGG.Compound.Record.__init__()=Bio.KEGG.Compound.Record-class.html#__init__,Method Bio.KEGG.Enzyme.Record.__init__()=Bio.KEGG.Enzyme.Record-class.html#__init__,Method Bio.LocusLink.Iterator.__init__()=Bio.LocusLink.Iterator-class.html#__init__,Method Bio.LocusLink.Record.__init__()=Bio.LocusLink.Record-class.html#__init__,Method Bio.LocusLink.RecordParser.__init__()=Bio.LocusLink.RecordParser-class.html#__init__,Method Bio.LocusLink._RecordConsumer.__init__()=Bio.LocusLink._RecordConsumer-class.html#__init__,Method Bio.LocusLink._Scanner.__init__()=Bio.LocusLink._Scanner-class.html#__init__,Method Bio.LocusLink.web_parse.Record.__init__()=Bio.LocusLink.web_parse.Record-class.html#__init__,Method Bio.LocusLink.web_parse.Token.__init__()=Bio.LocusLink.web_parse.Token-class.html#__init__,Method Bio.LocusLink.web_parse.Url.__init__()=Bio.LocusLink.web_parse.Url-class.html#__init__,Method Bio.LogisticRegression.LogisticRegression.__init__()=Bio.LogisticRegression.LogisticRegression-class.html#__init__,Method Bio.MEME.Motif.Instance.__init__()=Bio.MEME.Motif.Instance-class.html#__init__,Method Bio.MEME.Motif.MEMEMotif.__init__()=Bio.MEME.Motif.MEMEMotif-class.html#__init__,Method Bio.MEME.Motif.Motif.__init__()=Bio.MEME.Motif.Motif-class.html#__init__,Method Bio.MEME.Parser.MASTParser.__init__()=Bio.MEME.Parser.MASTParser-class.html#__init__,Method Bio.MEME.Parser.MASTRecord.__init__()=Bio.MEME.Parser.MASTRecord-class.html#__init__,Method Bio.MEME.Parser.MEMEParser.__init__()=Bio.MEME.Parser.MEMEParser-class.html#__init__,Method Bio.MEME.Parser.MEMERecord.__init__()=Bio.MEME.Parser.MEMERecord-class.html#__init__,Method Bio.MEME.Parser._MASTConsumer.__init__()=Bio.MEME.Parser._MASTConsumer-class.html#__init__,Method Bio.MEME.Parser._MEMEConsumer.__init__()=Bio.MEME.Parser._MEMEConsumer-class.html#__init__,Method Bio.MarkovModel.MarkovModel.__init__()=Bio.MarkovModel.MarkovModel-class.html#__init__,Method Bio.MaxEntropy.MaxEntropy.__init__()=Bio.MaxEntropy.MaxEntropy-class.html#__init__,Method Bio.Medline.Iterator.__init__()=Bio.Medline.Iterator-class.html#__init__,Method Bio.Medline.Record.__init__()=Bio.Medline.Record-class.html#__init__,Method Bio.Medline.RecordParser.__init__()=Bio.Medline.RecordParser-class.html#__init__,Method Bio.Medline._RecordConsumer.__init__()=Bio.Medline._RecordConsumer-class.html#__init__,Method Bio.MetaTool.Iterator.__init__()=Bio.MetaTool.Iterator-class.html#__init__,Method Bio.MetaTool.Record.Metabolite.__init__()=Bio.MetaTool.Record.Metabolite-class.html#__init__,Method Bio.MetaTool.Record.MetaboliteRole.__init__()=Bio.MetaTool.Record.MetaboliteRole-class.html#__init__,Method Bio.MetaTool.Record.PathwayTransform.__init__()=Bio.MetaTool.Record.PathwayTransform-class.html#__init__,Method Bio.MetaTool.Record.Record.__init__()=Bio.MetaTool.Record.Record-class.html#__init__,Method Bio.MetaTool.RecordParser.__init__()=Bio.MetaTool.RecordParser-class.html#__init__,Method Bio.MetaTool._RecordConsumer.__init__()=Bio.MetaTool._RecordConsumer-class.html#__init__,Method Bio.MetaTool._Scanner.__init__()=Bio.MetaTool._Scanner-class.html#__init__,Method Bio.Mindy.BaseDB.OpenDB.__init__()=Bio.Mindy.BaseDB.OpenDB-class.html#__init__,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#__init__,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#__init__,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.BaseFlatDB.__init__()=Bio.Mindy.FlatDB.BaseFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.BisectFile.__init__()=Bio.Mindy.FlatDB.BisectFile-class.html#__init__,Method Bio.Mindy.FlatDB.DiskFlatDB.__init__()=Bio.Mindy.FlatDB.DiskFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.MemoryFlatDB.__init__()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.PrimaryNamespace.__init__()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.PrimaryTable.__init__()=Bio.Mindy.FlatDB.PrimaryTable-class.html#__init__,Method Bio.Mindy.FlatDB.SecondaryNamespace.__init__()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.SecondaryTable.__init__()=Bio.Mindy.FlatDB.SecondaryTable-class.html#__init__,Method Bio.Mindy.Location.Location.__init__()=Bio.Mindy.Location.Location-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__()=Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.FunctionIndexer-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.SimpleIndexer-class.html#__init__,Method Bio.Mindy.XPath.GrabXPathNodes.__init__()=Bio.Mindy.XPath.GrabXPathNodes-class.html#__init__,Method Bio.NBRF.Iterator.__init__()=Bio.NBRF.Iterator-class.html#__init__,Method Bio.NBRF.Record.Record.__init__()=Bio.NBRF.Record.Record-class.html#__init__,Method Bio.NBRF.RecordParser.__init__()=Bio.NBRF.RecordParser-class.html#__init__,Method Bio.NBRF._RecordConsumer.__init__()=Bio.NBRF._RecordConsumer-class.html#__init__,Method Bio.NBRF._Scanner.__init__()=Bio.NBRF._Scanner-class.html#__init__,Method Bio.NMR.xpktools.Peaklist.__init__()=Bio.NMR.xpktools.Peaklist-class.html#__init__,Method Bio.NMR.xpktools.XpkEntry.__init__()=Bio.NMR.xpktools.XpkEntry-class.html#__init__,Method Bio.NaiveBayes.NaiveBayes.__init__()=Bio.NaiveBayes.NaiveBayes-class.html#__init__,Method Bio.Ndb.Record.__init__()=Bio.Ndb.Record-class.html#__init__,Method Bio.NetCatch.ExtractUrls.__init__()=Bio.NetCatch.ExtractUrls-class.html#__init__,Method Bio.NetCatch.NetCatch.__init__()=Bio.NetCatch.NetCatch-class.html#__init__,Method Bio.NetCatch.Url.__init__()=Bio.NetCatch.Url-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__()=Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork-class.html#__init__,Method Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__()=Bio.NeuralNetwork.Gene.Motif.MotifCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#__init__,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__()=Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__()=Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__()=Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__()=Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.Schema.__init__()=Bio.NeuralNetwork.Gene.Schema.Schema-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaFactory-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__()=Bio.NeuralNetwork.Gene.Schema.SimpleFinisher-class.html#__init__,Method Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__()=Bio.NeuralNetwork.Gene.Signature.SignatureCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#__init__,Method Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__()=Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-class.html#__init__,Method Bio.NeuralNetwork.Training.ExampleManager.__init__()=Bio.NeuralNetwork.Training.ExampleManager-class.html#__init__,Method Bio.NeuralNetwork.Training.TrainingExample.__init__()=Bio.NeuralNetwork.Training.TrainingExample-class.html#__init__,Method Bio.Nexus.Nexus.Block.__init__()=Bio.Nexus.Nexus.Block-class.html#__init__,Method Bio.Nexus.Nexus.CharBuffer.__init__()=Bio.Nexus.Nexus.CharBuffer-class.html#__init__,Method Bio.Nexus.Nexus.Commandline.__init__()=Bio.Nexus.Nexus.Commandline-class.html#__init__,Method Bio.Nexus.Nexus.Nexus.__init__()=Bio.Nexus.Nexus.Nexus-class.html#__init__,Method Bio.Nexus.Nexus.StepMatrix.__init__()=Bio.Nexus.Nexus.StepMatrix-class.html#__init__,Method Bio.Nexus.Nodes.Chain.__init__()=Bio.Nexus.Nodes.Chain-class.html#__init__,Method Bio.Nexus.Nodes.Node.__init__()=Bio.Nexus.Nodes.Node-class.html#__init__,Method Bio.Nexus.Trees.NodeData.__init__()=Bio.Nexus.Trees.NodeData-class.html#__init__,Method Bio.Nexus.Trees.Tree.__init__()=Bio.Nexus.Trees.Tree-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap-class.html#__init__,Method Bio.PDB.Atom.Atom.__init__()=Bio.PDB.Atom.Atom-class.html#__init__,Method Bio.PDB.Atom.DisorderedAtom.__init__()=Bio.PDB.Atom.DisorderedAtom-class.html#__init__,Method Bio.PDB.Chain.Chain.__init__()=Bio.PDB.Chain.Chain-class.html#__init__,Method Bio.PDB.DSSP'.DSSP.__init__()=Bio.PDB.DSSP%27.DSSP-class.html#__init__,Method Bio.PDB.Dice.ChainSelector.__init__()=Bio.PDB.Dice.ChainSelector-class.html#__init__,Method Bio.PDB.Entity.DisorderedEntityWrapper.__init__()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__init__,Method Bio.PDB.Entity.Entity.__init__()=Bio.PDB.Entity.Entity-class.html#__init__,Method Bio.PDB.FragmentMapper'.Fragment.__init__()=Bio.PDB.FragmentMapper%27.Fragment-class.html#__init__,Method Bio.PDB.FragmentMapper'.FragmentMapper.__init__()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#__init__,Method Bio.PDB.HSExposure.ExposureCN.__init__()=Bio.PDB.HSExposure.ExposureCN-class.html#__init__,Method Bio.PDB.HSExposure.HSExposureCA.__init__()=Bio.PDB.HSExposure.HSExposureCA-class.html#__init__,Method Bio.PDB.HSExposure.HSExposureCB.__init__()=Bio.PDB.HSExposure.HSExposureCB-class.html#__init__,Method Bio.PDB.HSExposure._AbstractHSExposure.__init__()=Bio.PDB.HSExposure._AbstractHSExposure-class.html#__init__,Method Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__()=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#__init__,Method Bio.PDB.Model.Model.__init__()=Bio.PDB.Model.Model-class.html#__init__,Method Bio.PDB.NACCESS.NACCESS.__init__()=Bio.PDB.NACCESS.NACCESS-class.html#__init__,Method Bio.PDB.NACCESS.NACCESS_atomic.__init__()=Bio.PDB.NACCESS.NACCESS_atomic-class.html#__init__,Method Bio.PDB.NeighborSearch.NeighborSearch.__init__()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#__init__,Method Bio.PDB.PDBIO'.PDBIO.__init__()=Bio.PDB.PDBIO%27.PDBIO-class.html#__init__,Method Bio.PDB.PDBList'.PDBList.__init__()=Bio.PDB.PDBList%27.PDBList-class.html#__init__,Method Bio.PDB.PDBParser'.PDBParser.__init__()=Bio.PDB.PDBParser%27.PDBParser-class.html#__init__,Method Bio.PDB.PSEA.PSEA.__init__()=Bio.PDB.PSEA.PSEA-class.html#__init__,Method Bio.PDB.Polypeptide.CaPPBuilder.__init__()=Bio.PDB.Polypeptide.CaPPBuilder-class.html#__init__,Method Bio.PDB.Polypeptide.PPBuilder.__init__()=Bio.PDB.Polypeptide.PPBuilder-class.html#__init__,Method Bio.PDB.Polypeptide._PPBuilder.__init__()=Bio.PDB.Polypeptide._PPBuilder-class.html#__init__,Method Bio.PDB.Residue.DisorderedResidue.__init__()=Bio.PDB.Residue.DisorderedResidue-class.html#__init__,Method Bio.PDB.Residue.Residue.__init__()=Bio.PDB.Residue.Residue-class.html#__init__,Method Bio.PDB.ResidueDepth'.ResidueDepth.__init__()=Bio.PDB.ResidueDepth%27.ResidueDepth-class.html#__init__,Method Bio.PDB.Structure.Structure.__init__()=Bio.PDB.Structure.Structure-class.html#__init__,Method Bio.PDB.StructureAlignment'.StructureAlignment.__init__()=Bio.PDB.StructureAlignment%27.StructureAlignment-class.html#__init__,Method Bio.PDB.StructureBuilder.StructureBuilder.__init__()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#__init__,Method Bio.PDB.Superimposer'.Superimposer.__init__()=Bio.PDB.Superimposer%27.Superimposer-class.html#__init__,Method Bio.PDB.Vector'.Vector.__init__()=Bio.PDB.Vector%27.Vector-class.html#__init__,Method Bio.ParserSupport.EventGenerator.__init__()=Bio.ParserSupport.EventGenerator-class.html#__init__,Method Bio.ParserSupport.SGMLStrippingConsumer.__init__()=Bio.ParserSupport.SGMLStrippingConsumer-class.html#__init__,Method Bio.ParserSupport.TaggingConsumer.__init__()=Bio.ParserSupport.TaggingConsumer-class.html#__init__,Method Bio.Parsers.spark.GenericASTBuilder.__init__()=Bio.Parsers.spark.GenericASTBuilder-class.html#__init__,Method Bio.Parsers.spark.GenericASTMatcher.__init__()=Bio.Parsers.spark.GenericASTMatcher-class.html#__init__,Method Bio.Parsers.spark.GenericASTTraversal.__init__()=Bio.Parsers.spark.GenericASTTraversal-class.html#__init__,Method Bio.Parsers.spark.GenericParser.__init__()=Bio.Parsers.spark.GenericParser-class.html#__init__,Method Bio.Parsers.spark.GenericScanner.__init__()=Bio.Parsers.spark.GenericScanner-class.html#__init__,Method Bio.Pathway.Network.__init__()=Bio.Pathway.Network-class.html#__init__,Method Bio.Pathway.Reaction.__init__()=Bio.Pathway.Reaction-class.html#__init__,Method Bio.Pathway.Rep.Graph.Graph.__init__()=Bio.Pathway.Rep.Graph.Graph-class.html#__init__,Method Bio.Pathway.Rep.HashSet.HashSet.__init__()=Bio.Pathway.Rep.HashSet.HashSet-class.html#__init__,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__init__,Method Bio.Pathway.System.__init__()=Bio.Pathway.System-class.html#__init__,Method Bio.PopGen.Async.Async.__init__()=Bio.PopGen.Async.Async-class.html#__init__,Method Bio.PopGen.Async.DirectoryRetriever.__init__()=Bio.PopGen.Async.DirectoryRetriever-class.html#__init__,Method Bio.PopGen.Async.FileRetriever.__init__()=Bio.PopGen.Async.FileRetriever-class.html#__init__,Method Bio.PopGen.Async.Local.Local.__init__()=Bio.PopGen.Async.Local.Local-class.html#__init__,Method Bio.PopGen.FDist.Async.FDistAsync.__init__()=Bio.PopGen.FDist.Async.FDistAsync-class.html#__init__,Method Bio.PopGen.FDist.Async.SplitFDist.__init__()=Bio.PopGen.FDist.Async.SplitFDist-class.html#__init__,Method Bio.PopGen.FDist.Controller.FDistController.__init__()=Bio.PopGen.FDist.Controller.FDistController-class.html#__init__,Method Bio.PopGen.FDist.Record.__init__()=Bio.PopGen.FDist.Record-class.html#__init__,Method Bio.PopGen.FDist.RecordParser.__init__()=Bio.PopGen.FDist.RecordParser-class.html#__init__,Method Bio.PopGen.FDist._RecordConsumer.__init__()=Bio.PopGen.FDist._RecordConsumer-class.html#__init__,Method Bio.PopGen.GenePop.Record.__init__()=Bio.PopGen.GenePop.Record-class.html#__init__,Method Bio.PopGen.GenePop.RecordParser.__init__()=Bio.PopGen.GenePop.RecordParser-class.html#__init__,Method Bio.PopGen.GenePop._RecordConsumer.__init__()=Bio.PopGen.GenePop._RecordConsumer-class.html#__init__,Method Bio.PopGen.SimCoal.Async.SimCoalCache.__init__()=Bio.PopGen.SimCoal.Async.SimCoalCache-class.html#__init__,Method Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__()=Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html#__init__,Method Bio.PopGen.SimCoal.Controller.SimCoalController.__init__()=Bio.PopGen.SimCoal.Controller.SimCoalController-class.html#__init__,Method Bio.PropertyManager.PropertyManager.__init__()=Bio.PropertyManager.PropertyManager-class.html#__init__,Method Bio.Prosite.Dictionary.__init__()=Bio.Prosite.Dictionary-class.html#__init__,Method Bio.Prosite.ExPASyDictionary.__init__()=Bio.Prosite.ExPASyDictionary-class.html#__init__,Method Bio.Prosite.Iterator.__init__()=Bio.Prosite.Iterator-class.html#__init__,Method Bio.Prosite.Pattern.Prosite.__init__()=Bio.Prosite.Pattern.Prosite-class.html#__init__,Method Bio.Prosite.Pattern.PrositeMatch.__init__()=Bio.Prosite.Pattern.PrositeMatch-class.html#__init__,Method Bio.Prosite.Pattern.PrositeTerm.__init__()=Bio.Prosite.Pattern.PrositeTerm-class.html#__init__,Method Bio.Prosite.PatternHit.__init__()=Bio.Prosite.PatternHit-class.html#__init__,Method Bio.Prosite.Prodoc.Dictionary.__init__()=Bio.Prosite.Prodoc.Dictionary-class.html#__init__,Method Bio.Prosite.Prodoc.ExPASyDictionary.__init__()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__init__,Method Bio.Prosite.Prodoc.Iterator.__init__()=Bio.Prosite.Prodoc.Iterator-class.html#__init__,Method Bio.Prosite.Prodoc.Record.__init__()=Bio.Prosite.Prodoc.Record-class.html#__init__,Method Bio.Prosite.Prodoc.RecordParser.__init__()=Bio.Prosite.Prodoc.RecordParser-class.html#__init__,Method Bio.Prosite.Prodoc.Reference.__init__()=Bio.Prosite.Prodoc.Reference-class.html#__init__,Method Bio.Prosite.Prodoc._RecordConsumer.__init__()=Bio.Prosite.Prodoc._RecordConsumer-class.html#__init__,Method Bio.Prosite.Record.__init__()=Bio.Prosite.Record-class.html#__init__,Method Bio.Prosite.RecordParser.__init__()=Bio.Prosite.RecordParser-class.html#__init__,Method Bio.Prosite._RecordConsumer.__init__()=Bio.Prosite._RecordConsumer-class.html#__init__,Method Bio.PubMed.Dictionary.__init__()=Bio.PubMed.Dictionary-class.html#__init__,Method Bio.Rebase.Dictionary.__init__()=Bio.Rebase.Dictionary-class.html#__init__,Method Bio.Rebase.Iterator.__init__()=Bio.Rebase.Iterator-class.html#__init__,Method Bio.Rebase.Record.__init__()=Bio.Rebase.Record-class.html#__init__,Method Bio.Rebase.RecordParser.__init__()=Bio.Rebase.RecordParser-class.html#__init__,Method Bio.Rebase._RecordConsumer.__init__()=Bio.Rebase._RecordConsumer-class.html#__init__,Method Bio.Restriction.PrintFormat.PrintFormat.__init__()=Bio.Restriction.PrintFormat.PrintFormat-class.html#__init__,Method Bio.Restriction.Restriction.Analysis.__init__()=Bio.Restriction.Restriction.Analysis-class.html#__init__,Method Bio.Restriction.Restriction.FormattedSeq.__init__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__init__,Method Bio.Restriction.Restriction.RestrictionBatch.__init__()=Bio.Restriction.Restriction.RestrictionBatch-class.html#__init__,Method Bio.Restriction.Restriction.RestrictionType.__init__()=Bio.Restriction.Restriction.RestrictionType-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__()=Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__()=Bio.Restriction._Update.RestrictionCompiler.newenzyme-class.html#__init__,Method Bio.Restriction._Update.Update.ConnectionError.__init__()=Bio.Restriction._Update.Update.ConnectionError-class.html#__init__,Method Bio.Restriction._Update.Update.FtpNameError.__init__()=Bio.Restriction._Update.Update.FtpNameError-class.html#__init__,Method Bio.Restriction._Update.Update.FtpPasswordError.__init__()=Bio.Restriction._Update.Update.FtpPasswordError-class.html#__init__,Method Bio.Restriction._Update.Update.RebaseUpdate.__init__()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#__init__,Method Bio.SCOP.Astral.__init__()=Bio.SCOP.Astral-class.html#__init__,Method Bio.SCOP.Cla.Index.__init__()=Bio.SCOP.Cla.Index-class.html#__init__,Method Bio.SCOP.Cla.Iterator.__init__()=Bio.SCOP.Cla.Iterator-class.html#__init__,Method Bio.SCOP.Cla.Parser.__init__()=Bio.SCOP.Cla.Parser-class.html#__init__,Method Bio.SCOP.Cla.Record.__init__()=Bio.SCOP.Cla.Record-class.html#__init__,Method Bio.SCOP.Des.Iterator.__init__()=Bio.SCOP.Des.Iterator-class.html#__init__,Method Bio.SCOP.Des.Parser.__init__()=Bio.SCOP.Des.Parser-class.html#__init__,Method Bio.SCOP.Des.Record.__init__()=Bio.SCOP.Des.Record-class.html#__init__,Method Bio.SCOP.Dom.Iterator.__init__()=Bio.SCOP.Dom.Iterator-class.html#__init__,Method Bio.SCOP.Dom.Record.__init__()=Bio.SCOP.Dom.Record-class.html#__init__,Method Bio.SCOP.Domain.__init__()=Bio.SCOP.Domain-class.html#__init__,Method Bio.SCOP.FileIndex.FileIndex.__init__()=Bio.SCOP.FileIndex.FileIndex-class.html#__init__,Method Bio.SCOP.FileIndex.defaultdict.__init__()=Bio.SCOP.FileIndex.defaultdict-class.html#__init__,Method Bio.SCOP.Hie.Iterator.__init__()=Bio.SCOP.Hie.Iterator-class.html#__init__,Method Bio.SCOP.Hie.Parser.__init__()=Bio.SCOP.Hie.Parser-class.html#__init__,Method Bio.SCOP.Hie.Record.__init__()=Bio.SCOP.Hie.Record-class.html#__init__,Method Bio.SCOP.Node.__init__()=Bio.SCOP.Node-class.html#__init__,Method Bio.SCOP.Raf.Iterator.__init__()=Bio.SCOP.Raf.Iterator-class.html#__init__,Method Bio.SCOP.Raf.Parser.__init__()=Bio.SCOP.Raf.Parser-class.html#__init__,Method Bio.SCOP.Raf.Res.__init__()=Bio.SCOP.Raf.Res-class.html#__init__,Method Bio.SCOP.Raf.SeqMap.__init__()=Bio.SCOP.Raf.SeqMap-class.html#__init__,Method Bio.SCOP.Raf.SeqMapIndex.__init__()=Bio.SCOP.Raf.SeqMapIndex-class.html#__init__,Method Bio.SCOP.Residues'.Residues.__init__()=Bio.SCOP.Residues%27.Residues-class.html#__init__,Method Bio.SCOP.Scop.__init__()=Bio.SCOP.Scop-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__()=Bio.SGMLExtractor.SGMLExtractor.LocalParser-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractor.__init__()=Bio.SGMLExtractor.SGMLExtractor-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractorHandle.__init__()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#__init__,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#__init__,Method Bio.Saf.Iterator.__init__()=Bio.Saf.Iterator-class.html#__init__,Method Bio.Saf.Record.Record.__init__()=Bio.Saf.Record.Record-class.html#__init__,Method Bio.Saf.RecordParser.__init__()=Bio.Saf.RecordParser-class.html#__init__,Method Bio.Saf._RecordConsumer.__init__()=Bio.Saf._RecordConsumer-class.html#__init__,Method Bio.Saf._Scanner.__init__()=Bio.Saf._Scanner-class.html#__init__,Method Bio.Search.Algorithm.__init__()=Bio.Search.Algorithm-class.html#__init__,Method Bio.Search.Database.__init__()=Bio.Search.Database-class.html#__init__,Method Bio.Search.HSP.__init__()=Bio.Search.HSP-class.html#__init__,Method Bio.Search.HSPSeq.__init__()=Bio.Search.HSPSeq-class.html#__init__,Method Bio.Search.Hit.__init__()=Bio.Search.Hit-class.html#__init__,Method Bio.Search.HomologySeq.__init__()=Bio.Search.HomologySeq-class.html#__init__,Method Bio.Search.Query.__init__()=Bio.Search.Query-class.html#__init__,Method Bio.Search.Search.__init__()=Bio.Search.Search-class.html#__init__,Method Bio.Search.TableInfo.__init__()=Bio.Search.TableInfo-class.html#__init__,Method Bio.Search._SeqLength.__init__()=Bio.Search._SeqLength-class.html#__init__,Method Bio.Seq.MutableSeq.__init__()=Bio.Seq.MutableSeq-class.html#__init__,Method Bio.Seq.Seq.__init__()=Bio.Seq.Seq-class.html#__init__,Method Bio.SeqFeature.AbstractPosition.__init__()=Bio.SeqFeature.AbstractPosition-class.html#__init__,Method Bio.SeqFeature.AfterPosition.__init__()=Bio.SeqFeature.AfterPosition-class.html#__init__,Method Bio.SeqFeature.BeforePosition.__init__()=Bio.SeqFeature.BeforePosition-class.html#__init__,Method Bio.SeqFeature.BetweenPosition.__init__()=Bio.SeqFeature.BetweenPosition-class.html#__init__,Method Bio.SeqFeature.ExactPosition.__init__()=Bio.SeqFeature.ExactPosition-class.html#__init__,Method Bio.SeqFeature.FeatureLocation.__init__()=Bio.SeqFeature.FeatureLocation-class.html#__init__,Method Bio.SeqFeature.OneOfPosition.__init__()=Bio.SeqFeature.OneOfPosition-class.html#__init__,Method Bio.SeqFeature.PositionGap.__init__()=Bio.SeqFeature.PositionGap-class.html#__init__,Method Bio.SeqFeature.Reference.__init__()=Bio.SeqFeature.Reference-class.html#__init__,Method Bio.SeqFeature.SeqFeature.__init__()=Bio.SeqFeature.SeqFeature-class.html#__init__,Method Bio.SeqFeature.WithinPosition.__init__()=Bio.SeqFeature.WithinPosition-class.html#__init__,Method Bio.SeqIO.ClustalIO.ClustalWriter.__init__()=Bio.SeqIO.ClustalIO.ClustalWriter-class.html#__init__,Method Bio.SeqIO.FastaIO.FastaWriter.__init__()=Bio.SeqIO.FastaIO.FastaWriter-class.html#__init__,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__init__,Method Bio.SeqIO.Interfaces.SequenceIterator.__init__()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#__init__,Method Bio.SeqIO.Interfaces.SequenceWriter.__init__()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#__init__,Method Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__()=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#__init__,Method Bio.SeqIO.PhylipIO.PhylipWriter.__init__()=Bio.SeqIO.PhylipIO.PhylipWriter-class.html#__init__,Method Bio.SeqIO.StockholmIO.StockholmIterator.__init__()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__init__,Method Bio.SeqIO.StockholmIO.StockholmWriter.__init__()=Bio.SeqIO.StockholmIO.StockholmWriter-class.html#__init__,Method Bio.SeqRecord.SeqRecord.__init__()=Bio.SeqRecord.SeqRecord-class.html#__init__,Method Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__()=Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#__init__,Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#__init__,Method Bio.SeqUtils.MissingTable.__init__()=Bio.SeqUtils.MissingTable-class.html#__init__,Method Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__()=Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#__init__,Method Bio.Sequencing.Ace.ACEFileRecord.__init__()=Bio.Sequencing.Ace.ACEFileRecord-class.html#__init__,Method Bio.Sequencing.Ace.ACEParser.__init__()=Bio.Sequencing.Ace.ACEParser-class.html#__init__,Method Bio.Sequencing.Ace.Contig.__init__()=Bio.Sequencing.Ace.Contig-class.html#__init__,Method Bio.Sequencing.Ace.Iterator.__init__()=Bio.Sequencing.Ace.Iterator-class.html#__init__,Method Bio.Sequencing.Ace.Reads.__init__()=Bio.Sequencing.Ace.Reads-class.html#__init__,Method Bio.Sequencing.Ace.RecordParser.__init__()=Bio.Sequencing.Ace.RecordParser-class.html#__init__,Method Bio.Sequencing.Ace._RecordConsumer.__init__()=Bio.Sequencing.Ace._RecordConsumer-class.html#__init__,Method Bio.Sequencing.Ace.af.__init__()=Bio.Sequencing.Ace.af-class.html#__init__,Method Bio.Sequencing.Ace.bs.__init__()=Bio.Sequencing.Ace.bs-class.html#__init__,Method Bio.Sequencing.Ace.ct.__init__()=Bio.Sequencing.Ace.ct-class.html#__init__,Method Bio.Sequencing.Ace.ds.__init__()=Bio.Sequencing.Ace.ds-class.html#__init__,Method Bio.Sequencing.Ace.qa.__init__()=Bio.Sequencing.Ace.qa-class.html#__init__,Method Bio.Sequencing.Ace.rd.__init__()=Bio.Sequencing.Ace.rd-class.html#__init__,Method Bio.Sequencing.Ace.rt.__init__()=Bio.Sequencing.Ace.rt-class.html#__init__,Method Bio.Sequencing.Ace.wa.__init__()=Bio.Sequencing.Ace.wa-class.html#__init__,Method Bio.Sequencing.Ace.wr.__init__()=Bio.Sequencing.Ace.wr-class.html#__init__,Method Bio.Sequencing.Phd.Iterator.__init__()=Bio.Sequencing.Phd.Iterator-class.html#__init__,Method Bio.Sequencing.Phd.Record.__init__()=Bio.Sequencing.Phd.Record-class.html#__init__,Method Bio.Sequencing.Phd.RecordParser.__init__()=Bio.Sequencing.Phd.RecordParser-class.html#__init__,Method Bio.Sequencing.Phd._RecordConsumer.__init__()=Bio.Sequencing.Phd._RecordConsumer-class.html#__init__,Method Bio.Std.StdTerm.__init__()=Bio.Std.StdTerm-class.html#__init__,Method Bio.StdHandler.ConvertDispatchHandler.__init__()=Bio.StdHandler.ConvertDispatchHandler-class.html#__init__,Method Bio.StdHandler.ConvertHandler.__init__()=Bio.StdHandler.ConvertHandler-class.html#__init__,Method Bio.StdHandler.Feature.__init__()=Bio.StdHandler.Feature-class.html#__init__,Method Bio.StdHandler.Handle_dbxref.__init__()=Bio.StdHandler.Handle_dbxref-class.html#__init__,Method Bio.StdHandler.Handle_feature_location.__init__()=Bio.StdHandler.Handle_feature_location-class.html#__init__,Method Bio.StdHandler.Handle_feature_qualifier.__init__()=Bio.StdHandler.Handle_feature_qualifier-class.html#__init__,Method Bio.StdHandler.Handle_features.__init__()=Bio.StdHandler.Handle_features-class.html#__init__,Method Bio.StdHandler.Handle_hsp.__init__()=Bio.StdHandler.Handle_hsp-class.html#__init__,Method Bio.StdHandler.RecognizeHandler.__init__()=Bio.StdHandler.RecognizeHandler-class.html#__init__,Method Bio.SubsMat.FreqTable.FreqTable.__init__()=Bio.SubsMat.FreqTable.FreqTable-class.html#__init__,Method Bio.SubsMat.SeqMat.__init__()=Bio.SubsMat.SeqMat-class.html#__init__,Method Bio.SwissProt.KeyWList.ListParser.__init__()=Bio.SwissProt.KeyWList.ListParser-class.html#__init__,Method Bio.SwissProt.KeyWList.Record.__init__()=Bio.SwissProt.KeyWList.Record-class.html#__init__,Method Bio.SwissProt.KeyWList._ListConsumer.__init__()=Bio.SwissProt.KeyWList._ListConsumer-class.html#__init__,Method Bio.SwissProt.KeyWList._Scanner.__init__()=Bio.SwissProt.KeyWList._Scanner-class.html#__init__,Method Bio.SwissProt.SProt.Dictionary.__init__()=Bio.SwissProt.SProt.Dictionary-class.html#__init__,Method Bio.SwissProt.SProt.ExPASyDictionary.__init__()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#__init__,Method Bio.SwissProt.SProt.Iterator.__init__()=Bio.SwissProt.SProt.Iterator-class.html#__init__,Method Bio.SwissProt.SProt.Record.__init__()=Bio.SwissProt.SProt.Record-class.html#__init__,Method Bio.SwissProt.SProt.RecordParser.__init__()=Bio.SwissProt.SProt.RecordParser-class.html#__init__,Method Bio.SwissProt.SProt.Reference.__init__()=Bio.SwissProt.SProt.Reference-class.html#__init__,Method Bio.SwissProt.SProt.SequenceParser.__init__()=Bio.SwissProt.SProt.SequenceParser-class.html#__init__,Method Bio.SwissProt.SProt._RecordConsumer.__init__()=Bio.SwissProt.SProt._RecordConsumer-class.html#__init__,Method Bio.SwissProt.SProt._SequenceConsumer.__init__()=Bio.SwissProt.SProt._SequenceConsumer-class.html#__init__,Method Bio.Transcribe.Transcribe.__init__()=Bio.Transcribe.Transcribe-class.html#__init__,Method Bio.Translate.Translator.__init__()=Bio.Translate.Translator-class.html#__init__,Method Bio.UniGene.Iterator.__init__()=Bio.UniGene.Iterator-class.html#__init__,Method Bio.UniGene.RecordParser.__init__()=Bio.UniGene.RecordParser-class.html#__init__,Method Bio.UniGene.UnigeneProtsimRecord.__init__()=Bio.UniGene.UnigeneProtsimRecord-class.html#__init__,Method Bio.UniGene.UnigeneRecord.__init__()=Bio.UniGene.UnigeneRecord-class.html#__init__,Method Bio.UniGene.UnigeneSTSRecord.__init__()=Bio.UniGene.UnigeneSTSRecord-class.html#__init__,Method Bio.UniGene.UnigeneSequenceRecord.__init__()=Bio.UniGene.UnigeneSequenceRecord-class.html#__init__,Method Bio.UniGene._RecordConsumer.__init__()=Bio.UniGene._RecordConsumer-class.html#__init__,Method Bio.WWW.RequestLimiter.__init__()=Bio.WWW.RequestLimiter-class.html#__init__,Method Bio.Wise.dnal.Statistics.__init__()=Bio.Wise.dnal.Statistics-class.html#__init__,Method Bio.Wise.psw.AlignmentColumn.__init__()=Bio.Wise.psw.AlignmentColumn-class.html#__init__,Method Bio.Wise.psw.ColumnUnit.__init__()=Bio.Wise.psw.ColumnUnit-class.html#__init__,Method Bio.Writer.Writer.__init__()=Bio.Writer.Writer-class.html#__init__,Method Bio.biblio.Biblio.__init__()=Bio.biblio.Biblio-class.html#__init__,Method Bio.biblio.BiblioCollection.__init__()=Bio.biblio.BiblioCollection-class.html#__init__,Method Bio.builders.Search.search.BuildSearch.__init__()=Bio.builders.Search.search.BuildSearch-class.html#__init__,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#__init__,Method Bio.config.DBRegistry.BioCorbaDB.__init__()=Bio.config.DBRegistry.BioCorbaDB-class.html#__init__,Method Bio.config.DBRegistry.BioSQLDB.__init__()=Bio.config.DBRegistry.BioSQLDB-class.html#__init__,Method Bio.config.DBRegistry.CGIDB.__init__()=Bio.config.DBRegistry.CGIDB-class.html#__init__,Method Bio.config.DBRegistry.DBGroup.__init__()=Bio.config.DBRegistry.DBGroup-class.html#__init__,Method Bio.config.DBRegistry.DBObject.__init__()=Bio.config.DBRegistry.DBObject-class.html#__init__,Method Bio.config.DBRegistry.DBRegistry.__init__()=Bio.config.DBRegistry.DBRegistry-class.html#__init__,Method Bio.config.DBRegistry.EUtilsDB.__init__()=Bio.config.DBRegistry.EUtilsDB-class.html#__init__,Method Bio.config.DBRegistry.IndexedFileDB.__init__()=Bio.config.DBRegistry.IndexedFileDB-class.html#__init__,Method Bio.config.FormatRegistry.FormatGroup.__init__()=Bio.config.FormatRegistry.FormatGroup-class.html#__init__,Method Bio.config.FormatRegistry.FormatObject.__init__()=Bio.config.FormatRegistry.FormatObject-class.html#__init__,Method Bio.config.FormatRegistry.FormatRegistry.__init__()=Bio.config.FormatRegistry.FormatRegistry-class.html#__init__,Method Bio.config.Registry.RegisterableGroup.__init__()=Bio.config.Registry.RegisterableGroup-class.html#__init__,Method Bio.config.Registry.RegisterableObject.__init__()=Bio.config.Registry.RegisterableObject-class.html#__init__,Method Bio.config.Registry.Registry.__init__()=Bio.config.Registry.Registry-class.html#__init__,Method Bio.config.SeqDBRegistry.SeqDBRegistry.__init__()=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#__init__,Method Bio.config._stanzaformat.Stanza.__init__()=Bio.config._stanzaformat.Stanza-class.html#__init__,Method Bio.config._stanzaformat.StanzaFormat.__init__()=Bio.config._stanzaformat.StanzaFormat-class.html#__init__,Method Bio.config._support.make_cached_expression.__init__()=Bio.config._support.make_cached_expression-class.html#__init__,Method Bio.config._support.make_rate_limited_function.__init__()=Bio.config._support.make_rate_limited_function-class.html#__init__,Method Bio.kNN.kNN.__init__()=Bio.kNN.kNN-class.html#__init__,Method Bio.pairwise2.affine_penalty.__init__()=Bio.pairwise2.affine_penalty-class.html#__init__,Method Bio.pairwise2.dictionary_match.__init__()=Bio.pairwise2.dictionary_match-class.html#__init__,Method Bio.pairwise2.identity_match.__init__()=Bio.pairwise2.identity_match-class.html#__init__,Method Bio.writers.SeqRecord.embl.WriteEmbl.__init__()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#__init__,Method Bio.writers.SeqRecord.fasta.WriteFasta.__init__()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#__init__,Method BioSQL.BioSeq.DBSeq.__init__()=BioSQL.BioSeq.DBSeq-class.html#__init__,Method BioSQL.BioSeq.DBSeqRecord.__init__()=BioSQL.BioSeq.DBSeqRecord-class.html#__init__,Method BioSQL.BioSeqDatabase.Adaptor.__init__()=BioSQL.BioSeqDatabase.Adaptor-class.html#__init__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__init__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__init__,Method BioSQL.BioSeqDatabase.DBServer.__init__()=BioSQL.BioSeqDatabase.DBServer-class.html#__init__,Method BioSQL.DBUtils.Generic_dbutils.__init__()=BioSQL.DBUtils.Generic_dbutils-class.html#__init__,Method BioSQL.Loader.DatabaseLoader.__init__()=BioSQL.Loader.DatabaseLoader-class.html#__init__,Method BioSQL.Loader.DatabaseRemover.__init__()=BioSQL.Loader.DatabaseRemover-class.html#__init__,Method Martel.Dispatch.Callback.__init__()=Martel.Dispatch.Callback-class.html#__init__,Method Martel.Dispatch.DispatchHandler.__init__()=Martel.Dispatch.DispatchHandler-class.html#__init__,Method Martel.Dispatch.Dispatcher.__init__()=Martel.Dispatch.Dispatcher-class.html#__init__,Method Martel.Dispatch.Multicall.__init__()=Martel.Dispatch.Multicall-class.html#__init__,Method Martel.Dispatch.RemapEnd.__init__()=Martel.Dispatch.RemapEnd-class.html#__init__,Method Martel.Dispatch.RemapStart.__init__()=Martel.Dispatch.RemapStart-class.html#__init__,Method Martel.Expression.Alt.__init__()=Martel.Expression.Alt-class.html#__init__,Method Martel.Expression.Any.__init__()=Martel.Expression.Any-class.html#__init__,Method Martel.Expression.Assert.__init__()=Martel.Expression.Assert-class.html#__init__,Method Martel.Expression.Debug.__init__()=Martel.Expression.Debug-class.html#__init__,Method Martel.Expression.FastFeature.__init__()=Martel.Expression.FastFeature-class.html#__init__,Method Martel.Expression.Group.__init__()=Martel.Expression.Group-class.html#__init__,Method Martel.Expression.GroupRef.__init__()=Martel.Expression.GroupRef-class.html#__init__,Method Martel.Expression.HeaderFooter.__init__()=Martel.Expression.HeaderFooter-class.html#__init__,Method Martel.Expression.Literal.__init__()=Martel.Expression.Literal-class.html#__init__,Method Martel.Expression.MaxRepeat.__init__()=Martel.Expression.MaxRepeat-class.html#__init__,Method Martel.Expression.NullOp.__init__()=Martel.Expression.NullOp-class.html#__init__,Method Martel.Expression.ParseRecords.__init__()=Martel.Expression.ParseRecords-class.html#__init__,Method Martel.Expression.PassThrough.__init__()=Martel.Expression.PassThrough-class.html#__init__,Method Martel.Expression.Seq.__init__()=Martel.Expression.Seq-class.html#__init__,Method Martel.Expression.Str.__init__()=Martel.Expression.Str-class.html#__init__,Method Martel.Generate.CheckAssert.__init__()=Martel.Generate.CheckAssert-class.html#__init__,Method Martel.Generate.CheckAssertNot.__init__()=Martel.Generate.CheckAssertNot-class.html#__init__,Method Martel.Generate.CheckGroupRef.__init__()=Martel.Generate.CheckGroupRef-class.html#__init__,Method Martel.Generate.GeneratorState.__init__()=Martel.Generate.GeneratorState-class.html#__init__,Method Martel.Generate.HandleRepeatCount.__init__()=Martel.Generate.HandleRepeatCount-class.html#__init__,Method Martel.Generate.SetGroupValue.__init__()=Martel.Generate.SetGroupValue-class.html#__init__,Method Martel.Generate._call_call.__init__()=Martel.Generate._call_call-class.html#__init__,Method Martel.Generate._call_calltag.__init__()=Martel.Generate._call_calltag-class.html#__init__,Method Martel.Generate.print_debug.__init__()=Martel.Generate.print_debug-class.html#__init__,Method Martel.Generate.print_info.__init__()=Martel.Generate.print_info-class.html#__init__,Method Martel.IterParser.IterHeaderFooter.__init__()=Martel.IterParser.IterHeaderFooter-class.html#__init__,Method Martel.IterParser.IterRecords.__init__()=Martel.IterParser.IterRecords-class.html#__init__,Method Martel.Iterator.EventStream.__init__()=Martel.Iterator.EventStream-class.html#__init__,Method Martel.Iterator.HeaderFooterEventStream.__init__()=Martel.Iterator.HeaderFooterEventStream-class.html#__init__,Method Martel.Iterator.Iterate.__init__()=Martel.Iterator.Iterate-class.html#__init__,Method Martel.Iterator.Iterator.__init__()=Martel.Iterator.Iterator-class.html#__init__,Method Martel.Iterator.IteratorHeaderFooter.__init__()=Martel.Iterator.IteratorHeaderFooter-class.html#__init__,Method Martel.Iterator.IteratorRecords.__init__()=Martel.Iterator.IteratorRecords-class.html#__init__,Method Martel.Iterator.RecordEventStream.__init__()=Martel.Iterator.RecordEventStream-class.html#__init__,Method Martel.Iterator.StoreEvents.__init__()=Martel.Iterator.StoreEvents-class.html#__init__,Method Martel.LAX.ElementInfo.__init__()=Martel.LAX.ElementInfo-class.html#__init__,Method Martel.LAX.LAX.__init__()=Martel.LAX.LAX-class.html#__init__,Method Martel.Parser.HeaderFooterParser.__init__()=Martel.Parser.HeaderFooterParser-class.html#__init__,Method Martel.Parser.Parser.__init__()=Martel.Parser.Parser-class.html#__init__,Method Martel.Parser.ParserIncompleteException.__init__()=Martel.Parser.ParserIncompleteException-class.html#__init__,Method Martel.Parser.ParserPositionException.__init__()=Martel.Parser.ParserPositionException-class.html#__init__,Method Martel.Parser.RecordParser.__init__()=Martel.Parser.RecordParser-class.html#__init__,Method Martel.RecordReader.CountLines.__init__()=Martel.RecordReader.CountLines-class.html#__init__,Method Martel.RecordReader.EndsWith.__init__()=Martel.RecordReader.EndsWith-class.html#__init__,Method Martel.RecordReader.Everything.__init__()=Martel.RecordReader.Everything-class.html#__init__,Method Martel.RecordReader.Nothing.__init__()=Martel.RecordReader.Nothing-class.html#__init__,Method Martel.RecordReader.RecordReader.__init__()=Martel.RecordReader.RecordReader-class.html#__init__,Method Martel.RecordReader.StartsWith.__init__()=Martel.RecordReader.StartsWith-class.html#__init__,Method Martel.RecordReader.Until.__init__()=Martel.RecordReader.Until-class.html#__init__,Method Martel.convert_re.GroupNames.__init__()=Martel.convert_re.GroupNames-class.html#__init__,Method Martel.msre_parse.Pattern.__init__()=Martel.msre_parse.Pattern-class.html#__init__,Method Martel.msre_parse.SubPattern.__init__()=Martel.msre_parse.SubPattern-class.html#__init__,Method Martel.msre_parse.Tokenizer.__init__()=Martel.msre_parse.Tokenizer-class.html#__init__,Method Martel.test.support.CheckGood.__init__()=Martel.test.support.CheckGood-class.html#__init__,Method Martel.test.support.Dump.__init__()=Martel.test.support.Dump-class.html#__init__,Method Martel.test.support.Storage.__init__()=Martel.test.support.Storage-class.html#__init__,Method Martel.test.test_Parser.CountErrors.__init__()=Martel.test.test_Parser.CountErrors-class.html#__init__,Method Martel.test.test_Parser.CountRecords.__init__()=Martel.test.test_Parser.CountRecords-class.html#__init__,Method Martel.test.test_delimiter.CatchFields.__init__()=Martel.test.test_delimiter.CatchFields-class.html#__init__,Method Martel.test.test_optimize.GetErrorPos.__init__()=Martel.test.test_optimize.GetErrorPos-class.html#__init__"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-10', '__init__', 'link-10');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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">self</tt><tt class="py-op">.</tt><tt class="py-name">dataclass</tt><tt class="py-op">=</tt><tt id="link-11" 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-11', 'data', 'link-11');">data</a></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">__values_are_support</tt><tt class="py-op">=</tt><tt class="py-name">values_are_support</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">max_support</tt><tt class="py-op">=</tt><tt class="py-name">max_support</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">=</tt><tt class="py-name">weight</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rooted</tt><tt class="py-op">=</tt><tt class="py-name">rooted</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-12', 'name', 'link-12');">name</a></tt><tt class="py-op">=</tt><tt id="link-13" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-12');">name</a></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">root</tt><tt class="py-op">=</tt><tt id="link-14" class="py-name"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-14', 'Nodes', 'link-0');">Nodes</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Class Bio.Nexus.Nodes.Node=Bio.Nexus.Nodes.Node-class.html,Class Bio.SCOP.Node=Bio.SCOP.Node-class.html"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-15', 'Node', 'link-15');">Node</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-16', 'data', 'link-11');">data</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'add', 'link-17');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">=</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-18" 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-18', 'id', 'link-18');">id</a></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tree</tt><tt class="py-op">:</tt> <tt class="py-comment"># use the tree we have</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-comment"># if Tree is called from outside Nexus parser, we need to get rid of linebreaks, etc</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">tree</tt><tt class="py-op">=</tt><tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-19', 'strip', 'link-19');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\r'</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-comment"># there's discrepancy whether newick allows semicolons et the end</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">tree</tt><tt class="py-op">=</tt><tt class="py-name">tree</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-string">';'</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 id="link-20" class="py-name" targets="Method Bio.Nexus.Trees.Tree._add_subtree()=Bio.Nexus.Trees.Tree-class.html#_add_subtree"><a title="Bio.Nexus.Trees.Tree._add_subtree" class="py-name" href="#" onclick="return doclink('link-20', '_add_subtree', 'link-20');">_add_subtree</a></tt><tt class="py-op">(</tt><tt class="py-name">parent_id</tt><tt class="py-op">=</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">tree</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer._parse()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#_parse,Method Bio.Nexus.Trees.Tree._parse()=Bio.Nexus.Trees.Tree-class.html#_parse,Method Bio.PDB.PDBParser'.PDBParser._parse()=Bio.PDB.PDBParser%27.PDBParser-class.html#_parse,Method Bio.SCOP.Residues'.Residues._parse()=Bio.SCOP.Residues%27.Residues-class.html#_parse,Function Martel.msre_parse._parse()=Martel.msre_parse-module.html#_parse"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer._parse
Bio.Nexus.Trees.Tree._parse
Bio.PDB.PDBParser'.PDBParser._parse
Bio.SCOP.Residues'.Residues._parse
Martel.msre_parse._parse" class="py-name" href="#" onclick="return doclink('link-22', '_parse', 'link-22');">_parse</a></tt><tt class="py-op">(</tt><tt class="py-name">tree</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt>
<a name="Tree._parse"></a><div id="Tree._parse-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="Tree._parse-toggle" onclick="return toggle('Tree._parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#_parse">_parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">tree</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree._parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree._parse-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively."""</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment">#Remove any leading/trailing white space - want any string starting</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#with " (..." should be recognised as a leaf, "(..."</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">tree</tt> <tt class="py-op">=</tt> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-23', 'strip', 'link-19');">strip</a></tt><tt class="py-op">(</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">if</tt> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-24', 'count', 'link-24');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">'('</tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-25', 'count', 'link-24');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">')'</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 id="link-26" class="py-name" targets="Class Bio.Nexus.Trees.TreeError=Bio.Nexus.Trees.TreeError-class.html"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-26', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Parentheses do not match in (sub)tree: '</tt><tt class="py-op">+</tt><tt class="py-name">tree</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-27', 'count', 'link-24');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">'('</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># a leaf</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">colon</tt><tt class="py-op">=</tt><tt class="py-name">tree</tt><tt class="py-op">.</tt><tt class="py-name">rfind</tt><tt class="py-op">(</tt><tt class="py-string">':'</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">colon</tt><tt class="py-op">></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">colon</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-28" class="py-name" targets="Method Bio.Nexus.Trees.Tree._get_values()=Bio.Nexus.Trees.Tree-class.html#_get_values"><a title="Bio.Nexus.Trees.Tree._get_values" class="py-name" href="#" onclick="return doclink('link-28', '_get_values', 'link-28');">_get_values</a></tt><tt class="py-op">(</tt><tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-name">colon</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">else</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 class="py-op">[</tt><tt class="py-name">tree</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">None</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">closing</tt><tt class="py-op">=</tt><tt class="py-name">tree</tt><tt class="py-op">.</tt><tt class="py-name">rfind</tt><tt class="py-op">(</tt><tt class="py-string">')'</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">val</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Nexus.Trees.Tree._get_values" class="py-name" href="#" onclick="return doclink('link-29', '_get_values', 'link-28');">_get_values</a></tt><tt class="py-op">(</tt><tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-name">closing</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="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">val</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">val</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">subtrees</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">plevel</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">prev</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">closing</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'('</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">plevel</tt><tt class="py-op">+=</tt><tt class="py-number">1</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">tree</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">')'</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">plevel</tt><tt class="py-op">-=</tt><tt class="py-number">1</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">','</tt> <tt class="py-keyword">and</tt> <tt class="py-name">plevel</tt><tt class="py-op">==</tt><tt class="py-number">0</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">subtrees</tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-name">prev</tt><tt class="py-op">:</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">prev</tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">subtrees</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">tree</tt><tt class="py-op">[</tt><tt class="py-name">prev</tt><tt class="py-op">:</tt><tt class="py-name">closing</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">subclades</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-32" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer._parse
Bio.Nexus.Trees.Tree._parse
Bio.PDB.PDBParser'.PDBParser._parse
Bio.SCOP.Residues'.Residues._parse
Martel.msre_parse._parse" class="py-name" href="#" onclick="return doclink('link-32', '_parse', 'link-22');">_parse</a></tt><tt class="py-op">(</tt><tt class="py-name">subtree</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">subtree</tt> <tt class="py-keyword">in</tt> <tt class="py-name">subtrees</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">return</tt> <tt class="py-op">[</tt><tt class="py-name">subclades</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">]</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="Tree._add_subtree"></a><div id="Tree._add_subtree-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="Tree._add_subtree-toggle" onclick="return toggle('Tree._add_subtree');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#_add_subtree">_add_subtree</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">parent_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">tree</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="Tree._add_subtree-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree._add_subtree-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-docstring">"""Adds leaf or tree (in newick format) to a parent_id. (self,parent_id,tree)."""</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parent_id</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-33" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-33', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Need node_id to connect to.'</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">for</tt> <tt class="py-name">st</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tree</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-34" 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-34', 'type', 'link-34');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt id="link-35" 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-35', 'list', 'link-35');">list</a></tt><tt class="py-op">:</tt> <tt class="py-comment"># it's a subtree</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dataclass</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</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">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">>=</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> <tt class="py-comment"># if there's two values, support comes first. Is that always so?</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-36', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</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">if</tt> <tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt 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="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-comment"># otherwise it could be real branchlengths or support as branchlengths</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 class="py-name">__values_are_support</tt><tt class="py-op">:</tt> <tt class="py-comment"># default</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-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</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">else</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-37', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">sn</tt><tt class="py-op">=</tt><tt id="link-38" class="py-name"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-38', 'Nodes', 'link-0');">Nodes</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-39', 'Node', 'link-15');">Node</a></tt><tt class="py-op">(</tt><tt class="py-name">nd</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'add', 'link-17');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">sn</tt><tt class="py-op">,</tt><tt class="py-name">parent_id</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 id="link-41" class="py-name"><a title="Bio.Nexus.Trees.Tree._add_subtree" class="py-name" href="#" onclick="return doclink('link-41', '_add_subtree', 'link-20');">_add_subtree</a></tt><tt class="py-op">(</tt><tt class="py-name">sn</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-18');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># it's a leaf</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dataclass</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</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">st</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</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">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">>=</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> <tt class="py-comment"># if there's two values, support comes first. Is that always so?</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-43', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt 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="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-comment"># otherwise it could be real branchlengths or support as branchlengths</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</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">__values_are_support</tt><tt class="py-op">:</tt> <tt class="py-comment"># default</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">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">nd</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-44', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">leaf</tt><tt class="py-op">=</tt><tt id="link-45" class="py-name"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-45', 'Nodes', 'link-0');">Nodes</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-46', 'Node', 'link-15');">Node</a></tt><tt class="py-op">(</tt><tt class="py-name">nd</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" 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-47', 'add', 'link-17');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">leaf</tt><tt class="py-op">,</tt><tt class="py-name">parent_id</tt><tt class="py-op">)</tt> </tt>
</div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="Tree._get_values"></a><div id="Tree._get_values-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="Tree._get_values-toggle" onclick="return toggle('Tree._get_values');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#_get_values">_get_values</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree._get_values-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree._get_values-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-docstring">"""Extracts values (support/branchlength) from xx[:yyy], xx."""</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-48" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-48', 'text', 'link-48');">text</a></tt><tt class="py-op">==</tt><tt class="py-string">''</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt id="link-49" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-49', 'text', 'link-48');">text</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-50', 'split', 'link-50');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">':'</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">t</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-51', 'strip', 'link-19');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="Tree._walk"></a><div id="Tree._walk-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="Tree._walk-toggle" onclick="return toggle('Tree._walk');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#_walk">_walk</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-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree._walk-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree._walk-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-docstring">"""Return all node_ids downwards from a node."""</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-52" 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-52', 'node', 'link-52');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-53', 'node', 'link-52');">node</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <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 id="link-54" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-54', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-55', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</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">yield</tt> <tt class="py-name">n</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</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 id="link-56" class="py-name" targets="Method Bio.Nexus.Trees.Tree._walk()=Bio.Nexus.Trees.Tree-class.html#_walk"><a title="Bio.Nexus.Trees.Tree._walk" class="py-name" href="#" onclick="return doclink('link-56', '_walk', 'link-56');">_walk</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">sn</tt> </tt>
</div><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
<a name="Tree.node"></a><div id="Tree.node-def"><a name="L153"></a><tt class="py-lineno">153</tt> <a class="py-toggle" href="#" id="Tree.node-toggle" onclick="return toggle('Tree.node');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#node">node</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">node_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.node-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.node-expanded"><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the instance of node_id.</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> node = node(self,node_id)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> """</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-name">node_id</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="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-57" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-57', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown node_id: %d'</tt> <tt class="py-op">%</tt> <tt class="py-name">node_id</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">node_id</tt><tt class="py-op">]</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="Tree.split"></a><div id="Tree.split-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="Tree.split-toggle" onclick="return toggle('Tree.split');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#split">split</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">parent_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">n</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-param">branchlength</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.split-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.split-expanded"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-docstring">"""Speciation: generates n (default two) descendants of a node.</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"> [new ids] = split(self,parent_id=None,n=2,branchlength=1.0):</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-keyword">if</tt> <tt class="py-name">parent_id</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-58" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-58', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Missing node_id.'</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt id="link-59" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-59', 'ids', 'link-59');">ids</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">parent_data</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">parent_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-60', 'data', 'link-11');">data</a></tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-61" 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-61', 'i', 'link-61');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt id="link-62" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-62', 'node', 'link-52');">node</a></tt><tt class="py-op">=</tt><tt id="link-63" class="py-name"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-63', 'Nodes', 'link-0');">Nodes</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-64', 'Node', 'link-15');">Node</a></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 class="py-keyword">if</tt> <tt class="py-name">parent_data</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt id="link-65" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-65', 'node', 'link-52');">node</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-66', 'data', 'link-11');">data</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dataclass</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment"># each node has taxon and branchlength attribute</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">parent_data</tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt id="link-67" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-67', 'node', 'link-52');">node</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-68', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt class="py-name">parent_data</tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-69" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-69', 'i', 'link-61');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt id="link-70" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-70', 'node', 'link-52');">node</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-71', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">branchlength</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt id="link-72" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-72', 'ids', 'link-59');">ids</a></tt><tt class="py-op">.</tt><tt id="link-73" 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-73', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" 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-74', 'add', 'link-17');">add</a></tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-75', 'node', 'link-52');">node</a></tt><tt class="py-op">,</tt><tt class="py-name">parent_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-76" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-76', 'ids', 'link-59');">ids</a></tt> </tt>
</div><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="Tree.search_taxon"></a><div id="Tree.search_taxon-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="Tree.search_taxon-toggle" onclick="return toggle('Tree.search_taxon');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#search_taxon">search_taxon</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">taxon</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.search_taxon-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.search_taxon-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the first matching taxon in self.data.taxon. Not restricted to terminal nodes.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> node_id = search_taxon(self,taxon)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-77" 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-77', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt><tt id="link-78" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-78', 'node', 'link-52');">node</a></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-79" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-79', 'items', 'link-79');">items</a></tt><tt class="py-op">(</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">if</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-52');">node</a></tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-81', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">==</tt><tt class="py-name">taxon</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">return</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-18');">id</a></tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="Tree.prune"></a><div id="Tree.prune-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="Tree.prune-toggle" onclick="return toggle('Tree.prune');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#prune">prune</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">taxon</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.prune-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.prune-expanded"><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-docstring">"""Prunes a terminal taxon from the tree.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> id_of_previous_node = prune(self,taxon)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> If taxon is from a bifurcation, the connectiong node will be collapsed</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"> and its branchlength added to remaining terminal node. This might be no</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> longer a meaningful value'</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt id="link-83" 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-83', 'id', 'link-18');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Method Bio.Nexus.Trees.Tree.search_taxon()=Bio.Nexus.Trees.Tree-class.html#search_taxon"><a title="Bio.Nexus.Trees.Tree.search_taxon" class="py-name" href="#" onclick="return doclink('link-84', 'search_taxon', 'link-84');">search_taxon</a></tt><tt class="py-op">(</tt><tt class="py-name">taxon</tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">if</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-18');">id</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-86" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-86', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Taxon not found: %s'</tt> <tt class="py-op">%</tt> <tt class="py-name">taxon</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-87" 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-87', 'id', 'link-18');">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 id="link-88" class="py-name" targets="Method Bio.Nexus.Trees.Tree.get_terminals()=Bio.Nexus.Trees.Tree-class.html#get_terminals"><a title="Bio.Nexus.Trees.Tree.get_terminals" class="py-name" href="#" onclick="return doclink('link-88', 'get_terminals', 'link-88');">get_terminals</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-89" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-89', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Not a terminal taxon: %s'</tt> <tt class="py-op">%</tt> <tt class="py-name">taxon</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">prev</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" 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-90', 'unlink', 'link-90');">unlink</a></tt><tt class="py-op">(</tt><tt id="link-91" 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-91', 'id', 'link-18');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" 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-92', 'kill', 'link-92');">kill</a></tt><tt class="py-op">(</tt><tt id="link-93" 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-93', 'id', 'link-18');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</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">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-94', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</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-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">prev</tt><tt class="py-op">==</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">:</tt> <tt class="py-comment"># we deleted one branch of a bifurcating root, then we have to move the root upwards</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">=</tt><tt class="py-name">self</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-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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-name">succ</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">self</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-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Nexus.Nodes.Chain.kill" class="py-name" href="#" onclick="return doclink('link-97', 'kill', 'link-92');">kill</a></tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">succ</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</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-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">new_bl</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-99', 'node', 'link-52');">node</a></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-100" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-100', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-101', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">succ</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-102', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.collapse()=Bio.Nexus.Nodes.Chain-class.html#collapse"><a title="Bio.Nexus.Nodes.Chain.collapse" class="py-name" href="#" onclick="return doclink('link-103', 'collapse', 'link-103');">collapse</a></tt><tt class="py-op">(</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-104', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">succ</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-105', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">new_bl</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">prev</tt> </tt>
</div><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> </tt>
<a name="Tree.get_taxa"></a><div id="Tree.get_taxa-def"><a name="L221"></a><tt class="py-lineno">221</tt> <a class="py-toggle" href="#" id="Tree.get_taxa-toggle" onclick="return toggle('Tree.get_taxa');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#get_taxa">get_taxa</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">node_id</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="Tree.get_taxa-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.get_taxa-expanded"><a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a list of all otus downwards from a node (self, node_id).</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> nodes = get_taxa(self,node_id=None)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">node_id</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">node_id</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">node_id</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="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-106" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-106', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Unknown node_id: %d.'</tt> <tt class="py-op">%</tt> <tt class="py-name">node_id</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">node_id</tt><tt class="py-op">]</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 class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">node_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-107', 'data', 'link-11');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">return</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">node_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-108', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">]</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt id="link-109" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-109', 'list', 'link-35');">list</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">succ</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">node_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt id="link-110" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-110', 'list', 'link-35');">list</a></tt><tt class="py-op">.</tt><tt id="link-111" 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-111', 'extend', 'link-111');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.Nexus.Trees.Tree.get_taxa()=Bio.Nexus.Trees.Tree-class.html#get_taxa"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-112', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-name">succ</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-113" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-113', 'list', 'link-35');">list</a></tt> </tt>
</div><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="Tree.get_terminals"></a><div id="Tree.get_terminals-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="Tree.get_terminals-toggle" onclick="return toggle('Tree.get_terminals');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#get_terminals">get_terminals</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="Tree.get_terminals-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.get_terminals-expanded"><a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a list of all terminal nodes."""</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-114" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-114', 'i', 'link-61');">i</a></tt> <tt class="py-keyword">for</tt> <tt id="link-115" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-115', 'i', 'link-61');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.all_ids()=Bio.Nexus.Nodes.Chain-class.html#all_ids"><a title="Bio.Nexus.Nodes.Chain.all_ids" class="py-name" href="#" onclick="return doclink('link-116', 'all_ids', 'link-116');">all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-117', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-118" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-118', 'i', 'link-61');">i</a></tt><tt class="py-op">)</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 class="py-op">]</tt> </tt>
</div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="Tree.sum_branchlength"></a><div id="Tree.sum_branchlength-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="Tree.sum_branchlength-toggle" onclick="return toggle('Tree.sum_branchlength');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#sum_branchlength">sum_branchlength</a><tt class="py-op">(</tt><tt class="py-param">self</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-param">node</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="Tree.sum_branchlength-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.sum_branchlength-expanded"><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-docstring">"""Adds up the branchlengths from root (default self.root) to node.</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> sum = sum_branchlength(self,root=None,node=None)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt 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="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">root</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-119" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-119', 'node', 'link-52');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-120" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-120', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Missing node id.'</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">blen</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-121" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-121', 'node', 'link-52');">node</a></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 id="link-122" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-122', 'node', 'link-52');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">root</tt><tt class="py-op">:</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">blen</tt><tt class="py-op">+=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-123', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-124" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-124', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-125', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt id="link-126" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-126', 'node', 'link-52');">node</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><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-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-128" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-128', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">blen</tt> </tt>
</div><a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="Tree.set_subtree"></a><div id="Tree.set_subtree-def"><a name="L262"></a><tt class="py-lineno">262</tt> <a class="py-toggle" href="#" id="Tree.set_subtree-toggle" onclick="return toggle('Tree.set_subtree');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#set_subtree">set_subtree</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="Tree.set_subtree-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.set_subtree-expanded"><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-docstring">"""Return subtree as a set of nested sets.</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> sets = set_subtree(self,node)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="L268"></a><tt class="py-lineno">268</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-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-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-130" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-130', 'node', 'link-52');">node</a></tt><tt class="py-op">)</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 class="py-op">:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</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-131" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-131', 'node', 'link-52');">node</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-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-133', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</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-134" class="py-name" targets="Method Bio.Nexus.Trees.Tree.set_subtree()=Bio.Nexus.Trees.Tree-class.html#set_subtree"><a title="Bio.Nexus.Trees.Tree.set_subtree" class="py-name" href="#" onclick="return doclink('link-134', 'set_subtree', 'link-134');">set_subtree</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</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 id="link-135" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-135', 'node', 'link-52');">node</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-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="Tree.is_identical"></a><div id="Tree.is_identical-def"><a name="L273"></a><tt class="py-lineno">273</tt> <a class="py-toggle" href="#" id="Tree.is_identical-toggle" onclick="return toggle('Tree.is_identical');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#is_identical">is_identical</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">tree2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.is_identical-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.is_identical-expanded"><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-docstring">"""Compare tree and tree2 for identity.</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-docstring"> result = is_identical(self,tree2)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</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-137" class="py-name"><a title="Bio.Nexus.Trees.Tree.set_subtree" class="py-name" href="#" onclick="return doclink('link-137', 'set_subtree', 'link-134');">set_subtree</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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-name">tree2</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.Nexus.Trees.Tree.set_subtree" class="py-name" href="#" onclick="return doclink('link-138', 'set_subtree', 'link-134');">set_subtree</a></tt><tt class="py-op">(</tt><tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
</div><a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> </tt>
<a name="Tree.is_compatible"></a><div id="Tree.is_compatible-def"><a name="L280"></a><tt class="py-lineno">280</tt> <a class="py-toggle" href="#" id="Tree.is_compatible-toggle" onclick="return toggle('Tree.is_compatible');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#is_compatible">is_compatible</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">tree2</tt><tt class="py-op">,</tt><tt class="py-param">threshold</tt><tt class="py-op">,</tt><tt class="py-param">strict</tt><tt class="py-op">=</tt><tt id="link-139" 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-139', 'True', 'link-139');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.is_compatible-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.is_compatible-expanded"><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-docstring">"""Compares branches with support>threshold for compatibility.</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-docstring"> result = is_compatible(self,tree2,threshold)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-comment"># check if both trees have the same set of taxa. strict=True enforces this.</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">missing2</tt><tt class="py-op">=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-140', 'get_taxa', 'link-112');">get_taxa</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-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-141', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">missing1</tt><tt class="py-op">=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-142', 'get_taxa', 'link-112');">get_taxa</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-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-143', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">strict</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-name">missing1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">missing2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">missing1</tt><tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Taxon/taxa %s is/are missing in tree %s'</tt> <tt class="py-op">%</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 class="py-name">missing1</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-144" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-144', 'name', 'link-12');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">missing2</tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Taxon/taxa %s is/are missing in tree %s'</tt> <tt class="py-op">%</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 class="py-name">missing2</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt> <tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-145', 'name', 'link-12');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-146" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-146', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Can\'t compare trees with different taxon compositions.'</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">t1</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-147', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</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-148" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-148', 'node', 'link-52');">node</a></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-149" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-149', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-150', 'support', 'link-3');">support</a></tt><tt class="py-op">)</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 id="link-151" class="py-name"><a title="Bio.Nexus.Nodes.Chain.all_ids" class="py-name" href="#" onclick="return doclink('link-151', 'all_ids', 'link-116');">all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> \ </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-152', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt> <tt class="py-keyword">and</tt>\ </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-153', 'node', 'link-52');">node</a></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-154" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-154', 'data', 'link-11');">data</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-155', 'node', 'link-52');">node</a></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-156" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-156', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-157', 'support', 'link-3');">support</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-158', 'node', 'link-52');">node</a></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-159" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-159', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-160', 'support', 'link-3');">support</a></tt><tt class="py-op">>=</tt><tt id="link-161" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.threshold()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#threshold,Method Bio.Compass._Consumer.threshold()=Bio.Compass._Consumer-class.html#threshold"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-161', 'threshold', 'link-161');">threshold</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">t2</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-162', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-163', 'node', 'link-52');">node</a></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-164" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-164', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-165', 'support', 'link-3');">support</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Nexus.Nodes.Chain.all_ids" class="py-name" href="#" onclick="return doclink('link-166', 'all_ids', 'link-116');">all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> \ </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-167', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt> <tt class="py-keyword">and</tt>\ </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-168', 'node', 'link-52');">node</a></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-169" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-169', 'data', 'link-11');">data</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-170', 'node', 'link-52');">node</a></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-171" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-171', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-172', 'support', 'link-3');">support</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">tree2</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-173', 'node', 'link-52');">node</a></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-174" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-174', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-175', 'support', 'link-3');">support</a></tt><tt class="py-op">>=</tt><tt id="link-176" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-176', 'threshold', 'link-161');">threshold</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">conflict</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">st1</tt><tt class="py-op">,</tt><tt class="py-name">sup1</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">t1</tt><tt class="py-op">:</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">st2</tt><tt class="py-op">,</tt><tt class="py-name">sup2</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">t2</tt><tt class="py-op">:</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">st1</tt><tt class="py-op">.</tt><tt class="py-name">issubset</tt><tt class="py-op">(</tt><tt class="py-name">st2</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">st2</tt><tt class="py-op">.</tt><tt class="py-name">issubset</tt><tt class="py-op">(</tt><tt class="py-name">st1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># don't hiccup on upstream nodes</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">intersect</tt><tt class="py-op">,</tt><tt class="py-name">notin1</tt><tt class="py-op">,</tt><tt class="py-name">notin2</tt><tt class="py-op">=</tt><tt class="py-name">st1</tt> <tt class="py-op">&</tt> <tt class="py-name">st2</tt><tt class="py-op">,</tt> <tt class="py-name">st2</tt><tt class="py-op">-</tt><tt class="py-name">st1</tt><tt class="py-op">,</tt> <tt class="py-name">st1</tt><tt class="py-op">-</tt><tt class="py-name">st2</tt> <tt class="py-comment"># all three are non-empty sets</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-comment"># if notin1==missing1 or notin2==missing2 <==> st1.issubset(st2) or st2.issubset(st1) ???</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">intersect</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">notin1</tt><tt class="py-op">.</tt><tt class="py-name">issubset</tt><tt class="py-op">(</tt><tt class="py-name">missing1</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">notin2</tt><tt class="py-op">.</tt><tt class="py-name">issubset</tt><tt class="py-op">(</tt><tt class="py-name">missing2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># omit conflicts due to missing taxa</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">conflict</tt><tt class="py-op">.</tt><tt id="link-177" 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-177', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">st1</tt><tt class="py-op">,</tt><tt class="py-name">sup1</tt><tt class="py-op">,</tt><tt class="py-name">st2</tt><tt class="py-op">,</tt><tt class="py-name">sup2</tt><tt class="py-op">,</tt><tt class="py-name">intersect</tt><tt class="py-op">,</tt><tt class="py-name">notin1</tt><tt class="py-op">,</tt><tt class="py-name">notin2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">conflict</tt> </tt>
</div><a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> </tt>
<a name="Tree.common_ancestor"></a><div id="Tree.common_ancestor-def"><a name="L311"></a><tt class="py-lineno">311</tt> <a class="py-toggle" href="#" id="Tree.common_ancestor-toggle" onclick="return toggle('Tree.common_ancestor');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#common_ancestor">common_ancestor</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">node1</tt><tt class="py-op">,</tt><tt class="py-param">node2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.common_ancestor-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.common_ancestor-expanded"><a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the common ancestor that connects to nodes.</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-docstring"> node_id = common_ancestor(self,node1,node2)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">l1</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</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-178" 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-178', 'trace', 'link-178');">trace</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">,</tt><tt class="py-name">node1</tt><tt class="py-op">)</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">l2</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</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-179" class="py-name"><a title="Bio.Nexus.Nodes.Chain.trace" class="py-name" href="#" onclick="return doclink('link-179', 'trace', 'link-178');">trace</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">,</tt><tt class="py-name">node2</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">n</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">l1</tt> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">l2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> </tt>
<a name="Tree.distance"></a><div id="Tree.distance-def"><a name="L322"></a><tt class="py-lineno">322</tt> <a class="py-toggle" href="#" id="Tree.distance-toggle" onclick="return toggle('Tree.distance');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#distance">distance</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">node1</tt><tt class="py-op">,</tt><tt class="py-param">node2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.distance-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.distance-expanded"><a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-docstring">"""Add and return the sum of the branchlengths between two nodes.</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-docstring"> dist = distance(self,node1,node2)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-name">ca</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name" targets="Method Bio.Nexus.Trees.Tree.common_ancestor()=Bio.Nexus.Trees.Tree-class.html#common_ancestor"><a title="Bio.Nexus.Trees.Tree.common_ancestor" class="py-name" href="#" onclick="return doclink('link-180', 'common_ancestor', 'link-180');">common_ancestor</a></tt><tt class="py-op">(</tt><tt class="py-name">node1</tt><tt class="py-op">,</tt><tt class="py-name">node2</tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</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-181" class="py-name" targets="Method Bio.Nexus.Trees.Tree.sum_branchlength()=Bio.Nexus.Trees.Tree-class.html#sum_branchlength"><a title="Bio.Nexus.Trees.Tree.sum_branchlength" class="py-name" href="#" onclick="return doclink('link-181', 'sum_branchlength', 'link-181');">sum_branchlength</a></tt><tt class="py-op">(</tt><tt class="py-name">ca</tt><tt class="py-op">,</tt><tt class="py-name">node1</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-182" class="py-name"><a title="Bio.Nexus.Trees.Tree.sum_branchlength" class="py-name" href="#" onclick="return doclink('link-182', 'sum_branchlength', 'link-181');">sum_branchlength</a></tt><tt class="py-op">(</tt><tt class="py-name">ca</tt><tt class="py-op">,</tt><tt class="py-name">node2</tt><tt class="py-op">)</tt> </tt>
</div><a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> </tt>
<a name="Tree.is_monophyletic"></a><div id="Tree.is_monophyletic-def"><a name="L330"></a><tt class="py-lineno">330</tt> <a class="py-toggle" href="#" id="Tree.is_monophyletic-toggle" onclick="return toggle('Tree.is_monophyletic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#is_monophyletic">is_monophyletic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">taxon_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.is_monophyletic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.is_monophyletic-expanded"><a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-docstring">"""Return node_id of common ancestor if taxon_list is monophyletic, -1 otherwise.</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-docstring"> result = is_monophyletic(self,taxon_list)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">taxon_list</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">taxon_set</tt><tt class="py-op">=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">taxon_list</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">taxon_set</tt><tt class="py-op">=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">taxon_list</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-name">node_id</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-name">subclade_taxa</tt><tt class="py-op">=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-183', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-name">node_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">subclade_taxa</tt><tt class="py-op">==</tt><tt class="py-name">taxon_set</tt><tt class="py-op">:</tt> <tt class="py-comment"># are we there?</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">node_id</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># check subnodes</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">subnode</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">node_id</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-184', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-name">subnode</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">issuperset</tt><tt class="py-op">(</tt><tt class="py-name">taxon_set</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># taxon_set is downstream</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">node_id</tt><tt class="py-op">=</tt><tt class="py-name">subnode</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> <tt class="py-comment"># out of for loop</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-comment"># taxon set was not with successors, for loop exhausted</tt> </tt>
</div><a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> </tt>
<a name="Tree.is_bifurcating"></a><div id="Tree.is_bifurcating-def"><a name="L352"></a><tt class="py-lineno">352</tt> <a class="py-toggle" href="#" id="Tree.is_bifurcating-toggle" onclick="return toggle('Tree.is_bifurcating');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#is_bifurcating">is_bifurcating</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-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.is_bifurcating-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.is_bifurcating-expanded"><a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-docstring">"""Return True if tree downstream of node is strictly bifurcating."""</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-185" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-185', 'node', 'link-52');">node</a></tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt id="link-186" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-186', 'node', 'link-52');">node</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-187" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-187', 'node', 'link-52');">node</a></tt><tt class="py-op">==</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-188', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-189" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-189', 'node', 'link-52');">node</a></tt><tt class="py-op">)</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-number">3</tt><tt class="py-op">:</tt> <tt class="py-comment">#root can be trifurcating, because it has no ancestor</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</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-190" class="py-name" targets="Method Bio.Nexus.Trees.Tree.is_bifurcating()=Bio.Nexus.Trees.Tree-class.html#is_bifurcating"><a title="Bio.Nexus.Trees.Tree.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-190', 'is_bifurcating', 'link-190');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-191', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-192" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-192', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-193', 'is_bifurcating', 'link-190');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-194', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-195', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</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-keyword">and</tt> \ </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-196', 'is_bifurcating', 'link-190');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-197', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-198" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-198', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-199', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-200" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-200', 'node', 'link-52');">node</a></tt><tt class="py-op">)</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-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-201', 'is_bifurcating', 'link-190');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-202', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-203" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-203', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-204', 'is_bifurcating', 'link-190');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-205', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-206" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-206', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</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="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-207', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-208" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-208', 'node', 'link-52');">node</a></tt><tt class="py-op">)</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-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-209" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-209', 'True', 'link-139');">True</a></tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-210" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-210', 'False', 'link-5');">False</a></tt> </tt>
</div><a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> </tt>
<a name="Tree.branchlength2support"></a><div id="Tree.branchlength2support-def"><a name="L369"></a><tt class="py-lineno">369</tt> <a class="py-toggle" href="#" id="Tree.branchlength2support-toggle" onclick="return toggle('Tree.branchlength2support');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#branchlength2support">branchlength2support</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="Tree.branchlength2support-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.branchlength2support-expanded"><a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-docstring">"""Move values stored in data.branchlength to data.support, and set branchlength to 0.0</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"><tt class="py-docstring"> This is necessary when support has been stored as branchlength (e.g. paup), and has thus</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-docstring"> been read in as branchlength. </tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <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">chain</tt><tt class="py-op">.</tt><tt id="link-211" 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-211', 'keys', 'link-211');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-212', 'node', 'link-52');">node</a></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-213" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-213', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-214', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-215', 'node', 'link-52');">node</a></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-216" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-216', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-217', 'node', 'link-52');">node</a></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-218" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-218', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
</div><a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="Tree.convert_absolute_support"></a><div id="Tree.convert_absolute_support-def"><a name="L380"></a><tt class="py-lineno">380</tt> <a class="py-toggle" href="#" id="Tree.convert_absolute_support-toggle" onclick="return toggle('Tree.convert_absolute_support');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#convert_absolute_support">convert_absolute_support</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">nrep</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.convert_absolute_support-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.convert_absolute_support-expanded"><a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert absolute support (clade-count) to rel. frequencies.</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"><tt class="py-docstring"> Some software (e.g. PHYLIP consense) just calculate how often clades appear, instead of</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-docstring"> calculating relative frequencies."""</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <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 id="link-219" class="py-name"><a title="Bio.Nexus.Trees.Tree._walk" class="py-name" href="#" onclick="return doclink('link-219', '_walk', 'link-56');">_walk</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</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-220" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-220', 'node', 'link-52');">node</a></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-221" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-221', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-222', 'support', 'link-3');">support</a></tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-223" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-223', 'node', 'link-52');">node</a></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-224" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-224', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-225', 'support', 'link-3');">support</a></tt><tt class="py-op">/=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">nrep</tt><tt class="py-op">)</tt> </tt>
</div><a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> </tt>
<a name="Tree.randomize"></a><div id="Tree.randomize-def"><a name="L390"></a><tt class="py-lineno">390</tt> <a class="py-toggle" href="#" id="Tree.randomize-toggle" onclick="return toggle('Tree.randomize');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#randomize">randomize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">ntax</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">taxon_list</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">branchlength</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt><tt class="py-param">branchlength_sd</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">bifurcate</tt><tt class="py-op">=</tt><tt id="link-226" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-226', 'True', 'link-139');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.randomize-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.randomize-expanded"><a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-docstring">"""Generates a random tree with ntax taxa and/or taxa from taxlabels.</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"> new_tree = randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True)</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> Trees are bifurcating by default. (Polytomies not yet supported).</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">ntax</tt> <tt class="py-keyword">and</tt> <tt class="py-name">taxon_list</tt><tt class="py-op">:</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">ntax</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taxon_list</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">taxon_list</tt> <tt class="py-keyword">and</tt> <tt class="py-name">ntax</tt><tt class="py-op">:</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-name">taxon_list</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'taxon'</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-227" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-227', 'i', 'link-61');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-228" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-228', 'i', 'link-61');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">ntax</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">ntax</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">taxon_list</tt><tt class="py-op">:</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-229" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-229', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Either numer of taxa or list of taxa must be specified.'</tt><tt class="py-op">)</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">ntax</tt><tt class="py-op"><></tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taxon_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-230" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-230', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Length of taxon list must correspond to ntax.'</tt><tt class="py-op">)</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-comment"># initiate self with empty root</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-231', '__init__', 'link-10');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">terminals</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_terminals" class="py-name" href="#" onclick="return doclink('link-232', 'get_terminals', 'link-88');">get_terminals</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-comment"># bifurcate randomly at terminal nodes until ntax is reached</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">terminals</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-name">ntax</tt><tt class="py-op">:</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">newsplit</tt><tt class="py-op">=</tt><tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">choice</tt><tt class="py-op">(</tt><tt class="py-name">terminals</tt><tt class="py-op">)</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">new_terminals</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-233', 'split', 'link-50');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">parent_id</tt><tt class="py-op">=</tt><tt class="py-name">newsplit</tt><tt class="py-op">,</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">branchlength</tt><tt class="py-op">)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-comment"># if desired, give some variation to the branch length</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">branchlength_sd</tt><tt class="py-op">:</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">nt</tt> <tt class="py-keyword">in</tt> <tt class="py-name">new_terminals</tt><tt class="py-op">:</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-name">bl</tt><tt class="py-op">=</tt><tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">gauss</tt><tt class="py-op">(</tt><tt class="py-name">branchlength</tt><tt class="py-op">,</tt><tt class="py-name">branchlength_sd</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">bl</tt><tt class="py-op"><</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">bl</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-234" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-234', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">nt</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-235" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-235', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">bl</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">terminals</tt><tt class="py-op">.</tt><tt id="link-236" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-236', 'extend', 'link-111');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">new_terminals</tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">terminals</tt><tt class="py-op">.</tt><tt id="link-237" 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-237', 'remove', 'link-237');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">newsplit</tt><tt class="py-op">)</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-comment"># distribute taxon labels randomly</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">shuffle</tt><tt class="py-op">(</tt><tt class="py-name">taxon_list</tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt id="link-238" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-238', 'node', 'link-52');">node</a></tt><tt class="py-op">,</tt><tt id="link-239" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-239', 'name', 'link-12');">name</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">terminals</tt><tt class="py-op">,</tt><tt class="py-name">taxon_list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-240', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-241" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-241', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-242" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-242', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt id="link-243" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-243', 'name', 'link-12');">name</a></tt> </tt>
</div><a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> </tt>
<a name="Tree.display"></a><div id="Tree.display-def"><a name="L426"></a><tt class="py-lineno">426</tt> <a class="py-toggle" href="#" id="Tree.display-toggle" onclick="return toggle('Tree.display');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#display">display</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="Tree.display-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.display-expanded"><a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-docstring">"""Quick and dirty lists of all nodes."""</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt id="link-244" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-244', 'table', 'link-244');">table</a></tt><tt class="py-op">=</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">'taxon'</tt><tt class="py-op">,</tt><tt class="py-string">'prev'</tt><tt class="py-op">,</tt><tt class="py-string">'succ'</tt><tt class="py-op">,</tt><tt class="py-string">'brlen'</tt><tt class="py-op">,</tt><tt class="py-string">'blen (sum)'</tt><tt class="py-op">,</tt><tt class="py-string">'support'</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-245" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-245', 'i', 'link-61');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.Nexus.Nodes.Chain.all_ids" class="py-name" href="#" onclick="return doclink('link-246', 'all_ids', 'link-116');">all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-247', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-248" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-248', 'i', 'link-61');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-249', 'data', 'link-11');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt id="link-250" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-250', 'table', 'link-244');">table</a></tt><tt class="py-op">.</tt><tt id="link-251" 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-251', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-252" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-252', 'i', 'link-61');">i</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-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</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-string">'-'</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-op">)</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-name">tx</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-253', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">tx</tt><tt class="py-op">:</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-name">tx</tt><tt class="py-op">=</tt><tt class="py-string">'-'</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-name">blength</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-254" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-254', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">blength</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-name">blength</tt><tt class="py-op">=</tt><tt class="py-string">'-'</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-name">sum_blength</tt><tt class="py-op">=</tt><tt class="py-string">'-'</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-name">sum_blength</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.Nexus.Trees.Tree.sum_branchlength" class="py-name" href="#" onclick="return doclink('link-255', 'sum_branchlength', 'link-181');">sum_branchlength</a></tt><tt class="py-op">(</tt><tt id="link-256" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-256', 'node', 'link-52');">node</a></tt><tt class="py-op">=</tt><tt id="link-257" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-257', 'i', 'link-61');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt id="link-258" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-258', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-259', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-260', 'support', 'link-3');">support</a></tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-261" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-261', 'support', 'link-3');">support</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt id="link-262" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-262', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-string">'-'</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt id="link-263" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-263', 'table', 'link-244');">table</a></tt><tt class="py-op">.</tt><tt id="link-264" 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-264', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-265" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-265', 'i', 'link-61');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">tx</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</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-name">blength</tt><tt class="py-op">,</tt><tt class="py-name">sum_blength</tt><tt class="py-op">,</tt><tt id="link-266" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-266', 'support', 'link-3');">support</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'%3s %32s %15s %15s %8s %10s %8s'</tt> <tt class="py-op">%</tt> <tt class="py-name">l</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt id="link-267" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-267', 'table', 'link-244');">table</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\nRoot: '</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> </tt>
</div><a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> </tt>
<a name="Tree.to_string"></a><div id="Tree.to_string-def"><a name="L450"></a><tt class="py-lineno">450</tt> <a class="py-toggle" href="#" id="Tree.to_string-toggle" onclick="return toggle('Tree.to_string');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#to_string">to_string</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">support_as_branchlengths</tt><tt class="py-op">=</tt><tt id="link-268" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-268', 'False', 'link-5');">False</a></tt><tt class="py-op">,</tt><tt class="py-param">branchlengths_only</tt><tt class="py-op">=</tt><tt id="link-269" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-269', 'False', 'link-5');">False</a></tt><tt class="py-op">,</tt><tt class="py-param">plain</tt><tt class="py-op">=</tt><tt id="link-270" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-270', 'True', 'link-139');">True</a></tt><tt class="py-op">,</tt><tt class="py-param">plain_newick</tt><tt class="py-op">=</tt><tt id="link-271" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-271', 'False', 'link-5');">False</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.to_string-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.to_string-expanded"><a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a paup compatible tree line.</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-docstring"> to_string(self,support_as_branchlengths=False,branchlengths_only=False,plain=True)</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-comment"># if there's a conflict in the arguments, we override plain=True</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">support_as_branchlengths</tt> <tt class="py-keyword">or</tt> <tt class="py-name">branchlengths_only</tt><tt class="py-op">:</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-name">plain</tt><tt class="py-op">=</tt><tt id="link-272" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-272', 'False', 'link-5');">False</a></tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">support_as_branchlengths</tt><tt class="py-op">=</tt><tt class="py-name">support_as_branchlengths</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">branchlengths_only</tt><tt class="py-op">=</tt><tt class="py-name">branchlengths_only</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plain</tt><tt class="py-op">=</tt><tt class="py-name">plain</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">make_info_string</tt><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">terminal</tt><tt class="py-op">=</tt><tt id="link-273" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-273', 'False', 'link-5');">False</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-docstring">"""Creates nicely formatted support/branchlengths."""</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-comment"># CHECK FORMATTING</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plain</tt><tt class="py-op">:</tt> <tt class="py-comment"># plain tree only. That's easy.</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">support_as_branchlengths</tt><tt class="py-op">:</tt> <tt class="py-comment"># support as branchlengths (eg. PAUP), ignore actual branchlengths</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-274" class="py-name" targets="Method Bio.Parsers.spark.GenericASTBuilder.terminal()=Bio.Parsers.spark.GenericASTBuilder-class.html#terminal"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-274', 'terminal', 'link-274');">terminal</a></tt><tt class="py-op">:</tt> <tt class="py-comment"># terminal branches have 100% support</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">':%1.2f'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_support</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">':%1.2f'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-275" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-275', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-276" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-276', 'support', 'link-3');">support</a></tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">branchlengths_only</tt><tt class="py-op">:</tt> <tt class="py-comment"># write only branchlengths, ignore support</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">':%1.5f'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-277" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-277', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">)</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># write suport and branchlengths (e.g. .con tree of mrbayes)</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-278" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-278', 'terminal', 'link-274');">terminal</a></tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">':%1.5f'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-279" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-279', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-280" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-280', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</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 id="link-281" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-281', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-282" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-282', 'support', 'link-3');">support</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 class="py-comment"># we have blen and suppport</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'%1.2f:%1.5f'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-283" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-283', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-284" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-284', 'support', 'link-3');">support</a></tt><tt class="py-op">,</tt><tt id="link-285" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-285', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-286" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-286', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</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 class="py-comment"># we have only blen</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'0.00000:%1.5f'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-287" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-287', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-288" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-288', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-289', 'support', 'link-3');">support</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 class="py-comment"># we have only support</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'%1.2f:0.00000'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-290" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-290', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-291', 'support', 'link-3');">support</a></tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'0.00:0.00000'</tt> </tt>
</div><a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">newickize</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert a node tree to a newick tree recursively."""</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> </tt>
<a name="L490"></a><tt class="py-lineno">490</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-292" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-292', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-293" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-293', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">:</tt> <tt class="py-comment">#terminal</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</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-294" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-294', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-295" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-295', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-296', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">+</tt><tt class="py-name">make_info_string</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-297', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-298" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-298', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-299" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-299', 'data', 'link-11');">data</a></tt><tt class="py-op">,</tt><tt id="link-300" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-300', 'terminal', 'link-274');">terminal</a></tt><tt class="py-op">=</tt><tt id="link-301" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-301', 'True', 'link-139');">True</a></tt><tt class="py-op">)</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'(%s)%s'</tt> <tt class="py-op">%</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-302" 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-302', 'map', 'link-302');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">newickize</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-303" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-303', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-304" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-304', 'node', 'link-52');">node</a></tt><tt class="py-op">)</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 class="py-name">make_info_string</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-305" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-305', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-306" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-306', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-307" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-307', 'data', 'link-11');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">subtree</tt> </tt>
</div><a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'tree'</tt><tt class="py-op">]</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</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-308" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-308', 'name', 'link-12');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-309" 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-309', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-310" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-310', 'name', 'link-12');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-311" 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-311', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'a_tree'</tt><tt class="py-op">)</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-312" 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-312', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'='</tt><tt class="py-op">)</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op"><></tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-313" 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-313', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'[&W%s]'</tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-314" class="py-name" targets="Method Bio.Blast.NCBIStandalone._BlastConsumer.round()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#round,Method Bio.Blast.NCBIStandalone._DescriptionConsumer.round()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#round"><a title="Bio.Blast.NCBIStandalone._BlastConsumer.round
Bio.Blast.NCBIStandalone._DescriptionConsumer.round" class="py-name" href="#" onclick="return doclink('link-314', 'round', 'link-314');">round</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rooted</tt><tt class="py-op">:</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-315" 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-315', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'[&R]'</tt><tt class="py-op">)</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-316" 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-316', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'(%s)'</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-317" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-317', 'map', 'link-302');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">newickize</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-318" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-318', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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-name">succ</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">plain_newick</tt><tt class="py-op">:</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">treeline</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">' '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">treeline</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">';'</tt> </tt>
</div><a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> </tt>
<a name="Tree.__str__"></a><div id="Tree.__str__-def"><a name="L512"></a><tt class="py-lineno">512</tt> <a class="py-toggle" href="#" id="Tree.__str__-toggle" onclick="return toggle('Tree.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-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="Tree.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.__str__-expanded"><a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-docstring">"""Short version of to_string(), gives plain tree"""</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</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-319" class="py-name" targets="Method Bio.Nexus.Trees.Tree.to_string()=Bio.Nexus.Trees.Tree-class.html#to_string"><a title="Bio.Nexus.Trees.Tree.to_string" class="py-name" href="#" onclick="return doclink('link-319', 'to_string', 'link-319');">to_string</a></tt><tt class="py-op">(</tt><tt class="py-name">plain</tt><tt class="py-op">=</tt><tt id="link-320" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-320', 'True', 'link-139');">True</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> </tt>
<a name="Tree.unroot"></a><div id="Tree.unroot-def"><a name="L516"></a><tt class="py-lineno">516</tt> <a class="py-toggle" href="#" id="Tree.unroot-toggle" onclick="return toggle('Tree.unroot');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#unroot">unroot</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="Tree.unroot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.unroot-expanded"><a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-docstring">"""Defines a unrooted Tree structure, using data of a rooted Tree."""</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-comment"># travel down the rooted tree structure and save all branches and the nodes they connect</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">_get_branches</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-name">branches</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-321" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-321', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-322" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-322', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">succ</tt><tt class="py-op">:</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-name">branches</tt><tt class="py-op">.</tt><tt id="link-323" 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-323', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-324" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-324', 'node', 'link-52');">node</a></tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-325" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-325', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-326" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-326', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-327" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-327', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-328" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-328', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-329" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-329', 'support', 'link-3');">support</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-name">branches</tt><tt class="py-op">.</tt><tt id="link-330" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-330', 'extend', 'link-111');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">_get_branches</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">branches</tt> </tt>
</div><a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">=</tt><tt class="py-name">_get_branches</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-comment"># if root is bifurcating, then it is eliminated</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-331" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-331', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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-name">succ</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-comment"># find the two branches that connect to root</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rootbranches</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">b</tt> <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> <tt class="py-keyword">in</tt> <tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">b1</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-332" 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-332', 'pop', 'link-332');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-333" 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-333', 'index', 'link-333');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">rootbranches</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-name">b2</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-334" class="py-name"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-334', 'pop', 'link-332');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-335" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-335', 'index', 'link-333');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">rootbranches</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="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-comment"># Connect them two each other. If both have support, it should be identical (or one set to None?).</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># If both have branchlengths, they will be added</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">newbranch</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-name">newbranch</tt><tt class="py-op">.</tt><tt id="link-336" 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-336', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># either None (both rootbranches are unsupported) or some support</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-name">newbranch</tt><tt class="py-op">.</tt><tt id="link-337" 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-337', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># dito</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-name">newbranch</tt><tt class="py-op">.</tt><tt id="link-338" 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-338', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># identical support</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">or</tt> <tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">3</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="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-name">newbranch</tt><tt class="py-op">.</tt><tt id="link-339" 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-339', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># one is 0, take the other</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-340" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-340', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Support mismatch in bifurcating root: %f, %f'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">b1</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">b2</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-341" 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-341', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">newbranch</tt><tt class="py-op">)</tt> </tt>
</div><a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> </tt>
<a name="Tree.root_with_outgroup"></a><div id="Tree.root_with_outgroup-def"><a name="L550"></a><tt class="py-lineno">550</tt> <a class="py-toggle" href="#" id="Tree.root_with_outgroup-toggle" onclick="return toggle('Tree.root_with_outgroup');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees.Tree-class.html#root_with_outgroup">root_with_outgroup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">outgroup</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="Tree.root_with_outgroup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.root_with_outgroup-expanded"><a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">_connect_subtree</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>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-docstring">"""Hook subtree starting with node child to parent."""</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-342" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-342', 'i', 'link-61');">i</a></tt><tt class="py-op">,</tt><tt class="py-name">branch</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parent</tt> <tt class="py-keyword">in</tt> <tt class="py-name">branch</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt class="py-name">branch</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-name">branch</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-343" class="py-name"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-343', 'pop', 'link-332');">pop</a></tt><tt class="py-op">(</tt><tt id="link-344" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-344', 'i', 'link-61');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-345" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-345', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Unable to connect nodes for rooting: nodes %d and %d are not connected'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">,</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-346" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.link()=Bio.Nexus.Nodes.Chain-class.html#link"><a title="Bio.Nexus.Nodes.Chain.link" class="py-name" href="#" onclick="return doclink('link-346', 'link', 'link-346');">link</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">,</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-347" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-347', 'node', 'link-52');">node</a></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-348" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-348', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">branchlength</tt><tt class="py-op">=</tt><tt class="py-name">branch</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-349" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-349', 'node', 'link-52');">node</a></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-350" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-350', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-351" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-351', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">branch</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-comment">#now check if there are more branches connected to the child, and if so, connect them</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">child_branches</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">b</tt> <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt> <tt class="py-keyword">if</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-name">child_branches</tt><tt class="py-op">:</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">child</tt><tt class="py-op">==</tt><tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-name">succ</tt><tt class="py-op">=</tt><tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-name">succ</tt><tt class="py-op">=</tt><tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-name">_connect_subtree</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">,</tt><tt class="py-name">succ</tt><tt class="py-op">)</tt> </tt>
</div><a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-comment"># check the outgroup we're supposed to root with</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">outgroup</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</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">root</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> <tt class="py-name">outgroup_node</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-352" class="py-name" targets="Method Bio.Nexus.Trees.Tree.is_monophyletic()=Bio.Nexus.Trees.Tree-class.html#is_monophyletic"><a title="Bio.Nexus.Trees.Tree.is_monophyletic" class="py-name" href="#" onclick="return doclink('link-352', 'is_monophyletic', 'link-352');">is_monophyletic</a></tt><tt class="py-op">(</tt><tt class="py-name">outgroup</tt><tt class="py-op">)</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">outgroup_node</tt><tt class="py-op">==</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt class="py-comment"># if tree is already rooted with outgroup on a bifurcating root,</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># or the outgroup includes all taxa on the tree, then we're fine</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</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 id="link-353" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-353', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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-name">succ</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt> <tt class="py-keyword">and</tt> <tt class="py-name">outgroup_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-354" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-354', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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-name">succ</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">outgroup_node</tt><tt class="py-op">==</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">:</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</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">root</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-355" class="py-name" targets="Method Bio.Nexus.Trees.Tree.unroot()=Bio.Nexus.Trees.Tree-class.html#unroot"><a title="Bio.Nexus.Trees.Tree.unroot" class="py-name" href="#" onclick="return doclink('link-355', 'unroot', 'link-355');">unroot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-comment"># now we find the branch that connects outgroup and ingroup</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print self.node(outgroup_node).prev</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-356" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-356', 'i', 'link-61');">i</a></tt><tt class="py-op">,</tt><tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">outgroup_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-357" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-357', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">outgroup_node</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt> <tt class="py-keyword">in</tt> <tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">root_branch</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-358" class="py-name"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-358', 'pop', 'link-332');">pop</a></tt><tt class="py-op">(</tt><tt id="link-359" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-359', 'i', 'link-61');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-360" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-360', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Unrooted and rooted Tree do not match'</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">outgroup_node</tt><tt class="py-op">==</tt><tt class="py-name">root_branch</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="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-name">ingroup_node</tt><tt class="py-op">=</tt><tt class="py-name">root_branch</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-name">ingroup_node</tt><tt class="py-op">=</tt><tt class="py-name">root_branch</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-comment"># now we destroy the old tree structure, but keep node data. Nodes will be reconnected according to new outgroup</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</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 id="link-361" class="py-name"><a title="Bio.Nexus.Nodes.Chain.all_ids" class="py-name" href="#" onclick="return doclink('link-361', 'all_ids', 'link-116');">all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-362" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-362', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">n</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="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-363" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-363', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</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>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> <tt class="py-comment"># now we just add both subtrees (outgroup and ingroup) branch for branch</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">root</tt><tt class="py-op">=</tt><tt id="link-364" class="py-name"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-364', 'Nodes', 'link-0');">Nodes</a></tt><tt class="py-op">.</tt><tt id="link-365" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-365', 'Node', 'link-15');">Node</a></tt><tt class="py-op">(</tt><tt id="link-366" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-366', 'data', 'link-11');">data</a></tt><tt class="py-op">=</tt><tt id="link-367" class="py-name"><a title="Bio.Nexus.Trees.NodeData" class="py-name" href="#" onclick="return doclink('link-367', 'NodeData', 'link-6');">NodeData</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment"># new root </tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-368" 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-368', 'add', 'link-17');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> <tt class="py-comment"># add to tree description</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">=</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-369" 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-369', 'id', 'link-18');">id</a></tt> <tt class="py-comment"># set as root</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-370" 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-370', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-371" 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-371', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">ingroup_node</tt><tt class="py-op">,</tt><tt class="py-name">root_branch</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">root_branch</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># add branch to ingroup to unrooted tree</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unrooted</tt><tt class="py-op">.</tt><tt id="link-372" 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-372', 'append', 'link-30');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-373" 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-373', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">outgroup_node</tt><tt class="py-op">,</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt><tt class="py-number">0.0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># add branch to outgroup to unrooted tree</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> <tt class="py-name">_connect_subtree</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-374" 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-374', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">ingroup_node</tt><tt class="py-op">)</tt> <tt class="py-comment"># add ingroup</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt class="py-name">_connect_subtree</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-375" 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-375', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">outgroup_node</tt><tt class="py-op">)</tt> <tt class="py-comment"># add outgroup</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-comment"># if theres still a lonely node in self.chain, then it's the old root, and we delete it</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">oldroot</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt id="link-376" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-376', 'i', 'link-61');">i</a></tt> <tt class="py-keyword">for</tt> <tt id="link-377" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-377', 'i', 'link-61');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-378" class="py-name"><a title="Bio.Nexus.Nodes.Chain.all_ids" class="py-name" href="#" onclick="return doclink('link-378', 'all_ids', 'link-116');">all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-379" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-379', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-380" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-380', 'i', 'link-61');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">prev</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt id="link-381" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-381', 'i', 'link-61');">i</a></tt><tt class="py-op">!=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">]</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</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">oldroot</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-382" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-382', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Isolated nodes in tree description: %s'</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 class="py-name">oldroot</tt><tt class="py-op">)</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">oldroot</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-383" class="py-name"><a title="Bio.Nexus.Nodes.Chain.kill" class="py-name" href="#" onclick="return doclink('link-383', 'kill', 'link-92');">kill</a></tt><tt class="py-op">(</tt><tt class="py-name">oldroot</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</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">root</tt> </tt>
</div></div><a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> </tt>
<a name="consensus"></a><div id="consensus-def"><a name="L617"></a><tt class="py-lineno">617</tt> <a class="py-toggle" href="#" id="consensus-toggle" onclick="return toggle('consensus');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Nexus.Trees-module.html#consensus">consensus</a><tt class="py-op">(</tt><tt class="py-param">trees</tt><tt class="py-op">,</tt> <tt class="py-param">threshold</tt><tt class="py-op">=</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt><tt class="py-param">outgroup</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="consensus-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="consensus-expanded"><a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-docstring">"""Compute a majority rule consensus tree of all clades with relative frequency>=threshold from a list of trees."""</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-name">total</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">trees</tt><tt class="py-op">)</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">total</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-comment"># shouldn't we make sure that it's NodeData or subclass??</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dataclass</tt><tt class="py-op">=</tt><tt class="py-name">trees</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dataclass</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt class="py-name">max_support</tt><tt class="py-op">=</tt><tt class="py-name">trees</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">max_support</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt class="py-name">clades</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-comment">#countclades={}</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">alltaxa</tt><tt class="py-op">=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">trees</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-384" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-384', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-comment"># calculate calde frequencies</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">trees</tt><tt class="py-op">:</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-comment">#print c</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#if c%1==0:</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># print c</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">alltaxa</tt><tt class="py-op">!=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt id="link-385" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-385', 'get_taxa', 'link-112');">get_taxa</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="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-386" class="py-name"><a title="Bio.Nexus.Trees.TreeError" class="py-name" href="#" onclick="return doclink('link-386', 'TreeError', 'link-26');">TreeError</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Trees for consensus must contain the same taxa'</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt class="py-name">t</tt><tt class="py-op">.</tt><tt id="link-387" class="py-name" targets="Method Bio.Nexus.Trees.Tree.root_with_outgroup()=Bio.Nexus.Trees.Tree-class.html#root_with_outgroup"><a title="Bio.Nexus.Trees.Tree.root_with_outgroup" class="py-name" href="#" onclick="return doclink('link-387', 'root_with_outgroup', 'link-387');">root_with_outgroup</a></tt><tt class="py-op">(</tt><tt class="py-name">outgroup</tt><tt class="py-op">=</tt><tt class="py-name">outgroup</tt><tt class="py-op">)</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">st_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">t</tt><tt class="py-op">.</tt><tt id="link-388" class="py-name"><a title="Bio.Nexus.Trees.Tree._walk" class="py-name" href="#" onclick="return doclink('link-388', '_walk', 'link-56');">_walk</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-name">subclade_taxa</tt><tt class="py-op">=</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt id="link-389" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_taxa" class="py-name" href="#" onclick="return doclink('link-389', 'get_taxa', 'link-112');">get_taxa</a></tt><tt class="py-op">(</tt><tt class="py-name">st_node</tt><tt class="py-op">)</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-name">subclade_taxa</tt><tt class="py-op">.</tt><tt id="link-390" 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-390', 'sort', 'link-390');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt class="py-name">subclade_taxa</tt><tt class="py-op">=</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">subclade_taxa</tt><tt class="py-op">)</tt> <tt class="py-comment"># lists are not hashable</tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">subclade_taxa</tt> <tt class="py-keyword">in</tt> <tt class="py-name">clades</tt><tt class="py-op">:</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-name">subclade_taxa</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">total</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-name">subclade_taxa</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">total</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-comment">#if subclade_taxa in countclades:</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># countclades[subclade_taxa]+=t.weight</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#else:</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># countclades[subclade_taxa]=t.weight</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># weed out clades below threshold</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-391" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-391', 'items', 'link-79');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">p</tt><tt class="py-op"><</tt><tt id="link-392" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-392', 'threshold', 'link-161');">threshold</a></tt><tt class="py-op">:</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-comment"># create a tree with a root node</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-393" class="py-name" targets="Function Bio.Nexus.Trees.consensus()=Bio.Nexus.Trees-module.html#consensus"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-393', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">=</tt><tt id="link-394" class="py-name" targets="Class Bio.Nexus.Trees.Tree=Bio.Nexus.Trees.Tree-class.html"><a title="Bio.Nexus.Trees.Tree" class="py-name" href="#" onclick="return doclink('link-394', 'Tree', 'link-394');">Tree</a></tt><tt class="py-op">(</tt><tt id="link-395" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-395', 'name', 'link-12');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">'consensus_%2.1f'</tt> <tt class="py-op">%</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-396" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-396', 'threshold', 'link-161');">threshold</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-397" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-397', 'data', 'link-11');">data</a></tt><tt class="py-op">=</tt><tt class="py-name">dataclass</tt><tt class="py-op">)</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"> <tt class="py-comment"># each clade needs a node in the new tree, add them as isolated nodes</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt id="link-398" 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-398', 's', 'link-398');">s</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-399" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-399', 'items', 'link-79');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt id="link-400" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-400', 'node', 'link-52');">node</a></tt><tt class="py-op">=</tt><tt id="link-401" class="py-name"><a title="Bio.Nexus.Nodes" class="py-name" href="#" onclick="return doclink('link-401', 'Nodes', 'link-0');">Nodes</a></tt><tt class="py-op">.</tt><tt id="link-402" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-402', 'Node', 'link-15');">Node</a></tt><tt class="py-op">(</tt><tt id="link-403" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-403', 'data', 'link-11');">data</a></tt><tt class="py-op">=</tt><tt class="py-name">dataclass</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt id="link-404" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-404', 'node', 'link-52');">node</a></tt><tt class="py-op">.</tt><tt id="link-405" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-405', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-406" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-406', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt id="link-407" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-407', 's', 'link-398');">s</a></tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt id="link-408" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-408', 'node', 'link-52');">node</a></tt><tt class="py-op">.</tt><tt id="link-409" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-409', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt class="py-name">sets</tt><tt class="py-op">.</tt><tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt id="link-410" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-410', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-411" 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-411', 'add', 'link-17');">add</a></tt><tt class="py-op">(</tt><tt id="link-412" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-412', 'node', 'link-52');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> <tt class="py-comment"># set root node data</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-413" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-413', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-414" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-414', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-415" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-415', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-416" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-416', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt id="link-417" class="py-name"><a title="Martel.test.support" class="py-name" href="#" onclick="return doclink('link-417', 'support', 'link-3');">support</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt id="link-418" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-418', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-419" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-419', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-420" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-420', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt class="py-name">root</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-421" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-421', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt class="py-name">alltaxa</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-comment"># we sort the nodes by no. of taxa in the clade, so root will be the last</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">consensus_ids</tt><tt class="py-op">=</tt><tt id="link-422" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-422', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-423" class="py-name"><a title="Bio.Nexus.Nodes.Chain.all_ids" class="py-name" href="#" onclick="return doclink('link-423', 'all_ids', 'link-116');">all_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-name">consensus_ids</tt><tt class="py-op">.</tt><tt id="link-424" 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-424', 'sort', 'link-390');">sort</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-425" 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-425', 'x', 'link-425');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-426" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-426', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-427" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-427', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt id="link-428" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-428', 'x', 'link-425');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-429" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-429', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-430" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-430', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-431" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-431', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-432" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-432', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-comment"># now we just have to hook each node to the next smallest node that includes all taxa of the current </tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-433" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-433', 'i', 'link-61');">i</a></tt><tt class="py-op">,</tt><tt class="py-name">current</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">consensus_ids</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># skip the last one which is the root</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-comment">#print '----'</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print 'current: ',consensus.node(current).data.taxon</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># search remaining nodes</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">parent</tt> <tt class="py-keyword">in</tt> <tt class="py-name">consensus_ids</tt><tt class="py-op">[</tt><tt id="link-434" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-434', 'i', 'link-61');">i</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="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"> <tt class="py-comment">#print 'parent: ',consensus.node(parent).data.taxon</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-435" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-435', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-436" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-436', 'node', 'link-52');">node</a></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-437" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-437', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">.</tt><tt class="py-name">issuperset</tt><tt class="py-op">(</tt><tt id="link-438" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-438', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-439" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-439', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-440" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-440', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">'corrupt tree structure?'</tt><tt class="py-op">)</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-comment"># internal nodes don't have taxa</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-441" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-441', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-442" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-442', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-443" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-443', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt id="link-444" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-444', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-445" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-445', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-446" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-446', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt id="link-447" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-447', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-448" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-448', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-449" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-449', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">.</tt><tt id="link-450" class="py-name"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-450', 'pop', 'link-332');">pop</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> <tt class="py-comment"># reset the support for terminal nodes to maximum</tt> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#consensus.node(current).data.support=max_support</tt> </tt>
<a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt id="link-451" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-451', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-452" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-452', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-453" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-453', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"> <tt id="link-454" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-454', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-455" class="py-name"><a title="Bio.Nexus.Nodes.Chain.link" class="py-name" href="#" onclick="return doclink('link-455', 'link', 'link-346');">link</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">,</tt><tt class="py-name">current</tt><tt class="py-op">)</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"> <tt class="py-comment"># eliminate root taxon name</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-456" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-456', 'consensus', 'link-393');">consensus</a></tt><tt class="py-op">.</tt><tt id="link-457" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-457', 'node', 'link-52');">node</a></tt><tt class="py-op">(</tt><tt class="py-name">consensus_ids</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-458" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-458', 'data', 'link-11');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">taxon</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-459" class="py-name"><a title="Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-459', 'consensus', 'link-393');">consensus</a></tt> </tt>
</div><a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:47 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
