<?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.Phylo.NewickIO</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.Phylo-module.html">Package Phylo</a> ::
Module NewickIO
</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.Phylo.NewickIO-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Phylo.NewickIO-module.html">Module Bio.Phylo.NewickIO</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># All rights reserved.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">"""I/O function wrappers for the Newick file format.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">See: http://evolution.genetics.washington.edu/phylip/newick_doc.html</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class Bio.BiopythonDeprecationWarning=Bio.BiopythonDeprecationWarning-class.html"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-1', 'BiopythonDeprecationWarning', 'link-1');">BiopythonDeprecationWarning</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Package Bio.Phylo=Bio.Phylo-module.html"><a title="Bio.Phylo" class="py-name" href="#" onclick="return doclink('link-3', 'Phylo', 'link-3');">Phylo</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module Bio.Phylo.Newick=Bio.Phylo.Newick-module.html"><a title="Bio.Phylo.Newick" class="py-name" href="#" onclick="return doclink('link-4', 'Newick', 'link-4');">Newick</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"># Definitions retrieved from Bio.Nexus.Trees</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable Bio.Nexus.Trees.NODECOMMENT_START=Bio.Nexus.Trees-module.html#NODECOMMENT_START,Variable Bio.Phylo.NewickIO.NODECOMMENT_START=Bio.Phylo.NewickIO-module.html#NODECOMMENT_START"><a title="Bio.Nexus.Trees.NODECOMMENT_START
Bio.Phylo.NewickIO.NODECOMMENT_START" class="py-name" href="#" onclick="return doclink('link-5', 'NODECOMMENT_START', 'link-5');">NODECOMMENT_START</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'[&'</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt id="link-6" class="py-name" targets="Variable Bio.Nexus.Trees.NODECOMMENT_END=Bio.Nexus.Trees-module.html#NODECOMMENT_END,Variable Bio.Phylo.NewickIO.NODECOMMENT_END=Bio.Phylo.NewickIO-module.html#NODECOMMENT_END"><a title="Bio.Nexus.Trees.NODECOMMENT_END
Bio.Phylo.NewickIO.NODECOMMENT_END" class="py-name" href="#" onclick="return doclink('link-6', 'NODECOMMENT_END', 'link-6');">NODECOMMENT_END</a></tt> <tt class="py-op">=</tt> <tt class="py-string">']'</tt> </tt>
<a name="NewickError"></a><div id="NewickError-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="NewickError-toggle" onclick="return toggle('NewickError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.NewickError-class.html">NewickError</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NewickError-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NewickError-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-docstring">"""Exception raised when Newick object construction cannot continue."""</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-comment"># ---------------------------------------------------------</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-comment"># Public API</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over the trees in a Newick file handle.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> :returns: generator of Bio.Phylo.Newick.Tree objects.</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-7" class="py-name" targets="Module Bio.Entrez.Parser=Bio.Entrez.Parser-module.html,Class Bio.ExPASy.ScanProsite.Parser=Bio.ExPASy.ScanProsite.Parser-class.html,Class Bio.Phylo.NewickIO.Parser=Bio.Phylo.NewickIO.Parser-class.html,Class Bio.Phylo.PhyloXMLIO.Parser=Bio.Phylo.PhyloXMLIO.Parser-class.html,Class Bio.SeqIO.UniprotIO.Parser=Bio.SeqIO.UniprotIO.Parser-class.html"><a title="Bio.Entrez.Parser
Bio.ExPASy.ScanProsite.Parser
Bio.Phylo.NewickIO.Parser
Bio.Phylo.PhyloXMLIO.Parser
Bio.SeqIO.UniprotIO.Parser" class="py-name" href="#" onclick="return doclink('link-7', 'Parser', 'link-7');">Parser</a></tt><tt class="py-op">(</tt><tt id="link-8" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-8', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-9', 'parse', 'link-9');">parse</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="write"></a><div id="write-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="write-toggle" onclick="return toggle('write');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO-module.html#write">write</a><tt class="py-op">(</tt><tt class="py-param">trees</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">plain</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="write-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="write-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-docstring">"""Write a trees in Newick format to the given file handle.</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> :returns: number of trees written.</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name" targets="Class Bio.Phylo.NewickIO.Writer=Bio.Phylo.NewickIO.Writer-class.html,Class Bio.Phylo.PhyloXMLIO.Writer=Bio.Phylo.PhyloXMLIO.Writer-class.html"><a title="Bio.Phylo.NewickIO.Writer
Bio.Phylo.PhyloXMLIO.Writer" class="py-name" href="#" onclick="return doclink('link-10', 'Writer', 'link-10');">Writer</a></tt><tt class="py-op">(</tt><tt class="py-name">trees</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-11', 'write', 'link-11');">write</a></tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-12', 'handle', 'link-8');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">plain</tt><tt class="py-op">=</tt><tt class="py-name">plain</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
</div><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="Parser"></a><div id="Parser-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"># ---------------------------------------------------------</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"># Input</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="Parser-toggle" onclick="return toggle('Parser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Parser-class.html">Parser</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Parser-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse a Newick tree given a file handle.</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> Based on the parser in `Bio.Nexus.Trees`.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="Parser.__init__"></a><div id="Parser.__init__-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="Parser.__init__-toggle" onclick="return toggle('Parser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Parser-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">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Parser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser.__init__-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-13', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-14', 'handle', 'link-8');">handle</a></tt> </tt>
</div><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">classmethod</tt> </tt>
<a name="Parser.from_string"></a><div id="Parser.from_string-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="Parser.from_string-toggle" onclick="return toggle('Parser.from_string');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Parser-class.html#from_string">from_string</a><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">,</tt> <tt class="py-param">treetext</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Parser.from_string-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser.from_string-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-15" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">treetext</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cls</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-16', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="Parser.parse"></a><div id="Parser.parse-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="Parser.parse-toggle" onclick="return toggle('Parser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Parser-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">values_are_confidence</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">rooted</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment"># XXX Deprecated kwarg -- remove after Biopython 1.58</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-param">values_are_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="Parser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser.parse-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse the text stream this object was initialized with."""</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># XXX Handling the deprecated kwarg -- remove after Biopython 1.58</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">values_are_support</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="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"use the argument values_are_confidence instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-17', 'BiopythonDeprecationWarning', 'link-1');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">values_are_confidence</tt> <tt class="py-op">=</tt> <tt class="py-name">values_are_support</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">values_are_confidence</tt> <tt class="py-op">=</tt> <tt class="py-name">values_are_confidence</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</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 class="py-comment"># XXX this attribue is useless</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">buf</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-18', 'handle', 'link-8');">handle</a></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">buf</tt> <tt class="py-op">+=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Seq.Seq.rstrip()=Bio.Seq.Seq-class.html#rstrip"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-19', 'rstrip', 'link-19');">rstrip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">buf</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.Seq.Seq.endswith()=Bio.Seq.Seq-class.html#endswith"><a title="Bio.Seq.Seq.endswith" class="py-name" href="#" onclick="return doclink('link-20', 'endswith', 'link-20');">endswith</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="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Phylo.NewickIO.Parser._parse_tree()=Bio.Phylo.NewickIO.Parser-class.html#_parse_tree"><a title="Bio.Phylo.NewickIO.Parser._parse_tree" class="py-name" href="#" onclick="return doclink('link-21', '_parse_tree', 'link-21');">_parse_tree</a></tt><tt class="py-op">(</tt><tt class="py-name">buf</tt><tt class="py-op">,</tt> <tt class="py-name">rooted</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">buf</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">buf</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-comment"># Last tree is missing a terminal ';' character -- that's OK</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Phylo.NewickIO.Parser._parse_tree" class="py-name" href="#" onclick="return doclink('link-22', '_parse_tree', 'link-21');">_parse_tree</a></tt><tt class="py-op">(</tt><tt class="py-name">buf</tt><tt class="py-op">,</tt> <tt class="py-name">rooted</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="Parser._parse_tree"></a><div id="Parser._parse_tree-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="Parser._parse_tree-toggle" onclick="return toggle('Parser._parse_tree');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Parser-class.html#_parse_tree">_parse_tree</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-param">rooted</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Parser._parse_tree-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser._parse_tree-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses the text representation into an Tree object."""</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-comment"># XXX Pass **kwargs along from Parser.parse?</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-23" class="py-name"><a title="Bio.Phylo.Newick" class="py-name" href="#" onclick="return doclink('link-23', 'Newick', 'link-4');">Newick</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Class Bio.Nexus.Trees.Tree=Bio.Nexus.Trees.Tree-class.html,Class Bio.Phylo.BaseTree.Tree=Bio.Phylo.BaseTree.Tree-class.html,Class Bio.Phylo.Newick.Tree=Bio.Phylo.Newick.Tree-class.html"><a title="Bio.Nexus.Trees.Tree
Bio.Phylo.BaseTree.Tree
Bio.Phylo.Newick.Tree" class="py-name" href="#" onclick="return doclink('link-24', 'Tree', 'link-24');">Tree</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name" targets="Variable Bio.Phylo.BaseTree.Clade.root=Bio.Phylo.BaseTree.Clade-class.html#root"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-25', 'root', 'link-25');">root</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Phylo.NewickIO.Parser._parse_subtree()=Bio.Phylo.NewickIO.Parser-class.html#_parse_subtree"><a title="Bio.Phylo.NewickIO.Parser._parse_subtree" class="py-name" href="#" onclick="return doclink('link-26', '_parse_subtree', 'link-26');">_parse_subtree</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">rooted</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rooted</tt><tt class="py-op">)</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="Parser._parse_subtree"></a><div id="Parser._parse_subtree-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="Parser._parse_subtree-toggle" onclick="return toggle('Parser._parse_subtree');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Parser-class.html#_parse_subtree">_parse_subtree</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="Parser._parse_subtree-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser._parse_subtree-expanded"><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse ``(a,b,c...)[[[xx]:]yy]`` into subcomponents, recursively."""</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-27', 'strip', 'link-27');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Seq.Seq.rstrip" class="py-name" href="#" onclick="return doclink('link-28', 'rstrip', 'link-19');">rstrip</a></tt><tt class="py-op">(</tt><tt class="py-string">';'</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-29" 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,Method Bio.Seq.UnknownSeq.count()=Bio.Seq.UnknownSeq-class.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-29', 'count', 'link-29');">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">text</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-30', 'count', 'link-29');">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="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-31" class="py-name" targets="Class Bio.Phylo.NewickIO.NewickError=Bio.Phylo.NewickIO.NewickError-class.html"><a title="Bio.Phylo.NewickIO.NewickError" class="py-name" href="#" onclick="return doclink('link-31', 'NewickError', 'link-31');">NewickError</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">text</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-comment"># Text is now "(...)..." (balanced parens) or "..." (leaf node)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-32', 'count', 'link-29');">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>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-comment"># Leaf/terminal node -- recursion stops here</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</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-33" class="py-name" targets="Method Bio.Phylo.NewickIO.Parser._parse_tag()=Bio.Phylo.NewickIO.Parser-class.html#_parse_tag"><a title="Bio.Phylo.NewickIO.Parser._parse_tag" class="py-name" href="#" onclick="return doclink('link-33', '_parse_tag', 'link-33');">_parse_tag</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-comment"># Handle one layer of the nested subtree</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment"># XXX what if there's a paren in a comment or other string?</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">close_posn</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.Seq.Seq.rfind()=Bio.Seq.Seq-class.html#rfind"><a title="Bio.Seq.Seq.rfind" class="py-name" href="#" onclick="return doclink('link-34', 'rfind', 'link-34');">rfind</a></tt><tt class="py-op">(</tt><tt class="py-string">')'</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</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="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-comment"># Locate subtrees by counting nesting levels of parens</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</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="L107"></a><tt class="py-lineno">107</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="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">posn</tt> <tt class="py-keyword">in</tt> <tt id="link-35" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-35', 'range', 'link-35');">range</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">close_posn</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">posn</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'('</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</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="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">posn</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">')'</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</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="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">posn</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="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">subtrees</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-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"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-36', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">prev</tt><tt class="py-op">:</tt><tt class="py-name">posn</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">prev</tt> <tt class="py-op">=</tt> <tt class="py-name">posn</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">subtrees</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">prev</tt><tt class="py-op">:</tt><tt class="py-name">close_posn</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-comment"># Construct a new clade from trailing text, then attach subclades</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt id="link-38" class="py-name" targets="Variable Bio.Phylo.BaseTree.Tree.clade=Bio.Phylo.BaseTree.Tree-class.html#clade,Method Bio.Phylo.PhyloXMLIO.Writer.clade()=Bio.Phylo.PhyloXMLIO.Writer-class.html#clade"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-38', 'clade', 'link-38');">clade</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Phylo.NewickIO.Parser._parse_tag" class="py-name" href="#" onclick="return doclink('link-39', '_parse_tag', 'link-33');">_parse_tag</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">close_posn</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="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-40" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-40', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</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-41" class="py-name"><a title="Bio.Phylo.NewickIO.Parser._parse_subtree" class="py-name" href="#" onclick="return doclink('link-41', '_parse_subtree', 'link-26');">_parse_subtree</a></tt><tt class="py-op">(</tt><tt class="py-name">st</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">st</tt> <tt class="py-keyword">in</tt> <tt class="py-name">subtrees</tt><tt class="py-op">]</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-42" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-42', 'clade', 'link-38');">clade</a></tt> </tt>
</div><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
<a name="Parser._parse_tag"></a><div id="Parser._parse_tag-def"><a name="L122"></a><tt class="py-lineno">122</tt> <a class="py-toggle" href="#" id="Parser._parse_tag-toggle" onclick="return toggle('Parser._parse_tag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Parser-class.html#_parse_tag">_parse_tag</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="Parser._parse_tag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Parser._parse_tag-expanded"><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-docstring">"""Extract the data for a node from text.</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> :returns: Clade instance containing any available data</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-comment"># Extract the comment</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">comment_start</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.Seq.Seq.find()=Bio.Seq.Seq-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.Seq.Seq.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-43', 'find', 'link-43');">find</a></tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="Bio.Nexus.Trees.NODECOMMENT_START
Bio.Phylo.NewickIO.NODECOMMENT_START" class="py-name" href="#" onclick="return doclink('link-44', 'NODECOMMENT_START', 'link-5');">NODECOMMENT_START</a></tt><tt class="py-op">)</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">comment_start</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="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">comment_end</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.Seq.Seq.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-45', 'find', 'link-43');">find</a></tt><tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Bio.Nexus.Trees.NODECOMMENT_END
Bio.Phylo.NewickIO.NODECOMMENT_END" class="py-name" href="#" onclick="return doclink('link-46', 'NODECOMMENT_END', 'link-6');">NODECOMMENT_END</a></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">if</tt> <tt class="py-name">comment_end</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="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-47" class="py-name"><a title="Bio.Phylo.NewickIO.NewickError" class="py-name" href="#" onclick="return doclink('link-47', 'NewickError', 'link-31');">NewickError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Error in tree description: '</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-string">'Found %s without matching %s'</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-48" class="py-name"><a title="Bio.Nexus.Trees.NODECOMMENT_START
Bio.Phylo.NewickIO.NODECOMMENT_START" class="py-name" href="#" onclick="return doclink('link-48', 'NODECOMMENT_START', 'link-5');">NODECOMMENT_START</a></tt><tt class="py-op">,</tt> <tt id="link-49" class="py-name"><a title="Bio.Nexus.Trees.NODECOMMENT_END
Bio.Phylo.NewickIO.NODECOMMENT_END" class="py-name" href="#" onclick="return doclink('link-49', 'NODECOMMENT_END', 'link-6');">NODECOMMENT_END</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt id="link-50" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.comment()=Bio.GenBank._FeatureConsumer-class.html#comment,Method Bio.GenBank._RecordConsumer.comment()=Bio.GenBank._RecordConsumer-class.html#comment"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-50', 'comment', 'link-50');">comment</a></tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">comment_start</tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.Nexus.Trees.NODECOMMENT_START
Bio.Phylo.NewickIO.NODECOMMENT_START" class="py-name" href="#" onclick="return doclink('link-51', 'NODECOMMENT_START', 'link-5');">NODECOMMENT_START</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-name">comment_end</tt><tt class="py-op">]</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">comment_start</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-name">comment_end</tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-52" class="py-name"><a title="Bio.Nexus.Trees.NODECOMMENT_END
Bio.Phylo.NewickIO.NODECOMMENT_END" class="py-name" href="#" onclick="return doclink('link-52', 'NODECOMMENT_END', 'link-6');">NODECOMMENT_END</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-53', 'comment', 'link-50');">comment</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-54', 'clade', 'link-38');">clade</a></tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Bio.Phylo.Newick" class="py-name" href="#" onclick="return doclink('link-55', 'Newick', 'link-4');">Newick</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Class Bio.Phylo.BaseTree.Clade=Bio.Phylo.BaseTree.Clade-class.html,Class Bio.Phylo.Newick.Clade=Bio.Phylo.Newick.Clade-class.html,Class Bio.Phylo.PhyloXML.Clade=Bio.Phylo.PhyloXML.Clade-class.html"><a title="Bio.Phylo.BaseTree.Clade
Bio.Phylo.Newick.Clade
Bio.Phylo.PhyloXML.Clade" class="py-name" href="#" onclick="return doclink('link-56', 'Clade', 'link-56');">Clade</a></tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-57', 'comment', 'link-50');">comment</a></tt><tt class="py-op">=</tt><tt id="link-58" class="py-name"><a title="Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment" class="py-name" href="#" onclick="return doclink('link-58', 'comment', 'link-50');">comment</a></tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-comment"># Extract name (taxon), and optionally support, branch length</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-comment"># Float values are support and branch length, the string is name/taxon</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt id="link-59" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.Phylo.PhyloXML.Events.values()=Bio.Phylo.PhyloXML.Events-class.html#values,Method Bio.SeqIO._index._IndexedSeqFileDict.values()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-59', 'values', 'link-59');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">part</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-60', 'strip', 'link-27');">strip</a></tt><tt class="py-op">(</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 class="py-name">text</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-61', 'split', 'link-61');">split</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-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">part</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt id="link-62" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-62', 'values', 'link-59');">values</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-63', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">part</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-64" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-64', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-65', 'name', 'link-65');">name</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Two string taxonomies?"</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-66', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-67', 'name', 'link-65');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">part</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-68', 'values', 'link-59');">values</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-comment"># Real branch length, or support as branch length</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</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">values_are_confidence</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt id="link-69" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-69', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Variable Bio.Phylo.PhyloXML.Clade.confidence=Bio.Phylo.PhyloXML.Clade-class.html#confidence,Variable Bio.Phylo.PhyloXML.Phylogeny.confidence=Bio.Phylo.PhyloXML.Phylogeny-class.html#confidence,Method Bio.Phylo.PhyloXMLIO.Parser.confidence()=Bio.Phylo.PhyloXMLIO.Parser-class.html#confidence,Method Bio.Phylo.PhyloXMLIO.Writer.confidence()=Bio.Phylo.PhyloXMLIO.Writer-class.html#confidence"><a title="Bio.Phylo.PhyloXML.Clade.confidence
Bio.Phylo.PhyloXML.Phylogeny.confidence
Bio.Phylo.PhyloXMLIO.Parser.confidence
Bio.Phylo.PhyloXMLIO.Writer.confidence" class="py-name" href="#" onclick="return doclink('link-70', 'confidence', 'link-70');">confidence</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-71', 'values', 'link-59');">values</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt id="link-72" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-72', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.branch_length()=Bio.Phylo.PhyloXMLIO.Writer-class.html#branch_length"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-73', 'branch_length', 'link-73');">branch_length</a></tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-74', 'values', 'link-59');">values</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-75', 'values', 'link-59');">values</a></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="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-comment"># Two non-taxon values: support comes first. (Is that always so?)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-76', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Phylo.PhyloXML.Clade.confidence
Bio.Phylo.PhyloXML.Phylogeny.confidence
Bio.Phylo.PhyloXMLIO.Parser.confidence
Bio.Phylo.PhyloXMLIO.Writer.confidence" class="py-name" href="#" onclick="return doclink('link-77', 'confidence', 'link-70');">confidence</a></tt><tt class="py-op">,</tt> <tt id="link-78" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-78', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-79', 'branch_length', 'link-73');">branch_length</a></tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-80', 'values', 'link-59');">values</a></tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-81" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-81', 'values', 'link-59');">values</a></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="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-82" class="py-name"><a title="Bio.Phylo.NewickIO.NewickError" class="py-name" href="#" onclick="return doclink('link-82', 'NewickError', 'link-31');">NewickError</a></tt><tt class="py-op">(</tt><tt class="py-string">"Too many colons in tag: "</tt> <tt class="py-op">+</tt> <tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-83" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-83', 'clade', 'link-38');">clade</a></tt> </tt>
</div></div><a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt>
<a name="Writer"></a><div id="Writer-def"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"># ---------------------------------------------------------</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-comment"># Output</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="Writer-toggle" onclick="return toggle('Writer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Writer-class.html">Writer</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Writer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Writer-expanded"><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-docstring">"""Based on the writer in Bio.Nexus.Trees (str, to_string)."""</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="Writer.__init__"></a><div id="Writer.__init__-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="Writer.__init__-toggle" onclick="return toggle('Writer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Writer-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">trees</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Writer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Writer.__init__-expanded"><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trees</tt> <tt class="py-op">=</tt> <tt class="py-name">trees</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="Writer.write"></a><div id="Writer.write-def"><a name="L173"></a><tt class="py-lineno">173</tt> <a class="py-toggle" href="#" id="Writer.write-toggle" onclick="return toggle('Writer.write');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Writer-class.html#write">write</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Writer.write-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Writer.write-expanded"><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-docstring">"""Write this instance's trees to a file handle."""</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt id="link-84" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-84', 'count', 'link-29');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">treestr</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Method Bio.Phylo.NewickIO.Writer.to_strings()=Bio.Phylo.NewickIO.Writer-class.html#to_strings"><a title="Bio.Phylo.NewickIO.Writer.to_strings" class="py-name" href="#" onclick="return doclink('link-85', 'to_strings', 'link-85');">to_strings</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt id="link-86" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-86', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-87', 'write', 'link-11');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">treestr</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt id="link-88" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-88', 'count', 'link-29');">count</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-89" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-89', 'count', 'link-29');">count</a></tt> </tt>
</div><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="Writer.to_strings"></a><div id="Writer.to_strings-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="Writer.to_strings-toggle" onclick="return toggle('Writer.to_strings');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Writer-class.html#to_strings">to_strings</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">confidence_as_branch_length</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-param">branch_length_only</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">plain</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-param">plain_newick</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">ladderize</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">max_confidence</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-param">format_confidence</tt><tt class="py-op">=</tt><tt class="py-string">'%1.2f'</tt><tt class="py-op">,</tt> <tt class="py-param">format_branch_length</tt><tt class="py-op">=</tt><tt class="py-string">'%1.5f'</tt><tt class="py-op">,</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment"># XXX Deprecated kwargs -- remove after Biopython 1.58</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-param">support_as_branchlengths</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">branchlengths_only</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-param">max_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="Writer.to_strings-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Writer.to_strings-expanded"><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-docstring">"""Return an iterable of PAUP-compatible tree lines."""</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-comment"># XXX Handling the deprecated kwargs -- remove after Biopython 1.58</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">support_as_branchlengths</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="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-string">"use the argument confidence_as_branch_length instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt id="link-90" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-90', 'BiopythonDeprecationWarning', 'link-1');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">confidence_as_branch_length</tt> <tt class="py-op">=</tt> <tt class="py-name">support_as_branchlengths</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">branchlengths_only</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="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"use the argument branch_length_only instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-91" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-91', 'BiopythonDeprecationWarning', 'link-1');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">branch_length_only</tt> <tt class="py-op">=</tt> <tt class="py-name">branchlengths_only</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">max_support</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="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"use the argument max_confidence instead"</tt><tt class="py-op">,</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt id="link-92" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-92', 'BiopythonDeprecationWarning', 'link-1');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">max_confidence</tt> <tt class="py-op">=</tt> <tt class="py-name">max_support</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</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="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">confidence_as_branch_length</tt> <tt class="py-keyword">or</tt> <tt class="py-name">branch_length_only</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">plain</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <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-93" class="py-name" targets="Method Bio.Phylo.NewickIO.Writer._info_factory()=Bio.Phylo.NewickIO.Writer-class.html#_info_factory"><a title="Bio.Phylo.NewickIO.Writer._info_factory" class="py-name" href="#" onclick="return doclink('link-93', '_info_factory', 'link-93');">_info_factory</a></tt><tt class="py-op">(</tt><tt class="py-name">plain</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">confidence_as_branch_length</tt><tt class="py-op">,</tt> <tt class="py-name">branch_length_only</tt><tt class="py-op">,</tt> <tt class="py-name">max_confidence</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">format_confidence</tt><tt class="py-op">,</tt> <tt class="py-name">format_branch_length</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">def</tt> <tt class="py-def-name">newickize</tt><tt class="py-op">(</tt><tt class="py-param">clade</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert a node tree to a Newick tree string, recursively."""</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-94" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-94', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Method Bio.Nexus.Trees.Tree.is_terminal()=Bio.Nexus.Trees.Tree-class.html#is_terminal,Method Bio.Phylo.BaseTree.Clade.is_terminal()=Bio.Phylo.BaseTree.Clade-class.html#is_terminal,Method Bio.Phylo.BaseTree.Tree.is_terminal()=Bio.Phylo.BaseTree.Tree-class.html#is_terminal"><a title="Bio.Nexus.Trees.Tree.is_terminal
Bio.Phylo.BaseTree.Clade.is_terminal
Bio.Phylo.BaseTree.Tree.is_terminal" class="py-name" href="#" onclick="return doclink('link-95', 'is_terminal', 'link-95');">is_terminal</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#terminal</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-96" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-96', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-97', 'name', 'link-65');">name</a></tt> <tt class="py-keyword">or</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-name">make_info_string</tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-98', 'clade', 'link-38');">clade</a></tt><tt class="py-op">,</tt> <tt id="link-99" 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-99', 'terminal', 'link-99');">terminal</a></tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</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">subtrees</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">newickize</tt><tt class="py-op">(</tt><tt class="py-name">sub</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sub</tt> <tt class="py-keyword">in</tt> <tt id="link-100" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-100', 'clade', 'link-38');">clade</a></tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'(%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 class="py-name">subtrees</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">make_info_string</tt><tt class="py-op">(</tt><tt id="link-101" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-101', 'clade', 'link-38');">clade</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-comment"># Convert each tree to a string</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">tree</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trees</tt><tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-102" class="py-name" targets="Method Bio.Phylo.BaseTree.TreeMixin.ladderize()=Bio.Phylo.BaseTree.TreeMixin-class.html#ladderize"><a title="Bio.Phylo.BaseTree.TreeMixin.ladderize" class="py-name" href="#" onclick="return doclink('link-102', 'ladderize', 'link-102');">ladderize</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">'left'</tt><tt class="py-op">,</tt> <tt class="py-string">'LEFT'</tt><tt class="py-op">,</tt> <tt class="py-string">'right'</tt><tt class="py-op">,</tt> <tt class="py-string">'RIGHT'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-comment"># Nexus compatibility shim, kind of</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.ladderize" class="py-name" href="#" onclick="return doclink('link-103', 'ladderize', 'link-102');">ladderize</a></tt><tt class="py-op">(</tt><tt id="link-104" class="py-name" targets="Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-104', 'reverse', 'link-104');">reverse</a></tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt id="link-105" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.ladderize" class="py-name" href="#" onclick="return doclink('link-105', 'ladderize', 'link-102');">ladderize</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">'right'</tt><tt class="py-op">,</tt> <tt class="py-string">'RIGHT'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">rawtree</tt> <tt class="py-op">=</tt> <tt class="py-name">newickize</tt><tt class="py-op">(</tt><tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-106', 'root', 'link-25');">root</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">';'</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</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="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">rawtree</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-comment"># Nexus-style (?) notation before the raw Newick tree</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</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 class="py-op">(</tt><tt class="py-name">tree</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-107', 'name', 'link-65');">name</a></tt> <tt class="py-keyword">or</tt> <tt class="py-string">'a_tree'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'='</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">if</tt> <tt class="py-name">tree</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="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-108', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'[&W%s]'</tt> <tt class="py-op">%</tt> <tt id="link-109" 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-109', 'round', 'link-109');">round</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">tree</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>
<a name="L232"></a><tt class="py-lineno">232</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">rooted</tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-110', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'[&R]'</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">treeline</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-111', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">rawtree</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">yield</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>
</div><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="Writer._info_factory"></a><div id="Writer._info_factory-def"><a name="L237"></a><tt class="py-lineno">237</tt> <a class="py-toggle" href="#" id="Writer._info_factory-toggle" onclick="return toggle('Writer._info_factory');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.NewickIO.Writer-class.html#_info_factory">_info_factory</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">plain</tt><tt class="py-op">,</tt> <tt class="py-param">confidence_as_branch_length</tt><tt class="py-op">,</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-param">branch_length_only</tt><tt class="py-op">,</tt> <tt class="py-param">max_confidence</tt><tt class="py-op">,</tt> <tt class="py-param">format_confidence</tt><tt class="py-op">,</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-param">format_branch_length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Writer._info_factory-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Writer._info_factory-expanded"><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a function that creates a nicely formatted node tag."""</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">plain</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-comment"># Plain tree only. That's easy.</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</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">clade</tt><tt class="py-op">,</tt> <tt class="py-param">terminal</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">confidence_as_branch_length</tt><tt class="py-op">:</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-comment"># Support as branchlengths (eg. PAUP), ignore actual branchlengths</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</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">clade</tt><tt class="py-op">,</tt> <tt class="py-param">terminal</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-112" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-112', 'terminal', 'link-99');">terminal</a></tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-comment"># terminal branches have 100% support</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</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">format_confidence</tt> <tt class="py-op">%</tt> <tt class="py-name">max_confidence</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">':'</tt> <tt class="py-op">+</tt> <tt class="py-name">format_confidence</tt> <tt class="py-op">%</tt> <tt id="link-113" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-113', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.Phylo.PhyloXML.Clade.confidence
Bio.Phylo.PhyloXML.Phylogeny.confidence
Bio.Phylo.PhyloXMLIO.Parser.confidence
Bio.Phylo.PhyloXMLIO.Writer.confidence" class="py-name" href="#" onclick="return doclink('link-114', 'confidence', 'link-70');">confidence</a></tt> </tt>
</div><a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">branch_length_only</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-comment"># write only branchlengths, ignore support</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</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">clade</tt><tt class="py-op">,</tt> <tt class="py-param">terminal</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</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">format_branch_length</tt> <tt class="py-op">%</tt> <tt id="link-115" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-115', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-116', 'branch_length', 'link-73');">branch_length</a></tt> </tt>
</div><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-comment"># write support and branchlengths (e.g. .con tree of mrbayes)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</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">clade</tt><tt class="py-op">,</tt> <tt class="py-param">terminal</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt id="link-117" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-117', 'terminal', 'link-99');">terminal</a></tt> <tt class="py-keyword">or</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt id="link-118" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-118', 'clade', 'link-38');">clade</a></tt><tt class="py-op">,</tt> <tt class="py-string">'confidence'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt id="link-119" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-119', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="Bio.Phylo.PhyloXML.Clade.confidence
Bio.Phylo.PhyloXML.Phylogeny.confidence
Bio.Phylo.PhyloXMLIO.Parser.confidence
Bio.Phylo.PhyloXMLIO.Writer.confidence" class="py-name" href="#" onclick="return doclink('link-120', 'confidence', 'link-70');">confidence</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-string">':'</tt> <tt class="py-op">+</tt> <tt class="py-name">format_branch_length</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-op">)</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-121', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-122', 'branch_length', 'link-73');">branch_length</a></tt> <tt class="py-keyword">or</tt> <tt class="py-number">0.0</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">else</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-op">(</tt><tt class="py-name">format_confidence</tt> <tt class="py-op">+</tt> <tt class="py-string">':'</tt> <tt class="py-op">+</tt> <tt class="py-name">format_branch_length</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-op">)</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-123', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.Phylo.PhyloXML.Clade.confidence
Bio.Phylo.PhyloXML.Phylogeny.confidence
Bio.Phylo.PhyloXMLIO.Parser.confidence
Bio.Phylo.PhyloXMLIO.Writer.confidence" class="py-name" href="#" onclick="return doclink('link-124', 'confidence', 'link-70');">confidence</a></tt><tt class="py-op">,</tt> <tt id="link-125" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-125', 'clade', 'link-38');">clade</a></tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-126', 'branch_length', 'link-73');">branch_length</a></tt> <tt class="py-keyword">or</tt> <tt class="py-number">0.0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">make_info_string</tt> </tt>
</div></div><a name="L273"></a><tt class="py-lineno">273</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 Thu Aug 18 18:22:51 2011
</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>
