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<a href="Bio-module.html">Package Bio</a> ::
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Module BaseTree
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<h1 class="epydoc">Source Code for <a href="Bio.Phylo.BaseTree-module.html">Module Bio.Phylo.BaseTree</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"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Base classes for Bio.Phylo objects.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">All object representations for phylogenetic trees should derive from these base</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">classes in order to use the common methods defined on them.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</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="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">collections</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.SeqIO._index._IndexedSeqFileDict.copy()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.PDB.Vector'.Vector.copy
Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-0', 'copy', 'link-0');">copy</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">itertools</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.Phylo=Bio.Phylo-module.html"><a title="Bio.Phylo" class="py-name" href="#" onclick="return doclink('link-2', 'Phylo', 'link-2');">Phylo</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Module Bio.Phylo._sugar=Bio.Phylo._sugar-module.html"><a title="Bio.Phylo._sugar" class="py-name" href="#" onclick="return doclink('link-3', '_sugar', 'link-3');">_sugar</a></tt> </tt>
<a name="_level_traverse"></a><div id="_level_traverse-def"><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"># General tree-traversal algorithms</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="_level_traverse-toggle" onclick="return toggle('_level_traverse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_level_traverse">_level_traverse</a><tt class="py-op">(</tt><tt class="py-param">root</tt><tt class="py-op">,</tt> <tt class="py-param">get_children</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_level_traverse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_level_traverse-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-docstring">"""Traverse a tree in breadth-first (level) order."""</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-name">Q</tt> <tt class="py-op">=</tt> <tt class="py-name">collections</tt><tt class="py-op">.</tt><tt class="py-name">deque</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-4" 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-4', 'root', 'link-4');">root</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">Q</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">v</tt> <tt class="py-op">=</tt> <tt class="py-name">Q</tt><tt class="py-op">.</tt><tt class="py-name">popleft</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">v</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">Q</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.extend()=Bio.Align.MultipleSeqAlignment-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-5', 'extend', 'link-5');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">get_children</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="_preorder_traverse"></a><div id="_preorder_traverse-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="_preorder_traverse-toggle" onclick="return toggle('_preorder_traverse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_preorder_traverse">_preorder_traverse</a><tt class="py-op">(</tt><tt class="py-param">root</tt><tt class="py-op">,</tt> <tt class="py-param">get_children</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_preorder_traverse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_preorder_traverse-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-docstring">"""Traverse a tree in depth-first pre-order (parent before children)."""</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">dfs</tt><tt class="py-op">(</tt><tt class="py-param">elem</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">elem</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">get_children</tt><tt class="py-op">(</tt><tt class="py-name">elem</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">u</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dfs</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">u</tt> </tt>
</div><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">elem</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dfs</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-6', 'root', 'link-4');">root</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">elem</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="_postorder_traverse"></a><div id="_postorder_traverse-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="_postorder_traverse-toggle" onclick="return toggle('_postorder_traverse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_postorder_traverse">_postorder_traverse</a><tt class="py-op">(</tt><tt class="py-param">root</tt><tt class="py-op">,</tt> <tt class="py-param">get_children</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_postorder_traverse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_postorder_traverse-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-docstring">"""Traverse a tree in depth-first post-order (children before parent)."""</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">dfs</tt><tt class="py-op">(</tt><tt class="py-param">elem</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">get_children</tt><tt class="py-op">(</tt><tt class="py-name">elem</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">u</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dfs</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">u</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">elem</tt> </tt>
</div><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">elem</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dfs</tt><tt class="py-op">(</tt><tt id="link-7" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-7', 'root', 'link-4');">root</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">elem</tt> </tt>
</div><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="_sorted_attrs"></a><div id="_sorted_attrs-def"><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="_sorted_attrs-toggle" onclick="return toggle('_sorted_attrs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_sorted_attrs">_sorted_attrs</a><tt class="py-op">(</tt><tt class="py-param">elem</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_sorted_attrs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_sorted_attrs-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""Get a flat list of elem's attributes, sorted for consistency."""</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">singles</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">lists</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-comment"># Sort attributes for consistent results</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">attrname</tt><tt class="py-op">,</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sorted</tt><tt class="py-op">(</tt><tt class="py-name">elem</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.SeqIO._index._IndexedSeqFileDict.iteritems()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#iteritems,Method BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#iteritems,Method BioSQL.BioSeqDatabase.DBServer.iteritems()=BioSQL.BioSeqDatabase.DBServer-class.html#iteritems"><a title="Bio.SeqIO._index._IndexedSeqFileDict.iteritems
BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems
BioSQL.BioSeqDatabase.DBServer.iteritems" class="py-name" href="#" onclick="return doclink('link-8', 'iteritems', 'link-8');">iteritems</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">kv</tt><tt class="py-op">:</tt> <tt class="py-name">kv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">child</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-9', 'list', 'link-9');">list</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">lists</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-10', 'extend', 'link-5');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">singles</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'append', 'link-11');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-12" class="py-name" targets="Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-12', 'x', 'link-12');">x</a></tt> <tt class="py-keyword">for</tt> <tt id="link-13" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-13', 'x', 'link-12');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">singles</tt> <tt class="py-op">+</tt> <tt class="py-name">lists</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-14', 'x', 'link-12');">x</a></tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name" targets="Class Bio.Phylo.BaseTree.TreeElement=Bio.Phylo.BaseTree.TreeElement-class.html"><a title="Bio.Phylo.BaseTree.TreeElement" class="py-name" href="#" onclick="return doclink('link-15', 'TreeElement', 'link-15');">TreeElement</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
<a name="_identity_matcher"></a><div id="_identity_matcher-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"># Factory functions to generalize searching for clades/nodes</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="_identity_matcher-toggle" onclick="return toggle('_identity_matcher');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_identity_matcher">_identity_matcher</a><tt class="py-op">(</tt><tt class="py-param">target</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_identity_matcher-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_identity_matcher-expanded"><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-docstring">"""Match a node to the target object by identity."""</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">match</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-16" class="py-name" targets="Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-16', 'node', 'link-16');">node</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">target</tt><tt class="py-op">)</tt> </tt>
</div><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-17" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-17', 'match', 'link-17');">match</a></tt> </tt>
</div><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="_class_matcher"></a><div id="_class_matcher-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="_class_matcher-toggle" onclick="return toggle('_class_matcher');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_class_matcher">_class_matcher</a><tt class="py-op">(</tt><tt class="py-param">target_cls</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_class_matcher-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_class_matcher-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-docstring">"""Match a node if it's an instance of the given class."""</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">match</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-18', 'node', 'link-16');">node</a></tt><tt class="py-op">,</tt> <tt class="py-name">target_cls</tt><tt class="py-op">)</tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-19" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-19', 'match', 'link-17');">match</a></tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="_string_matcher"></a><div id="_string_matcher-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="_string_matcher-toggle" onclick="return toggle('_string_matcher');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_string_matcher">_string_matcher</a><tt class="py-op">(</tt><tt class="py-param">target</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_string_matcher-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_string_matcher-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">match</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">unicode</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-20', 'node', 'link-16');">node</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">target</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-21" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-21', 'match', 'link-17');">match</a></tt> </tt>
</div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="_attribute_matcher"></a><div id="_attribute_matcher-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="_attribute_matcher-toggle" onclick="return toggle('_attribute_matcher');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_attribute_matcher">_attribute_matcher</a><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="_attribute_matcher-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_attribute_matcher-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""Match a node by specified attribute values.</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> ``terminal`` is a special case: True restricts the search to external (leaf)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> nodes, False restricts to internal nodes, and None allows all tree elements</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> to be searched, including phyloXML annotations.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> Otherwise, for a tree element to match the specification (i.e. for the</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> function produced by `_attribute_matcher` to return True when given a tree</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> element), it must have each of the attributes specified by the keys and</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> match each of the corresponding values -- think 'and', not 'or', for</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> multiple keys.</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">match</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'terminal'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwargs</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-comment"># Special case: restrict to internal/external/any nodes</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">kwa_copy</tt> <tt class="py-op">=</tt> <tt class="py-name">kwargs</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.PDB.Vector'.Vector.copy
Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-22', 'copy', 'link-0');">copy</a></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-name">pattern</tt> <tt class="py-op">=</tt> <tt class="py-name">kwa_copy</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop,Method Bio.SeqIO._index._IndexedSeqFileDict.pop()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#pop"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-23', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-string">'terminal'</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">pattern</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-24', 'node', 'link-16');">node</a></tt><tt class="py-op">,</tt> <tt class="py-string">'is_terminal'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt id="link-25" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-25', 'node', 'link-16');">node</a></tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'is_terminal', 'link-26');">is_terminal</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">pattern</tt><tt class="py-op">)</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">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">kwa_copy</tt> <tt class="py-op">=</tt> <tt class="py-name">kwargs</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">pattern</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwa_copy</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.SeqIO._index._IndexedSeqFileDict.iteritems
BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems
BioSQL.BioSeqDatabase.DBServer.iteritems" class="py-name" href="#" onclick="return doclink('link-27', 'iteritems', 'link-8');">iteritems</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-comment"># Nodes must match all other specified attributes</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-28', 'node', 'link-16');">node</a></tt><tt class="py-op">,</tt> <tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">target</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-29', 'node', 'link-16');">node</a></tt><tt class="py-op">,</tt> <tt class="py-name">key</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">pattern</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-30', 'match', 'link-17');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">pattern</tt><tt class="py-op">+</tt><tt class="py-string">'$'</tt><tt class="py-op">,</tt> <tt class="py-name">target</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">pattern</tt><tt class="py-op">,</tt> <tt class="py-name">bool</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">pattern</tt> <tt class="py-op">==</tt> <tt class="py-name">bool</tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">pattern</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">pattern</tt> <tt class="py-op">==</tt> <tt class="py-name">target</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pattern</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">target</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">'invalid query type: %s'</tt> <tt class="py-op">%</tt> <tt id="link-31" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type,Method Bio.Phylo.PhyloXMLIO.Writer.type()=Bio.Phylo.PhyloXMLIO.Writer-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-31', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">pattern</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-32" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-32', 'match', 'link-17');">match</a></tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="_function_matcher"></a><div id="_function_matcher-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="_function_matcher-toggle" onclick="return toggle('_function_matcher');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_function_matcher">_function_matcher</a><tt class="py-op">(</tt><tt class="py-param">matcher_func</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_function_matcher-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_function_matcher-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-docstring">"""Safer attribute lookup -- returns False instead of raising an error."""</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">match</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">matcher_func</tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-33', 'node', 'link-16');">node</a></tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-op">(</tt><tt class="py-name">LookupError</tt><tt class="py-op">,</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-name">TypeError</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-34" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-34', 'match', 'link-17');">match</a></tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="_object_matcher"></a><div id="_object_matcher-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="_object_matcher-toggle" onclick="return toggle('_object_matcher');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_object_matcher">_object_matcher</a><tt class="py-op">(</tt><tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_object_matcher-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_object_matcher-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve a matcher function by passing an arbitrary object.</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> i.e. passing a `TreeElement` such as a `Clade` or `Tree` instance returns an</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> identity matcher, passing a type such as the `PhyloXML.Taxonomy` class</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> returns a class matcher, and passing a dictionary returns an attribute</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> matcher.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> The resulting 'match' function returns True when given an object matching</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> the specification (identity, type or attribute values), otherwise False.</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> This is useful for writing functions that search the tree, and probably</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> shouldn't be used directly by the end user.</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> """</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">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name"><a title="Bio.Phylo.BaseTree.TreeElement" class="py-name" href="#" onclick="return doclink('link-35', 'TreeElement', 'link-15');">TreeElement</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-36" class="py-name" targets="Function Bio.Phylo.BaseTree._identity_matcher()=Bio.Phylo.BaseTree-module.html#_identity_matcher"><a title="Bio.Phylo.BaseTree._identity_matcher" class="py-name" href="#" onclick="return doclink('link-36', '_identity_matcher', 'link-36');">_identity_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">obj</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">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt id="link-37" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-37', 'type', 'link-31');">type</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-38" class="py-name" targets="Function Bio.Phylo.BaseTree._class_matcher()=Bio.Phylo.BaseTree-module.html#_class_matcher"><a title="Bio.Phylo.BaseTree._class_matcher" class="py-name" href="#" onclick="return doclink('link-38', '_class_matcher', 'link-38');">_class_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">obj</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">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-39" class="py-name" targets="Function Bio.Phylo.BaseTree._string_matcher()=Bio.Phylo.BaseTree-module.html#_string_matcher"><a title="Bio.Phylo.BaseTree._string_matcher" class="py-name" href="#" onclick="return doclink('link-39', '_string_matcher', 'link-39');">_string_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-40" class="py-name" targets="Function Bio.Phylo.BaseTree._attribute_matcher()=Bio.Phylo.BaseTree-module.html#_attribute_matcher"><a title="Bio.Phylo.BaseTree._attribute_matcher" class="py-name" href="#" onclick="return doclink('link-40', '_attribute_matcher', 'link-40');">_attribute_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">obj</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">if</tt> <tt class="py-name">callable</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">)</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-41" class="py-name" targets="Function Bio.Phylo.BaseTree._function_matcher()=Bio.Phylo.BaseTree-module.html#_function_matcher"><a title="Bio.Phylo.BaseTree._function_matcher" class="py-name" href="#" onclick="return doclink('link-41', '_function_matcher', 'link-41');">_function_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"%s (type %s) is not a valid type for comparison."</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-42', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
<a name="_combine_matchers"></a><div id="_combine_matchers-def"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <a class="py-toggle" href="#" id="_combine_matchers-toggle" onclick="return toggle('_combine_matchers');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_combine_matchers">_combine_matchers</a><tt class="py-op">(</tt><tt class="py-param">target</tt><tt class="py-op">,</tt> <tt class="py-param">kwargs</tt><tt class="py-op">,</tt> <tt class="py-param">require_spec</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_combine_matchers-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_combine_matchers-expanded"><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-docstring">"""Merge target specifications with keyword arguments.</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> Dispatch the components to the various matcher functions, then merge into a</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> single boolean function.</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">target</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">kwargs</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">require_spec</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"you must specify a target object or keyword "</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-string">"arguments."</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-keyword">lambda</tt> <tt id="link-43" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-43', 'x', 'link-12');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">True</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-44" class="py-name"><a title="Bio.Phylo.BaseTree._attribute_matcher" class="py-name" href="#" onclick="return doclink('link-44', '_attribute_matcher', 'link-40');">_attribute_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">match_obj</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name" targets="Function Bio.Phylo.BaseTree._object_matcher()=Bio.Phylo.BaseTree-module.html#_object_matcher"><a title="Bio.Phylo.BaseTree._object_matcher" class="py-name" href="#" onclick="return doclink('link-45', '_object_matcher', 'link-45');">_object_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">kwargs</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">match_obj</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">match_kwargs</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.Phylo.BaseTree._attribute_matcher" class="py-name" href="#" onclick="return doclink('link-46', '_attribute_matcher', 'link-40');">_attribute_matcher</a></tt><tt class="py-op">(</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-47" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-47', 'x', 'link-12');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">match_obj</tt><tt class="py-op">(</tt><tt id="link-48" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-48', 'x', 'link-12');">x</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">match_kwargs</tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-49', 'x', 'link-12');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> </tt>
<a name="_combine_args"></a><div id="_combine_args-def"><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="_combine_args-toggle" onclick="return toggle('_combine_args');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree-module.html#_combine_args">_combine_args</a><tt class="py-op">(</tt><tt class="py-param">first</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">rest</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_combine_args-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_combine_args-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert ``[targets]`` or ``*targets`` arguments to a single iterable.</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> This helps other functions work like the built-in functions `max` and</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> `min`.</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-comment"># Background: is_monophyletic takes a single list or iterable (like the</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-comment"># same method in Bio.Nexus.Trees); root_with_outgroup and common_ancestor</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-comment"># take separate arguments. This mismatch was in the initial release and I</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-comment"># didn't notice the inconsistency until after Biopython 1.55. I can think</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-comment"># of cases where either style is more convenient, so let's support both</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-comment"># (for backward compatibility and consistency between methods).</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">first</tt><tt class="py-op">,</tt> <tt class="py-string">'__iter__'</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">first</tt><tt class="py-op">,</tt> <tt id="link-50" class="py-name"><a title="Bio.Phylo.BaseTree.TreeElement" class="py-name" href="#" onclick="return doclink('link-50', 'TreeElement', 'link-15');">TreeElement</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">first</tt><tt class="py-op">,</tt> <tt id="link-51" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-51', 'type', 'link-31');">type</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">first</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">first</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment"># `terminals` is an iterable of targets</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-52" class="py-name" targets="Method Bio.Nexus.Nexus.CharBuffer.rest()=Bio.Nexus.Nexus.CharBuffer-class.html#rest"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-52', 'rest', 'link-52');">rest</a></tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Arguments must be either a single list of "</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-string">"targets, or separately specified targets "</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-string">"(e.g. foo(t1, t2, t3)), but not both."</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">first</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-comment"># `terminals` is a single target -- wrap in a container</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">itertools</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">first</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.Nexus.Nexus.CharBuffer.rest" class="py-name" href="#" onclick="return doclink('link-53', 'rest', 'link-52');">rest</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="TreeElement"></a><div id="TreeElement-def"><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-comment"># Class definitions</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <a class="py-toggle" href="#" id="TreeElement-toggle" onclick="return toggle('TreeElement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeElement-class.html">TreeElement</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="TreeElement-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TreeElement-expanded"><a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for all Bio.Phylo classes."""</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> </tt>
<a name="TreeElement.__repr__"></a><div id="TreeElement.__repr__-def"><a name="L216"></a><tt class="py-lineno">216</tt> <a class="py-toggle" href="#" id="TreeElement.__repr__-toggle" onclick="return toggle('TreeElement.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeElement-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeElement.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeElement.__repr__-expanded"><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-docstring">"""Show this object's constructor with its primitive arguments."""</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">pair_as_kwarg_string</tt><tt class="py-op">(</tt><tt class="py-param">key</tt><tt class="py-op">,</tt> <tt class="py-param">val</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</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-name">key</tt><tt class="py-op">,</tt> <tt id="link-54" class="py-name"><a title="Bio.Phylo._sugar" class="py-name" href="#" onclick="return doclink('link-54', '_sugar', 'link-3');">_sugar</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Function Bio.Phylo._sugar.trim_str()=Bio.Phylo._sugar-module.html#trim_str"><a title="Bio.Phylo._sugar.trim_str" class="py-name" href="#" onclick="return doclink('link-55', 'trim_str', 'link-55');">trim_str</a></tt><tt class="py-op">(</tt><tt class="py-name">unicode</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt><tt class="py-op">)</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">return</tt> <tt class="py-string">"%s=%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
</div><a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">u'%s(%s)'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <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">pair_as_kwarg_string</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.SeqIO._index._IndexedSeqFileDict.iteritems
BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems
BioSQL.BioSeqDatabase.DBServer.iteritems" class="py-name" href="#" onclick="return doclink('link-56', 'iteritems', 'link-8');">iteritems</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">val</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
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<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> </tt>
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Bio.PopGen.FDist.Record.__str__
Bio.PopGen.GenePop.FileParser.FileRecord.__str__
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Bio.Restriction.Restriction.RestrictionBatch.__str__
Bio.Restriction.Restriction.RestrictionType.__str__
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Bio.Pathway.Rep.MultiGraph.MultiGraph.__repr__()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__repr__,Method Bio.Pathway.System.__repr__()=Bio.Pathway.System-class.html#__repr__,Method Bio.Phylo.BaseTree.TreeElement.__repr__()=Bio.Phylo.BaseTree.TreeElement-class.html#__repr__,Method Bio.Phylo.PhyloXML.BranchColor.__repr__()=Bio.Phylo.PhyloXML.BranchColor-class.html#__repr__,Method Bio.Restriction.Restriction.Analysis.__repr__()=Bio.Restriction.Restriction.Analysis-class.html#__repr__,Method Bio.Restriction.Restriction.FormattedSeq.__repr__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__repr__,Method Bio.Restriction.Restriction.RestrictionBatch.__repr__()=Bio.Restriction.Restriction.RestrictionBatch-class.html#__repr__,Method Bio.Restriction.Restriction.RestrictionType.__repr__()=Bio.Restriction.Restriction.RestrictionType-class.html#__repr__,Method Bio.Seq.MutableSeq.__repr__()=Bio.Seq.MutableSeq-class.html#__repr__,Method Bio.Seq.Seq.__repr__()=Bio.Seq.Seq-class.html#__repr__,Method Bio.Seq.UnknownSeq.__repr__()=Bio.Seq.UnknownSeq-class.html#__repr__,Method Bio.SeqFeature.AbstractPosition.__repr__()=Bio.SeqFeature.AbstractPosition-class.html#__repr__,Method Bio.SeqFeature.AfterPosition.__repr__()=Bio.SeqFeature.AfterPosition-class.html#__repr__,Method Bio.SeqFeature.BeforePosition.__repr__()=Bio.SeqFeature.BeforePosition-class.html#__repr__,Method Bio.SeqFeature.ExactPosition.__repr__()=Bio.SeqFeature.ExactPosition-class.html#__repr__,Method Bio.SeqFeature.FeatureLocation.__repr__()=Bio.SeqFeature.FeatureLocation-class.html#__repr__,Method Bio.SeqFeature.OneOfPosition.__repr__()=Bio.SeqFeature.OneOfPosition-class.html#__repr__,Method Bio.SeqFeature.PositionGap.__repr__()=Bio.SeqFeature.PositionGap-class.html#__repr__,Method Bio.SeqFeature.Reference.__repr__()=Bio.SeqFeature.Reference-class.html#__repr__,Method Bio.SeqFeature.SeqFeature.__repr__()=Bio.SeqFeature.SeqFeature-class.html#__repr__,Method Bio.SeqFeature.UnknownPosition.__repr__()=Bio.SeqFeature.UnknownPosition-class.html#__repr__,Method Bio.SeqIO._index._IndexedSeqFileDict.__repr__()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#__repr__,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.__repr__()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#__repr__,Method Bio.SeqRecord.SeqRecord.__repr__()=Bio.SeqRecord.SeqRecord-class.html#__repr__,Method Bio.UniGene.ProtsimLine.__repr__()=Bio.UniGene.ProtsimLine-class.html#__repr__,Method Bio.UniGene.Record.__repr__()=Bio.UniGene.Record-class.html#__repr__,Method Bio.UniGene.STSLine.__repr__()=Bio.UniGene.STSLine-class.html#__repr__,Method Bio.UniGene.SequenceLine.__repr__()=Bio.UniGene.SequenceLine-class.html#__repr__,Method Bio.UniGene.UnigeneProtsimRecord.__repr__()=Bio.UniGene.UnigeneProtsimRecord-class.html#__repr__,Method Bio.UniGene.UnigeneRecord.__repr__()=Bio.UniGene.UnigeneRecord-class.html#__repr__,Method Bio.UniGene.UnigeneSTSRecord.__repr__()=Bio.UniGene.UnigeneSTSRecord-class.html#__repr__,Method Bio.UniGene.UnigeneSequenceRecord.__repr__()=Bio.UniGene.UnigeneSequenceRecord-class.html#__repr__,Method Bio.Wise.psw.AlignmentColumn.__repr__()=Bio.Wise.psw.AlignmentColumn-class.html#__repr__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__repr__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__repr__,Method BioSQL.BioSeqDatabase.DBServer.__repr__()=BioSQL.BioSeqDatabase.DBServer-class.html#__repr__"><a title="Bio.Align.Generic.Alignment.__repr__
Bio.Alphabet.Alphabet.__repr__
Bio.Alphabet.AlphabetEncoder.__repr__
Bio.Application.AbstractCommandline.__repr__
Bio.Application.ApplicationError.__repr__
Bio.Crystal.Crystal.__repr__
Bio.Crystal.Hetero.__repr__
Bio.DocSQL.Query.__repr__
Bio.Entrez.Parser.DictionaryElement.__repr__
Bio.Entrez.Parser.IntegerElement.__repr__
Bio.Entrez.Parser.ListElement.__repr__
Bio.Entrez.Parser.StringElement.__repr__
Bio.Entrez.Parser.StructureElement.__repr__
Bio.Entrez.Parser.UnicodeElement.__repr__
Bio.ExPASy.Enzyme.Record.__repr__
Bio.FSSP.FSSPSumRec.__repr__
Bio.FSSP.PosAlign.__repr__
Bio.FSSP.fssp_rec.fff_rec.__repr__
Bio.GenBank.LocationParser.AbsoluteLocation.__repr__
Bio.GenBank.LocationParser.Between.__repr__
Bio.GenBank.LocationParser.FeatureName.__repr__
Bio.GenBank.LocationParser.Function.__repr__
Bio.GenBank.LocationParser.HighBound.__repr__
Bio.GenBank.LocationParser.Integer.__repr__
Bio.GenBank.LocationParser.LowBound.__repr__
Bio.GenBank.LocationParser.Path.__repr__
Bio.GenBank.LocationParser.Range.__repr__
Bio.GenBank.LocationParser.Symbol.__repr__
Bio.GenBank.LocationParser.Token.__repr__
Bio.GenBank.LocationParser.TwoBound.__repr__
Bio.GenBank.LocationParser.UnsignedInteger.__repr__
Bio.PDB.Atom.Atom.__repr__
Bio.PDB.Atom.DisorderedAtom.__repr__
Bio.PDB.Chain.Chain.__repr__
Bio.PDB.FragmentMapper'.Fragment.__repr__
Bio.PDB.Model.Model.__repr__
Bio.PDB.PDBIO'.Select.__repr__
Bio.PDB.Polypeptide.Polypeptide.__repr__
Bio.PDB.Residue.DisorderedResidue.__repr__
Bio.PDB.Residue.Residue.__repr__
Bio.PDB.Structure.Structure.__repr__
Bio.PDB.Vector'.Vector.__repr__
Bio.Pathway.Interaction.__repr__
Bio.Pathway.Network.__repr__
Bio.Pathway.Reaction.__repr__
Bio.Pathway.Rep.Graph.Graph.__repr__
Bio.Pathway.Rep.HashSet.HashSet.__repr__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__repr__
Bio.Pathway.System.__repr__
Bio.Phylo.BaseTree.TreeElement.__repr__
Bio.Phylo.PhyloXML.BranchColor.__repr__
Bio.Restriction.Restriction.Analysis.__repr__
Bio.Restriction.Restriction.FormattedSeq.__repr__
Bio.Restriction.Restriction.RestrictionBatch.__repr__
Bio.Restriction.Restriction.RestrictionType.__repr__
Bio.Seq.MutableSeq.__repr__
Bio.Seq.Seq.__repr__
Bio.Seq.UnknownSeq.__repr__
Bio.SeqFeature.AbstractPosition.__repr__
Bio.SeqFeature.AfterPosition.__repr__
Bio.SeqFeature.BeforePosition.__repr__
Bio.SeqFeature.ExactPosition.__repr__
Bio.SeqFeature.FeatureLocation.__repr__
Bio.SeqFeature.OneOfPosition.__repr__
Bio.SeqFeature.PositionGap.__repr__
Bio.SeqFeature.Reference.__repr__
Bio.SeqFeature.SeqFeature.__repr__
Bio.SeqFeature.UnknownPosition.__repr__
Bio.SeqIO._index._IndexedSeqFileDict.__repr__
Bio.SeqIO._index._SQLiteManySeqFilesDict.__repr__
Bio.SeqRecord.SeqRecord.__repr__
Bio.UniGene.ProtsimLine.__repr__
Bio.UniGene.Record.__repr__
Bio.UniGene.STSLine.__repr__
Bio.UniGene.SequenceLine.__repr__
Bio.UniGene.UnigeneProtsimRecord.__repr__
Bio.UniGene.UnigeneRecord.__repr__
Bio.UniGene.UnigeneSTSRecord.__repr__
Bio.UniGene.UnigeneSequenceRecord.__repr__
Bio.Wise.psw.AlignmentColumn.__repr__
BioSQL.BioSeqDatabase.BioSeqDatabase.__repr__
BioSQL.BioSeqDatabase.DBServer.__repr__" class="py-name" href="#" onclick="return doclink('link-59', '__repr__', 'link-59');">__repr__</a></tt> </tt>
</div><a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> </tt>
<a name="TreeMixin"></a><div id="TreeMixin-def"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <a class="py-toggle" href="#" id="TreeMixin-toggle" onclick="return toggle('TreeMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html">TreeMixin</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="TreeMixin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TreeMixin-expanded"><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-docstring">"""Methods for Tree- and Clade-based classes.</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"> This lets `Tree` and `Clade` support the same traversal and searching</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> operations without requiring Clade to inherit from Tree, so Clade isn't</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> required to have all of Tree's attributes -- just ``root`` (a Clade</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> instance) and ``is_terminal``.</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-comment"># Traversal methods</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="TreeMixin._filter_search"></a><div id="TreeMixin._filter_search-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="TreeMixin._filter_search-toggle" onclick="return toggle('TreeMixin._filter_search');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#_filter_search">_filter_search</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filter_func</tt><tt class="py-op">,</tt> <tt class="py-param">order</tt><tt class="py-op">,</tt> <tt class="py-param">follow_attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin._filter_search-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin._filter_search-expanded"><a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-docstring">"""Perform a BFS or DFS traversal through all elements in this tree.</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"> :returns: generator of all elements for which `filter_func` is True.</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">order_opts</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'preorder'</tt><tt class="py-op">:</tt> <tt id="link-60" class="py-name" targets="Function Bio.Phylo.BaseTree._preorder_traverse()=Bio.Phylo.BaseTree-module.html#_preorder_traverse"><a title="Bio.Phylo.BaseTree._preorder_traverse" class="py-name" href="#" onclick="return doclink('link-60', '_preorder_traverse', 'link-60');">_preorder_traverse</a></tt><tt class="py-op">,</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-string">'postorder'</tt><tt class="py-op">:</tt> <tt id="link-61" class="py-name" targets="Function Bio.Phylo.BaseTree._postorder_traverse()=Bio.Phylo.BaseTree-module.html#_postorder_traverse"><a title="Bio.Phylo.BaseTree._postorder_traverse" class="py-name" href="#" onclick="return doclink('link-61', '_postorder_traverse', 'link-61');">_postorder_traverse</a></tt><tt class="py-op">,</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-string">'level'</tt><tt class="py-op">:</tt> <tt id="link-62" class="py-name" targets="Function Bio.Phylo.BaseTree._level_traverse()=Bio.Phylo.BaseTree-module.html#_level_traverse"><a title="Bio.Phylo.BaseTree._level_traverse" class="py-name" href="#" onclick="return doclink('link-62', '_level_traverse', 'link-62');">_level_traverse</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-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">order_func</tt> <tt class="py-op">=</tt> <tt class="py-name">order_opts</tt><tt class="py-op">[</tt><tt class="py-name">order</tt><tt class="py-op">]</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid order '%s'; must be one of: %s"</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">order</tt><tt class="py-op">,</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">order_opts</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Phylo.PhyloXML.Events.keys()=Bio.Phylo.PhyloXML.Events-class.html#keys,Method Bio.SeqIO._index._IndexedSeqFileDict.keys()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#keys,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.keys()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-63', 'keys', 'link-63');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">follow_attrs</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">get_children</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name" targets="Function Bio.Phylo.BaseTree._sorted_attrs()=Bio.Phylo.BaseTree-module.html#_sorted_attrs"><a title="Bio.Phylo.BaseTree._sorted_attrs" class="py-name" href="#" onclick="return doclink('link-64', '_sorted_attrs', 'link-64');">_sorted_attrs</a></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt id="link-65" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-65', 'root', 'link-4');">root</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">get_children</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">elem</tt><tt class="py-op">:</tt> <tt class="py-name">elem</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-66', 'root', 'link-4');">root</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-67', 'root', 'link-4');">root</a></tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">itertools</tt><tt class="py-op">.</tt><tt class="py-name">ifilter</tt><tt class="py-op">(</tt><tt class="py-name">filter_func</tt><tt class="py-op">,</tt> <tt class="py-name">order_func</tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-68', 'root', 'link-4');">root</a></tt><tt class="py-op">,</tt> <tt class="py-name">get_children</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.find_any"></a><div id="TreeMixin.find_any-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="TreeMixin.find_any-toggle" onclick="return toggle('TreeMixin.find_any');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_any">find_any</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</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="TreeMixin.find_any-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.find_any-expanded"><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the first element found by find_elements(), or None.</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> This is also useful for checking whether any matching element exists in</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> the tree, and can be used in a conditional expression.</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">hits</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.Phylo.BaseTree.TreeMixin.find_elements()=Bio.Phylo.BaseTree.TreeMixin-class.html#find_elements"><a title="Bio.Phylo.BaseTree.TreeMixin.find_elements" class="py-name" href="#" onclick="return doclink('link-69', 'find_elements', 'link-69');">find_elements</a></tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">hits</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.File.UndoHandle.next()=Bio.File.UndoHandle-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.PopGen.GenePop.Controller._FileIterator.next()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-70', 'next', 'link-70');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.find_elements"></a><div id="TreeMixin.find_elements-def"><a name="L275"></a><tt class="py-lineno">275</tt> <a class="py-toggle" href="#" id="TreeMixin.find_elements-toggle" onclick="return toggle('TreeMixin.find_elements');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_elements">find_elements</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">terminal</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">order</tt><tt class="py-op">=</tt><tt class="py-string">'preorder'</tt><tt class="py-op">,</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <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="TreeMixin.find_elements-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.find_elements-expanded"><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-docstring">"""Find all tree elements matching the given attributes.</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-docstring"> The arbitrary keyword arguments indicate the attribute name of the</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-docstring"> sub-element and the value to match: string, integer or boolean. Strings</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-docstring"> are evaluated as regular expression matches; integers are compared</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-docstring"> directly for equality, and booleans evaluate the attribute's truth value</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-docstring"> (True or False) before comparing. To handle nonzero floats, search with</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"> a boolean argument, then filter the result manually.</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-docstring"> If no keyword arguments are given, then just the class type is used for</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-docstring"> matching.</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-docstring"> The result is an iterable through all matching objects, by depth-first</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"> search. (Not necessarily the same order as the elements appear in the</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-docstring"> source file!)</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"> :Parameters:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"> target : TreeElement instance, type, dict, or callable</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> Specifies the characteristics to search for. (The default,</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> TreeElement, matches any standard Bio.Phylo type.)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> terminal : bool</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> A boolean value to select for or against terminal nodes (a.k.a.</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> leaf nodes). True searches for only terminal nodes, False</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> excludes terminal nodes, and the default, None, searches both</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> terminal and non-terminal nodes, as well as any tree elements</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> lacking the ``is_terminal`` method.</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"> order : {'preorder', 'postorder', 'level'}</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> Tree traversal order: 'preorder' (default) is depth-first</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"> search, 'postorder' is DFS with child nodes preceding parents,</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> and 'level' is breadth-first search.</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-docstring"> Example</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-docstring"> -------</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Phylo.IO import PhyloXMIO</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-docstring"> >>> phx = PhyloXMLIO.read('phyloxml_examples.xml')</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-docstring"> >>> matches = phx.phylogenies[5].find_elements(code='OCTVU')</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-docstring"> >>> matches.next()</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-docstring"> Taxonomy(code='OCTVU', scientific_name='Octopus vulgaris')</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-71" 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-71', 'terminal', 'link-71');">terminal</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">kwargs</tt><tt class="py-op">[</tt><tt class="py-string">'terminal'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-72', 'terminal', 'link-71');">terminal</a></tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">is_matching_elem</tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name" targets="Function Bio.Phylo.BaseTree._combine_matchers()=Bio.Phylo.BaseTree-module.html#_combine_matchers"><a title="Bio.Phylo.BaseTree._combine_matchers" class="py-name" href="#" onclick="return doclink('link-73', '_combine_matchers', 'link-73');">_combine_matchers</a></tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">,</tt> <tt class="py-name">kwargs</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name" targets="Method Bio.Phylo.BaseTree.TreeMixin._filter_search()=Bio.Phylo.BaseTree.TreeMixin-class.html#_filter_search"><a title="Bio.Phylo.BaseTree.TreeMixin._filter_search" class="py-name" href="#" onclick="return doclink('link-74', '_filter_search', 'link-74');">_filter_search</a></tt><tt class="py-op">(</tt><tt class="py-name">is_matching_elem</tt><tt class="py-op">,</tt> <tt class="py-name">order</tt><tt class="py-op">,</tt> <tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
</div><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.find_clades"></a><div id="TreeMixin.find_clades-def"><a name="L323"></a><tt class="py-lineno">323</tt> <a class="py-toggle" href="#" id="TreeMixin.find_clades-toggle" onclick="return toggle('TreeMixin.find_clades');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_clades">find_clades</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">terminal</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">order</tt><tt class="py-op">=</tt><tt class="py-string">'preorder'</tt><tt class="py-op">,</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <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="TreeMixin.find_clades-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.find_clades-expanded"><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-docstring">"""Find each clade containing a matching element.</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-docstring"> That is, find each element as with find_elements(), but return the</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-docstring"> corresponding clade object. (This is usually what you want.)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-docstring"> :returns: an iterable through all matching objects, searching</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-docstring"> depth-first (preorder) by default.</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">match_attrs</tt><tt class="py-op">(</tt><tt class="py-param">elem</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-name">orig_clades</tt> <tt class="py-op">=</tt> <tt class="py-name">elem</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-75', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-string">'clades'</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">found</tt> <tt class="py-op">=</tt> <tt class="py-name">elem</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name" targets="Method Bio.Phylo.BaseTree.TreeMixin.find_any()=Bio.Phylo.BaseTree.TreeMixin-class.html#find_any"><a title="Bio.Phylo.BaseTree.TreeMixin.find_any" class="py-name" href="#" onclick="return doclink('link-76', 'find_any', 'link-76');">find_any</a></tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">elem</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt> <tt class="py-op">=</tt> <tt class="py-name">orig_clades</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">found</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>
</div><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-77" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-77', 'terminal', 'link-71');">terminal</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-name">is_matching_elem</tt> <tt class="py-op">=</tt> <tt class="py-name">match_attrs</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">is_matching_elem</tt><tt class="py-op">(</tt><tt class="py-param">elem</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">elem</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><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-78', 'is_terminal', 'link-26');">is_terminal</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-79" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-79', 'terminal', 'link-71');">terminal</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">match_attrs</tt><tt class="py-op">(</tt><tt class="py-name">elem</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L344"></a><tt class="py-lineno">344</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-80" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin._filter_search" class="py-name" href="#" onclick="return doclink('link-80', '_filter_search', 'link-74');">_filter_search</a></tt><tt class="py-op">(</tt><tt class="py-name">is_matching_elem</tt><tt class="py-op">,</tt> <tt class="py-name">order</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
</div><a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.get_path"></a><div id="TreeMixin.get_path-def"><a name="L346"></a><tt class="py-lineno">346</tt> <a class="py-toggle" href="#" id="TreeMixin.get_path-toggle" onclick="return toggle('TreeMixin.get_path');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_path">get_path</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target</tt><tt class="py-op">=</tt><tt class="py-name">None</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="TreeMixin.get_path-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.get_path-expanded"><a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-docstring">"""List the clades directly between this root and the given target.</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"> :returns: list of all clade objects along this path, ending with the</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-docstring"> given target, but excluding the root clade.</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-comment"># Only one path will work -- ignore weights and visits</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt id="link-81" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-81', 'match', 'link-17');">match</a></tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="Bio.Phylo.BaseTree._combine_matchers" class="py-name" href="#" onclick="return doclink('link-82', '_combine_matchers', 'link-73');">_combine_matchers</a></tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">,</tt> <tt class="py-name">kwargs</tt><tt class="py-op">,</tt> <tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">check_in_path</tt><tt class="py-op">(</tt><tt class="py-param">v</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-83" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-83', 'match', 'link-17');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-84" 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-84', 'append', 'link-11');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">v</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><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-85', 'is_terminal', 'link-26');">is_terminal</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt class="py-name">v</tt><tt class="py-op">:</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">check_in_path</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'append', 'link-11');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">check_in_path</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-87', 'root', 'link-4');">root</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">path</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.get_nonterminals"></a><div id="TreeMixin.get_nonterminals-def"><a name="L370"></a><tt class="py-lineno">370</tt> <a class="py-toggle" href="#" id="TreeMixin.get_nonterminals-toggle" onclick="return toggle('TreeMixin.get_nonterminals');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_nonterminals">get_nonterminals</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">order</tt><tt class="py-op">=</tt><tt class="py-string">'preorder'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.get_nonterminals-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.get_nonterminals-expanded"><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-docstring">"""Get a list of all of this tree's nonterminal (internal) nodes."""</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-88" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-88', 'list', 'link-9');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Method Bio.Phylo.BaseTree.TreeMixin.find_clades()=Bio.Phylo.BaseTree.TreeMixin-class.html#find_clades"><a title="Bio.Phylo.BaseTree.TreeMixin.find_clades" class="py-name" href="#" onclick="return doclink('link-89', 'find_clades', 'link-89');">find_clades</a></tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-90', 'terminal', 'link-71');">terminal</a></tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">order</tt><tt class="py-op">=</tt><tt class="py-name">order</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.get_terminals"></a><div id="TreeMixin.get_terminals-def"><a name="L374"></a><tt class="py-lineno">374</tt> <a class="py-toggle" href="#" id="TreeMixin.get_terminals-toggle" onclick="return toggle('TreeMixin.get_terminals');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_terminals">get_terminals</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">order</tt><tt class="py-op">=</tt><tt class="py-string">'preorder'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.get_terminals-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.get_terminals-expanded"><a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-docstring">"""Get a list of all of this tree's terminal (leaf) nodes."""</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-91" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-91', 'list', 'link-9');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.find_clades" class="py-name" href="#" onclick="return doclink('link-92', 'find_clades', 'link-89');">find_clades</a></tt><tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-93', 'terminal', 'link-71');">terminal</a></tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-name">order</tt><tt class="py-op">=</tt><tt class="py-name">order</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.trace"></a><div id="TreeMixin.trace-def"><a name="L378"></a><tt class="py-lineno">378</tt> <a class="py-toggle" href="#" id="TreeMixin.trace-toggle" onclick="return toggle('TreeMixin.trace');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#trace">trace</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">finish</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.trace-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.trace-expanded"><a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-docstring">"""List of all clade object between two targets in this tree.</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-docstring"> Excluding `start`, including `finish`.</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">mrca</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method Bio.Nexus.Trees.Tree.common_ancestor()=Bio.Nexus.Trees.Tree-class.html#common_ancestor,Method Bio.Phylo.BaseTree.TreeMixin.common_ancestor()=Bio.Phylo.BaseTree.TreeMixin-class.html#common_ancestor"><a title="Bio.Nexus.Trees.Tree.common_ancestor
Bio.Phylo.BaseTree.TreeMixin.common_ancestor" class="py-name" href="#" onclick="return doclink('link-94', 'common_ancestor', 'link-94');">common_ancestor</a></tt><tt class="py-op">(</tt><tt id="link-95" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Variable Bio.SeqFeature.FeatureLocation.start=Bio.SeqFeature.FeatureLocation-class.html#start"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-95', 'start', 'link-95');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">finish</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">fromstart</tt> <tt class="py-op">=</tt> <tt class="py-name">mrca</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Method Bio.Phylo.BaseTree.TreeMixin.get_path()=Bio.Phylo.BaseTree.TreeMixin-class.html#get_path"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-96', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-97', 'start', 'link-95');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">to</tt> <tt class="py-op">=</tt> <tt class="py-name">mrca</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-98', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt class="py-name">finish</tt><tt class="py-op">)</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">fromstart</tt> <tt class="py-op">+</tt> <tt class="py-op">[</tt><tt class="py-name">mrca</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">to</tt> </tt>
</div><a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-comment"># Information methods</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.common_ancestor"></a><div id="TreeMixin.common_ancestor-def"><a name="L390"></a><tt class="py-lineno">390</tt> <a class="py-toggle" href="#" id="TreeMixin.common_ancestor-toggle" onclick="return toggle('TreeMixin.common_ancestor');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#common_ancestor">common_ancestor</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">targets</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">more_targets</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.common_ancestor-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.common_ancestor-expanded"><a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-docstring">"""Most recent common ancestor (clade) of all the given targets.</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"> Edge cases: </tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> - If no target is given, returns self.root</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> - If 1 target is given, returns the target</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-docstring"> - If any target is not found in this tree, raises a ValueError</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">paths</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-99" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-99', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt id="link-100" class="py-name" targets="Function Bio.Phylo.BaseTree._combine_args()=Bio.Phylo.BaseTree-module.html#_combine_args"><a title="Bio.Phylo.BaseTree._combine_args" class="py-name" href="#" onclick="return doclink('link-100', '_combine_args', 'link-100');">_combine_args</a></tt><tt class="py-op">(</tt><tt class="py-name">targets</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">more_targets</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-comment"># Validation -- otherwise izip throws a spooky error below</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">paths</tt><tt class="py-op">,</tt> <tt class="py-name">targets</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">p</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"target %s is not in this tree"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-name">mrca</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-101', 'root', 'link-4');">root</a></tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">level</tt> <tt class="py-keyword">in</tt> <tt class="py-name">itertools</tt><tt class="py-op">.</tt><tt class="py-name">izip</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">paths</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">ref</tt> <tt class="py-op">=</tt> <tt class="py-name">level</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-102" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.other()=Bio.Phylo.PhyloXMLIO.Parser-class.html#other,Method Bio.Phylo.PhyloXMLIO.Writer.other()=Bio.Phylo.PhyloXMLIO.Writer-class.html#other"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-102', 'other', 'link-102');">other</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">level</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="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ref</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt id="link-103" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-103', 'other', 'link-102');">other</a></tt><tt class="py-op">:</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">mrca</tt> <tt class="py-op">=</tt> <tt class="py-name">ref</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ref</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">mrca</tt><tt class="py-op">:</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mrca</tt> </tt>
</div><a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.count_terminals"></a><div id="TreeMixin.count_terminals-def"><a name="L416"></a><tt class="py-lineno">416</tt> <a class="py-toggle" href="#" id="TreeMixin.count_terminals-toggle" onclick="return toggle('TreeMixin.count_terminals');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#count_terminals">count_terminals</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.count_terminals-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.count_terminals-expanded"><a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-docstring">"""Counts the number of terminal (leaf) nodes within this tree."""</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-104" class="py-name"><a title="Bio.Phylo._sugar" class="py-name" href="#" onclick="return doclink('link-104', '_sugar', 'link-3');">_sugar</a></tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Function Bio.Phylo._sugar.iterlen()=Bio.Phylo._sugar-module.html#iterlen"><a title="Bio.Phylo._sugar.iterlen" class="py-name" href="#" onclick="return doclink('link-105', 'iterlen', 'link-105');">iterlen</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.find_clades" class="py-name" href="#" onclick="return doclink('link-106', 'find_clades', 'link-89');">find_clades</a></tt><tt class="py-op">(</tt><tt id="link-107" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-107', 'terminal', 'link-71');">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>
</div><a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.depths"></a><div id="TreeMixin.depths-def"><a name="L420"></a><tt class="py-lineno">420</tt> <a class="py-toggle" href="#" id="TreeMixin.depths-toggle" onclick="return toggle('TreeMixin.depths');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#depths">depths</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">unit_branch_lengths</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.depths-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.depths-expanded"><a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a mapping of tree clades to depths (by branch length).</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-docstring"> :Parameters:</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"><tt class="py-docstring"> unit_branch_lengths : bool</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-docstring"> If True, count only the number of branches (levels in the tree).</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"><tt class="py-docstring"> By default the distance is the cumulative branch length leading</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"><tt class="py-docstring"> to the clade.</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"><tt class="py-docstring"> :returns: dict of {clade: depth}, where keys are all of the Clade</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"><tt class="py-docstring"> instances in the tree, and values are the distance from the root to</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"><tt class="py-docstring"> each clade (including terminals).</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">unit_branch_lengths</tt><tt class="py-op">:</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-name">depth_of</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> <tt class="py-number">1</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-name">depth_of</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-108" 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-108', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-keyword">or</tt> <tt class="py-number">0</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt id="link-109" class="py-name" targets="Method Bio.Phylo.BaseTree.TreeMixin.depths()=Bio.Phylo.BaseTree.TreeMixin-class.html#depths"><a title="Bio.Phylo.BaseTree.TreeMixin.depths" class="py-name" href="#" onclick="return doclink('link-109', 'depths', 'link-109');">depths</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">update_depths</tt><tt class="py-op">(</tt><tt class="py-param">node</tt><tt class="py-op">,</tt> <tt class="py-param">curr_depth</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt id="link-110" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.depths" class="py-name" href="#" onclick="return doclink('link-110', 'depths', 'link-109');">depths</a></tt><tt class="py-op">[</tt><tt id="link-111" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-111', 'node', 'link-16');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">curr_depth</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt id="link-112" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-112', 'node', 'link-16');">node</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-name">new_depth</tt> <tt class="py-op">=</tt> <tt class="py-name">curr_depth</tt> <tt class="py-op">+</tt> <tt class="py-name">depth_of</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-name">update_depths</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">,</tt> <tt class="py-name">new_depth</tt><tt class="py-op">)</tt> </tt>
</div><a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-name">update_depths</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-113', 'root', 'link-4');">root</a></tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-114" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.depths" class="py-name" href="#" onclick="return doclink('link-114', 'depths', 'link-109');">depths</a></tt> </tt>
</div><a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.distance"></a><div id="TreeMixin.distance-def"><a name="L446"></a><tt class="py-lineno">446</tt> <a class="py-toggle" href="#" id="TreeMixin.distance-toggle" onclick="return toggle('TreeMixin.distance');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#distance">distance</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target1</tt><tt class="py-op">,</tt> <tt class="py-param">target2</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="TreeMixin.distance-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.distance-expanded"><a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-docstring">"""Calculate the sum of the branch lengths between two targets.</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-docstring"> If only one target is specified, the other is the root of this tree.</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">target2</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-115" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Method Bio.SubsMat.SeqMat.sum()=Bio.SubsMat.SeqMat-class.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-115', 'sum', 'link-115');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">n</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-108');">branch_length</a></tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-117', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt class="py-name">target1</tt><tt class="py-op">)</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-118', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-name">mrca</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Nexus.Trees.Tree.common_ancestor
Bio.Phylo.BaseTree.TreeMixin.common_ancestor" class="py-name" href="#" onclick="return doclink('link-119', 'common_ancestor', 'link-94');">common_ancestor</a></tt><tt class="py-op">(</tt><tt class="py-name">target1</tt><tt class="py-op">,</tt> <tt class="py-name">target2</tt><tt class="py-op">)</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mrca</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Method Bio.Nexus.Trees.Tree.distance()=Bio.Nexus.Trees.Tree-class.html#distance,Method Bio.Phylo.BaseTree.TreeMixin.distance()=Bio.Phylo.BaseTree.TreeMixin-class.html#distance"><a title="Bio.Nexus.Trees.Tree.distance
Bio.Phylo.BaseTree.TreeMixin.distance" class="py-name" href="#" onclick="return doclink('link-120', 'distance', 'link-120');">distance</a></tt><tt class="py-op">(</tt><tt class="py-name">target1</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">mrca</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.Nexus.Trees.Tree.distance
Bio.Phylo.BaseTree.TreeMixin.distance" class="py-name" href="#" onclick="return doclink('link-121', 'distance', 'link-120');">distance</a></tt><tt class="py-op">(</tt><tt class="py-name">target2</tt><tt class="py-op">)</tt> </tt>
</div><a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.is_bifurcating"></a><div id="TreeMixin.is_bifurcating-def"><a name="L457"></a><tt class="py-lineno">457</tt> <a class="py-toggle" href="#" id="TreeMixin.is_bifurcating-toggle" onclick="return toggle('TreeMixin.is_bifurcating');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_bifurcating">is_bifurcating</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.is_bifurcating-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.is_bifurcating-expanded"><a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-docstring">"""Return True if tree downstream of node is strictly bifurcating.</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-docstring"> I.e., all nodes have either 2 or 0 children (internal or external,</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"><tt class="py-docstring"> respectively). The root may have 3 descendents and still be considered</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-docstring"> part of a bifurcating tree, because it has no ancestor.</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-comment"># Root can be trifurcating</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-122" 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-122', 'Tree', 'link-122');">Tree</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-123', 'root', 'link-4');">root</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-124', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name" targets="Method Bio.Nexus.Trees.Tree.is_bifurcating()=Bio.Nexus.Trees.Tree-class.html#is_bifurcating,Method Bio.Phylo.BaseTree.TreeMixin.is_bifurcating()=Bio.Phylo.BaseTree.TreeMixin-class.html#is_bifurcating"><a title="Bio.Nexus.Trees.Tree.is_bifurcating
Bio.Phylo.BaseTree.TreeMixin.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-125', 'is_bifurcating', 'link-125');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-126', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating
Bio.Phylo.BaseTree.TreeMixin.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-127', 'is_bifurcating', 'link-125');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-128', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating
Bio.Phylo.BaseTree.TreeMixin.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-129', 'is_bifurcating', 'link-125');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-130', 'root', 'link-4');">root</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="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-131', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating
Bio.Phylo.BaseTree.TreeMixin.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-132', 'is_bifurcating', 'link-125');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-133', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="Bio.Nexus.Trees.Tree.is_bifurcating
Bio.Phylo.BaseTree.TreeMixin.is_bifurcating" class="py-name" href="#" onclick="return doclink('link-134', 'is_bifurcating', 'link-125');">is_bifurcating</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-135', 'root', 'link-4');">root</a></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="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.is_monophyletic"></a><div id="TreeMixin.is_monophyletic-def"><a name="L476"></a><tt class="py-lineno">476</tt> <a class="py-toggle" href="#" id="TreeMixin.is_monophyletic-toggle" onclick="return toggle('TreeMixin.is_monophyletic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_monophyletic">is_monophyletic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">terminals</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">more_terminals</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.is_monophyletic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.is_monophyletic-expanded"><a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-docstring">"""MRCA of terminals if they comprise a complete subclade, or False.</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"><tt class="py-docstring"> I.e., there exists a clade such that its terminals are the same set as</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"><tt class="py-docstring"> the given targets.</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"><tt class="py-docstring"> The given targets must be terminals of the tree.</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"><tt class="py-docstring"> To match both `Bio.Nexus.Trees` and the other multi-target methods in</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"><tt class="py-docstring"> Bio.Phylo, arguments to this method can be specified either of two ways:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"><tt class="py-docstring"> (i) as a single list of targets, or (ii) separately specified targets,</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"><tt class="py-docstring"> e.g. is_monophyletic(t1, t2, t3) -- but not both.</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-docstring"> For convenience, this method returns the common ancestor (MCRA) of the</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt class="py-docstring"> targets if they are monophyletic (instead of the value True), and False</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"> otherwise.</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-docstring"> :returns: common ancestor if terminals are monophyletic, otherwise False.</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-name">target_set</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.set()=Bio.Nexus.Nexus.StepMatrix-class.html#set,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#set"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-136', 'set', 'link-136');">set</a></tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.Phylo.BaseTree._combine_args" class="py-name" href="#" onclick="return doclink('link-137', '_combine_args', 'link-100');">_combine_args</a></tt><tt class="py-op">(</tt><tt class="py-name">terminals</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">more_terminals</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-name">current</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-138', 'root', 'link-4');">root</a></tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-139" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-139', 'set', 'link-136');">set</a></tt><tt class="py-op">(</tt><tt class="py-name">current</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name" targets="Method Bio.Nexus.Trees.Tree.get_terminals()=Bio.Nexus.Trees.Tree-class.html#get_terminals,Method Bio.Phylo.BaseTree.TreeMixin.get_terminals()=Bio.Phylo.BaseTree.TreeMixin-class.html#get_terminals"><a title="Bio.Nexus.Trees.Tree.get_terminals
Bio.Phylo.BaseTree.TreeMixin.get_terminals" class="py-name" href="#" onclick="return doclink('link-140', 'get_terminals', 'link-140');">get_terminals</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">target_set</tt><tt class="py-op">:</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">current</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-comment"># Try a narrower subclade</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">subclade</tt> <tt class="py-keyword">in</tt> <tt class="py-name">current</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">:</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-141" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-141', 'set', 'link-136');">set</a></tt><tt class="py-op">(</tt><tt class="py-name">subclade</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Nexus.Trees.Tree.get_terminals
Bio.Phylo.BaseTree.TreeMixin.get_terminals" class="py-name" href="#" onclick="return doclink('link-142', 'get_terminals', 'link-140');">get_terminals</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">issuperset</tt><tt class="py-op">(</tt><tt class="py-name">target_set</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-name">current</tt> <tt class="py-op">=</tt> <tt class="py-name">subclade</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.is_parent_of"></a><div id="TreeMixin.is_parent_of-def"><a name="L508"></a><tt class="py-lineno">508</tt> <a class="py-toggle" href="#" id="TreeMixin.is_parent_of-toggle" onclick="return toggle('TreeMixin.is_parent_of');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_parent_of">is_parent_of</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target</tt><tt class="py-op">=</tt><tt class="py-name">None</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="TreeMixin.is_parent_of-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.is_parent_of-expanded"><a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-docstring">"""True if target is a descendent of this tree.</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-docstring"> Not required to be a direct descendent.</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"><tt class="py-docstring"> To check only direct descendents of a clade, simply use list membership</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"><tt class="py-docstring"> testing: ``if subclade in clade: ...``</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-143', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt class="py-name">target</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-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.is_preterminal"></a><div id="TreeMixin.is_preterminal-def"><a name="L518"></a><tt class="py-lineno">518</tt> <a class="py-toggle" href="#" id="TreeMixin.is_preterminal-toggle" onclick="return toggle('TreeMixin.is_preterminal');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_preterminal">is_preterminal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.is_preterminal-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.is_preterminal-expanded"><a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-docstring">"""True if all direct descendents are terminal."""</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-144', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><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-145', 'is_terminal', 'link-26');">is_terminal</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-146" 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-146', 'clade', 'link-146');">clade</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-147', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">:</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-148" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-148', 'clade', 'link-146');">clade</a></tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><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-149', 'is_terminal', 'link-26');">is_terminal</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.total_branch_length"></a><div id="TreeMixin.total_branch_length-def"><a name="L527"></a><tt class="py-lineno">527</tt> <a class="py-toggle" href="#" id="TreeMixin.total_branch_length-toggle" onclick="return toggle('TreeMixin.total_branch_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#total_branch_length">total_branch_length</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.total_branch_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.total_branch_length-expanded"><a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-docstring">"""Calculate the sum of all the branch lengths in this tree."""</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-150" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-150', 'sum', 'link-115');">sum</a></tt><tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-151', 'node', 'link-16');">node</a></tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-152', 'branch_length', 'link-108');">branch_length</a></tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-153" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-153', 'node', 'link-16');">node</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.find_clades" class="py-name" href="#" onclick="return doclink('link-154', 'find_clades', 'link-89');">find_clades</a></tt><tt class="py-op">(</tt><tt id="link-155" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-155', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-comment"># Tree manipulation methods</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.collapse"></a><div id="TreeMixin.collapse-def"><a name="L534"></a><tt class="py-lineno">534</tt> <a class="py-toggle" href="#" id="TreeMixin.collapse-toggle" onclick="return toggle('TreeMixin.collapse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#collapse">collapse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target</tt><tt class="py-op">=</tt><tt class="py-name">None</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="TreeMixin.collapse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.collapse-expanded"><a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-docstring">"""Deletes target from the tree, relinking its children to its parent.</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"><tt class="py-docstring"> :returns: the parent clade.</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-156', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">path</tt><tt class="py-op">:</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"couldn't collapse %s in this tree"</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">target</tt> <tt class="py-keyword">or</tt> <tt class="py-name">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">path</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="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-157', 'root', 'link-4');">root</a></tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">path</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="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-name">popped</tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-158', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index,Function Bio.SeqIO.index()=Bio.SeqIO-module.html#index"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-159', 'index', 'link-159');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-name">extra_length</tt> <tt class="py-op">=</tt> <tt class="py-name">popped</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-160', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-keyword">or</tt> <tt class="py-number">0</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt class="py-name">popped</tt><tt class="py-op">:</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-name">child</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-161', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">extra_length</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-162', 'extend', 'link-5');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">popped</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">)</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">parent</tt> </tt>
</div><a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.collapse_all"></a><div id="TreeMixin.collapse_all-def"><a name="L554"></a><tt class="py-lineno">554</tt> <a class="py-toggle" href="#" id="TreeMixin.collapse_all-toggle" onclick="return toggle('TreeMixin.collapse_all');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#collapse_all">collapse_all</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target</tt><tt class="py-op">=</tt><tt class="py-name">None</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="TreeMixin.collapse_all-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.collapse_all-expanded"><a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-docstring">"""Collapse all the descendents of this tree, leaving only terminals.</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"><tt class="py-docstring"> Total branch lengths are preserved, i.e. the distance to each terminal</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"><tt class="py-docstring"> stays the same.</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"><tt class="py-docstring"> For example, this will safely collapse nodes with poor bootstrap</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"><tt class="py-docstring"> support:</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"><tt class="py-docstring"> >>> tree.collapse_all(lambda c: c.confidence is not None and</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"><tt class="py-docstring"> ... c.confidence < 70)</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"><tt class="py-docstring"> This implementation avoids strange side-effects by using level-order</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"><tt class="py-docstring"> traversal and testing all clade properties (versus the target</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"><tt class="py-docstring"> specification) up front. In particular, if a clade meets the target</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"><tt class="py-docstring"> specification in the original tree, it will be collapsed. For example,</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"><tt class="py-docstring"> if the condition is:</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"><tt class="py-docstring"> >>> tree.collapse_all(lambda c: c.branch_length < 0.1)</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"><tt class="py-docstring"> Collapsing a clade's parent node adds the parent's branch length to the</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"><tt class="py-docstring"> child, so during the execution of collapse_all, a clade's branch_length</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"><tt class="py-docstring"> may increase. In this implementation, clades are collapsed according to</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"><tt class="py-docstring"> their properties in the original tree, not the properties when tree</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-docstring"> traversal reaches the clade. (It's easier to debug.) If you want the</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"><tt class="py-docstring"> other behavior (incremental testing), modifying the source code of this</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"><tt class="py-docstring"> function is straightforward.</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-comment"># Read the iterable into a list to protect against in-place changes</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-name">internals</tt> <tt class="py-op">=</tt> <tt id="link-163" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-163', 'list', 'link-9');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.find_clades" class="py-name" href="#" onclick="return doclink('link-164', 'find_clades', 'link-89');">find_clades</a></tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-string">'level'</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="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-comment"># Skip the root node -- it can't be collapsed</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">internals</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-165', 'root', 'link-4');">root</a></tt><tt class="py-op">:</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-name">internals</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-166', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-167" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-167', 'clade', 'link-146');">clade</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">internals</tt><tt class="py-op">:</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name" targets="Method Bio.Nexus.Nodes.Chain.collapse()=Bio.Nexus.Nodes.Chain-class.html#collapse,Method Bio.Phylo.BaseTree.TreeMixin.collapse()=Bio.Phylo.BaseTree.TreeMixin-class.html#collapse"><a title="Bio.Nexus.Nodes.Chain.collapse
Bio.Phylo.BaseTree.TreeMixin.collapse" class="py-name" href="#" onclick="return doclink('link-168', 'collapse', 'link-168');">collapse</a></tt><tt class="py-op">(</tt><tt id="link-169" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-169', 'clade', 'link-146');">clade</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.ladderize"></a><div id="TreeMixin.ladderize-def"><a name="L590"></a><tt class="py-lineno">590</tt> <a class="py-toggle" href="#" id="TreeMixin.ladderize-toggle" onclick="return toggle('TreeMixin.ladderize');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#ladderize">ladderize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">reverse</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.ladderize-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.ladderize-expanded"><a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-docstring">"""Sort clades in-place according to the number of terminal nodes.</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"><tt class="py-docstring"> Deepest clades are last by default. Use ``reverse=True`` to sort clades</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"><tt class="py-docstring"> deepest-to-shallowest.</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-170', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.sort()=Bio.Align.MultipleSeqAlignment-class.html#sort,Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-171', 'sort', 'link-171');">sort</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name" targets="Method Bio.Nexus.Trees.Tree.count_terminals()=Bio.Nexus.Trees.Tree-class.html#count_terminals,Method Bio.Phylo.BaseTree.TreeMixin.count_terminals()=Bio.Phylo.BaseTree.TreeMixin-class.html#count_terminals"><a title="Bio.Nexus.Trees.Tree.count_terminals
Bio.Phylo.BaseTree.TreeMixin.count_terminals" class="py-name" href="#" onclick="return doclink('link-172', 'count_terminals', 'link-172');">count_terminals</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt id="link-173" 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-173', 'reverse', 'link-173');">reverse</a></tt><tt class="py-op">=</tt><tt id="link-174" class="py-name"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-174', 'reverse', 'link-173');">reverse</a></tt><tt class="py-op">)</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">subclade</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-175', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">:</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-name">subclade</tt><tt class="py-op">.</tt><tt id="link-176" 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-176', 'ladderize', 'link-176');">ladderize</a></tt><tt class="py-op">(</tt><tt id="link-177" class="py-name"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-177', 'reverse', 'link-173');">reverse</a></tt><tt class="py-op">=</tt><tt id="link-178" class="py-name"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-178', 'reverse', 'link-173');">reverse</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.prune"></a><div id="TreeMixin.prune-def"><a name="L601"></a><tt class="py-lineno">601</tt> <a class="py-toggle" href="#" id="TreeMixin.prune-toggle" onclick="return toggle('TreeMixin.prune');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#prune">prune</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">target</tt><tt class="py-op">=</tt><tt class="py-name">None</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="TreeMixin.prune-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.prune-expanded"><a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-docstring">"""Prunes a terminal clade from the tree.</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"><tt class="py-docstring"> If taxon is from a bifurcation, the connecting node will be collapsed</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"><tt class="py-docstring"> and its branch length added to remaining terminal node. This might be no</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"><tt class="py-docstring"> longer be a meaningful value.</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"><tt class="py-docstring"> :returns: parent clade of the pruned target</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'terminal'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwargs</tt> <tt class="py-keyword">and</tt> <tt class="py-name">kwargs</tt><tt class="py-op">[</tt><tt class="py-string">'terminal'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"target must be terminal"</tt><tt class="py-op">)</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-179', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">,</tt> <tt id="link-180" class="py-name"><a title="Bio.Parsers.spark.GenericASTBuilder.terminal" class="py-name" href="#" onclick="return doclink('link-180', 'terminal', 'link-71');">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 class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">path</tt><tt class="py-op">:</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"can't find a matching target below this root"</tt><tt class="py-op">)</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">path</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="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-181', 'root', 'link-4');">root</a></tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">path</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="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-182', 'remove', 'link-182');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">parent</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="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-comment"># We deleted a branch from a bifurcation</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parent</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-183', 'root', 'link-4');">root</a></tt><tt class="py-op">:</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-comment"># If we're at the root, move the root upwards</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-comment"># NB: This loses the length of the original branch</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt class="py-name">newroot</tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt class="py-name">newroot</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-184', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-185" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-185', 'root', 'link-4');">root</a></tt> <tt class="py-op">=</tt> <tt class="py-name">newroot</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-comment"># If we're not at the root, collapse this parent</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-name">child</tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">child</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-186', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-name">child</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-187', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-188', 'branch_length', 'link-108');">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="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-name">grandparent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-189', 'root', 'link-4');">root</a></tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-name">grandparent</tt> <tt class="py-op">=</tt> <tt class="py-name">path</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt class="py-comment"># Replace parent with child at the same place in grandparent</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt id="link-190" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-190', 'index', 'link-159');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">grandparent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-191', 'index', 'link-159');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt class="py-name">grandparent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-192', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt id="link-193" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-193', 'index', 'link-159');">index</a></tt><tt class="py-op">)</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-name">grandparent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-194', 'insert', 'link-194');">insert</a></tt><tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-195', 'index', 'link-159');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">child</tt><tt class="py-op">)</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">grandparent</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">parent</tt> </tt>
</div><a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> </tt>
<a name="TreeMixin.split"></a><div id="TreeMixin.split-def"><a name="L644"></a><tt class="py-lineno">644</tt> <a class="py-toggle" href="#" id="TreeMixin.split-toggle" onclick="return toggle('TreeMixin.split');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.TreeMixin-class.html#split">split</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-param">branch_length</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TreeMixin.split-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TreeMixin.split-expanded"><a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-docstring">"""Generate n (default 2) new descendants.</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"><tt class="py-docstring"> In a species tree, this is a speciation event.</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"><tt class="py-docstring"> New clades have the given branch_length and the same name as this</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"><tt class="py-docstring"> clade's root plus an integer suffix (counting from 0). For example,</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"><tt class="py-docstring"> splitting a clade named "A" produces sub-clades named "A0" and "A1".</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-name">clade_cls</tt> <tt class="py-op">=</tt> <tt id="link-196" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-196', 'type', 'link-31');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-197', 'root', 'link-4');">root</a></tt><tt class="py-op">)</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-name">base_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-198', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt id="link-199" 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-199', 'name', 'link-199');">name</a></tt> <tt class="py-keyword">or</tt> <tt class="py-string">''</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-200" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-200', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-201" 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-201', 'range', 'link-201');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt id="link-202" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-202', 'clade', 'link-146');">clade</a></tt> <tt class="py-op">=</tt> <tt class="py-name">clade_cls</tt><tt class="py-op">(</tt><tt id="link-203" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-203', 'name', 'link-199');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">base_name</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-204" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-204', 'i', 'link-200');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"> <tt id="link-205" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-205', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">=</tt><tt id="link-206" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-206', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-207', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-208" 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-208', 'append', 'link-11');">append</a></tt><tt class="py-op">(</tt><tt id="link-209" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-209', 'clade', 'link-146');">clade</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> </tt>
<a name="Tree"></a><div id="Tree-def"><a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <a class="py-toggle" href="#" id="Tree-toggle" onclick="return toggle('Tree');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html">Tree</a><tt class="py-op">(</tt><tt class="py-base-class">TreeElement</tt><tt class="py-op">,</tt> <tt class="py-base-class">TreeMixin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Tree-expanded"><a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt class="py-docstring">"""A phylogenetic tree, containing global info for the phylogeny.</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"><tt class="py-docstring"> The structure and node-specific data is accessible through the 'root'</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"><tt class="py-docstring"> clade attached to the Tree instance.</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"><tt class="py-docstring"> :Parameters:</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"><tt class="py-docstring"> root : Clade</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"><tt class="py-docstring"> The starting node of the tree. If the tree is rooted, this will</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"><tt class="py-docstring"> usually be the root node.</tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"><tt class="py-docstring"> rooted : bool</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"><tt class="py-docstring"> Whether or not the tree is rooted. By default, a tree is assumed to</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"><tt class="py-docstring"> be rooted.</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"><tt class="py-docstring"> id : str</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"><tt class="py-docstring"> The identifier of the tree, if there is one.</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"><tt class="py-docstring"> name : str</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"><tt class="py-docstring"> The name of the tree, in essence a label.</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Tree.__init__"></a><div id="Tree.__init__-def"><a name="L679"></a><tt class="py-lineno">679</tt> <a class="py-toggle" href="#" id="Tree.__init__-toggle" onclick="return toggle('Tree.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">root</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">rooted</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.__init__-expanded"><a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-210', 'root', 'link-4');">root</a></tt> <tt class="py-op">=</tt> <tt id="link-211" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-211', 'root', 'link-4');">root</a></tt> <tt class="py-keyword">or</tt> <tt id="link-212" 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-212', 'Clade', 'link-212');">Clade</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rooted</tt> <tt class="py-op">=</tt> <tt class="py-name">rooted</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-213" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.id()=Bio.Phylo.PhyloXMLIO.Parser-class.html#id,Method Bio.Phylo.PhyloXMLIO.Writer.id()=Bio.Phylo.PhyloXMLIO.Writer-class.html#id"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-213', 'id', 'link-213');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-214" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-214', 'id', 'link-213');">id</a></tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-215', 'name', 'link-199');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-216" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-216', 'name', 'link-199');">name</a></tt> </tt>
</div><a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">classmethod</tt> </tt>
<a name="Tree.from_clade"></a><div id="Tree.from_clade-def"><a name="L686"></a><tt class="py-lineno">686</tt> <a class="py-toggle" href="#" id="Tree.from_clade-toggle" onclick="return toggle('Tree.from_clade');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#from_clade">from_clade</a><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">,</tt> <tt class="py-param">clade</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="Tree.from_clade-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.from_clade-expanded"><a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a new Tree object given a clade.</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"><tt class="py-docstring"> Keyword arguments are the usual `Tree` constructor parameters.</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"> <tt id="link-217" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-217', 'root', 'link-4');">root</a></tt> <tt class="py-op">=</tt> <tt id="link-218" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.PDB.Vector'.Vector.copy
Bio.SeqIO._index._IndexedSeqFileDict.copy" class="py-name" href="#" onclick="return doclink('link-218', 'copy', 'link-0');">copy</a></tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt id="link-219" class="py-name"><a title="Bio.Phylo.BaseTree.Tree.clade
Bio.Phylo.PhyloXMLIO.Writer.clade" class="py-name" href="#" onclick="return doclink('link-219', 'clade', 'link-146');">clade</a></tt><tt class="py-op">)</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</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-220" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-220', 'root', 'link-4');">root</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="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">classmethod</tt> </tt>
<a name="Tree.randomized"></a><div id="Tree.randomized-def"><a name="L695"></a><tt class="py-lineno">695</tt> <a class="py-toggle" href="#" id="Tree.randomized-toggle" onclick="return toggle('Tree.randomized');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#randomized">randomized</a><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">,</tt> <tt class="py-param">taxa</tt><tt class="py-op">,</tt> <tt class="py-param">branch_length</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">branch_stdev</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.randomized-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.randomized-expanded"><a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a randomized bifurcating tree given a list of taxa.</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"><tt class="py-docstring"> :param taxa: Either an integer specifying the number of taxa to create</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt class="py-docstring"> (automatically named taxon#), or an iterable of taxon names, as</tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"><tt class="py-docstring"> strings.</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"><tt class="py-docstring"> :returns: a tree of the same type as this class.</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-name">taxa</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'taxon%s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-221" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-221', 'i', 'link-200');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-222" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-222', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-223" class="py-name"><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-223', 'range', 'link-201');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">,</tt> <tt class="py-string">'__iter__'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"> <tt class="py-name">taxa</tt> <tt class="py-op">=</tt> <tt id="link-224" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-224', 'list', 'link-9');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">)</tt> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"taxa argument must be integer (# taxa) or "</tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> <tt class="py-string">"iterable of taxon names."</tt><tt class="py-op">)</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"> <tt class="py-name">rtree</tt> <tt class="py-op">=</tt> <tt class="py-name">cls</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"> <tt class="py-name">terminals</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">rtree</tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-225', 'root', 'link-4');">root</a></tt><tt class="py-op">]</tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">terminals</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> <tt class="py-name">newsplit</tt> <tt class="py-op">=</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">choice</tt><tt class="py-op">(</tt><tt class="py-name">terminals</tt><tt class="py-op">)</tt> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"> <tt class="py-name">newterms</tt> <tt class="py-op">=</tt> <tt class="py-name">newsplit</tt><tt class="py-op">.</tt><tt id="link-226" 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-226', 'split', 'link-226');">split</a></tt><tt class="py-op">(</tt><tt id="link-227" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-227', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">=</tt><tt id="link-228" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-228', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">branch_stdev</tt><tt class="py-op">:</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> <tt class="py-comment"># Add some noise to the branch lengths</tt> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">nt</tt> <tt class="py-keyword">in</tt> <tt class="py-name">newterms</tt><tt class="py-op">:</tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt class="py-name">nt</tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-229', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">gauss</tt><tt class="py-op">(</tt><tt id="link-230" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-230', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">,</tt> <tt class="py-name">branch_stdev</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"> <tt class="py-name">terminals</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-231', 'remove', 'link-182');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">newsplit</tt><tt class="py-op">)</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> <tt class="py-name">terminals</tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-232', 'extend', 'link-5');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">newterms</tt><tt class="py-op">)</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"> <tt class="py-comment"># Distribute taxon labels randomly</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">shuffle</tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">)</tt> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-233" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-233', 'node', 'link-16');">node</a></tt><tt class="py-op">,</tt> <tt id="link-234" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-234', 'name', 'link-199');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">terminals</tt><tt class="py-op">,</tt> <tt class="py-name">taxa</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt id="link-235" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-235', 'node', 'link-16');">node</a></tt><tt class="py-op">.</tt><tt id="link-236" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-236', 'name', 'link-199');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-237" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-237', 'name', 'link-199');">name</a></tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rtree</tt> </tt>
</div><a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Tree.clade"></a><div id="Tree.clade-def"><a name="L730"></a><tt class="py-lineno">730</tt> <a class="py-toggle" href="#" id="Tree.clade-toggle" onclick="return toggle('Tree.clade');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#clade">clade</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.clade-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.clade-expanded"><a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-docstring">"""The first clade in this tree (not itself)."""</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</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-238" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-238', 'root', 'link-4');">root</a></tt> </tt>
</div><a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> </tt>
<a name="Tree.as_phyloxml"></a><div id="Tree.as_phyloxml-def"><a name="L734"></a><tt class="py-lineno">734</tt> <a class="py-toggle" href="#" id="Tree.as_phyloxml-toggle" onclick="return toggle('Tree.as_phyloxml');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#as_phyloxml">as_phyloxml</a><tt class="py-op">(</tt><tt class="py-param">self</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="Tree.as_phyloxml-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.as_phyloxml-expanded"><a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert this tree to a PhyloXML-compatible Phylogeny.</tt> </tt>
<a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"><tt class="py-docstring"> This lets you use the additional annotation types PhyloXML defines, and</tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"><tt class="py-docstring"> save this information when you write this tree as 'phyloxml'.</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-239" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-239', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.Phylo" class="py-name" href="#" onclick="return doclink('link-240', 'Phylo', 'link-2');">Phylo</a></tt><tt class="py-op">.</tt><tt id="link-241" class="py-name" targets="Module Bio.Phylo.PhyloXML=Bio.Phylo.PhyloXML-module.html"><a title="Bio.Phylo.PhyloXML" class="py-name" href="#" onclick="return doclink('link-241', 'PhyloXML', 'link-241');">PhyloXML</a></tt> <tt class="py-keyword">import</tt> <tt id="link-242" class="py-name" targets="Class Bio.Phylo.PhyloXML.Phylogeny=Bio.Phylo.PhyloXML.Phylogeny-class.html"><a title="Bio.Phylo.PhyloXML.Phylogeny" class="py-name" href="#" onclick="return doclink('link-242', 'Phylogeny', 'link-242');">Phylogeny</a></tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-243" class="py-name"><a title="Bio.Phylo.PhyloXML.Phylogeny" class="py-name" href="#" onclick="return doclink('link-243', 'Phylogeny', 'link-242');">Phylogeny</a></tt><tt class="py-op">.</tt><tt id="link-244" class="py-name" targets="Class Method Bio.Phylo.PhyloXML.Phylogeny.from_tree()=Bio.Phylo.PhyloXML.Phylogeny-class.html#from_tree"><a title="Bio.Phylo.PhyloXML.Phylogeny.from_tree" class="py-name" href="#" onclick="return doclink('link-244', 'from_tree', 'link-244');">from_tree</a></tt><tt class="py-op">(</tt><tt class="py-name">self</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="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"> </tt>
<a name="Tree.root_with_outgroup"></a><div id="Tree.root_with_outgroup-def"><a name="L743"></a><tt class="py-lineno">743</tt> <a class="py-toggle" href="#" id="Tree.root_with_outgroup-toggle" onclick="return toggle('Tree.root_with_outgroup');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#root_with_outgroup">root_with_outgroup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">outgroup_targets</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">more_targets</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.root_with_outgroup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.root_with_outgroup-expanded"><a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"> <tt class="py-docstring">"""Reroot this tree with the outgroup clade containing outgroup_targets.</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"><tt class="py-docstring"> Operates in-place.</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"><tt class="py-docstring"> Edge cases:</tt> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"><tt class="py-docstring"> - If ``outgroup == self.root``, no change</tt> </tt>
<a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"><tt class="py-docstring"> - If outgroup is terminal, create new bifurcating root node with a</tt> </tt>
<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"><tt class="py-docstring"> 0-length branch to the outgroup</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"><tt class="py-docstring"> - If outgroup is internal, use the given outgroup node as the new</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"><tt class="py-docstring"> trifurcating root, keeping branches the same</tt> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"><tt class="py-docstring"> - If the original root was bifurcating, drop it from the tree,</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"><tt class="py-docstring"> preserving total branch lengths</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> <tt class="py-comment"># This raises a ValueError if any target is not in this tree</tt> </tt>
<a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"> <tt class="py-comment"># Otherwise, common_ancestor guarantees outgroup is in this tree</tt> </tt>
<a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"> <tt class="py-name">outgroup</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name"><a title="Bio.Nexus.Trees.Tree.common_ancestor
Bio.Phylo.BaseTree.TreeMixin.common_ancestor" class="py-name" href="#" onclick="return doclink('link-245', 'common_ancestor', 'link-94');">common_ancestor</a></tt><tt class="py-op">(</tt><tt class="py-name">outgroup_targets</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">more_targets</tt><tt class="py-op">)</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"> <tt class="py-name">outgroup_path</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.Phylo.BaseTree.TreeMixin.get_path" class="py-name" href="#" onclick="return doclink('link-246', 'get_path', 'link-96');">get_path</a></tt><tt class="py-op">(</tt><tt class="py-name">outgroup</tt><tt class="py-op">)</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">outgroup_path</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="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"> <tt class="py-comment"># Outgroup is the current root -- no change</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"> <tt class="py-name">prev_blen</tt> <tt class="py-op">=</tt> <tt class="py-name">outgroup</tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-247', 'branch_length', 'link-108');">branch_length</a></tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">outgroup</tt><tt class="py-op">.</tt><tt id="link-248" class="py-name"><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-248', 'is_terminal', 'link-26');">is_terminal</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"> <tt class="py-comment"># Create a new root with a 0-length branch to the outgroup</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"> <tt class="py-name">outgroup</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-249', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"> <tt class="py-name">new_root</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-250" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-250', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"> <tt id="link-251" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-251', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-252" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-252', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-253', 'branch_length', 'link-108');">branch_length</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">outgroup</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"> <tt class="py-comment"># The first branch reversal (see the upcoming loop) is modified</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">outgroup_path</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="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> <tt class="py-comment"># Trivial tree like '(A,B);</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> <tt class="py-name">new_parent</tt> <tt class="py-op">=</tt> <tt class="py-name">new_root</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">outgroup_path</tt><tt class="py-op">.</tt><tt id="link-254" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-254', 'pop', 'link-23');">pop</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="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-255', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-256" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-256', 'index', 'link-159');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">outgroup</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"> <tt class="py-name">prev_blen</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-257', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-258', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">,</tt> <tt class="py-name">prev_blen</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-name">new_root</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-259', 'insert', 'link-194');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-name">new_parent</tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-comment"># Use the given outgroup node as the new (trifurcating) root</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-name">new_root</tt> <tt class="py-op">=</tt> <tt class="py-name">outgroup</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> <tt class="py-name">new_root</tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-260', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-261', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-262', 'branch_length', 'link-108');">branch_length</a></tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> <tt class="py-name">new_parent</tt> <tt class="py-op">=</tt> <tt class="py-name">new_root</tt> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"> <tt class="py-comment"># Tracing the outgroup lineage backwards, reattach the subclades under a</tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"> <tt class="py-comment"># new root clade. Reverse the branches directly above the outgroup in</tt> </tt>
<a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"> <tt class="py-comment"># the tree, but keep the descendants of those clades as they are.</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">parent</tt> <tt class="py-keyword">in</tt> <tt class="py-name">outgroup_path</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-263" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-263', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-264" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-264', 'index', 'link-159');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">new_parent</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"> <tt class="py-name">prev_blen</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt id="link-265" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-265', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt><tt class="py-op">.</tt><tt id="link-266" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-266', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">,</tt> <tt class="py-name">prev_blen</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt class="py-name">new_parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-267', 'insert', 'link-194');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">)</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> <tt class="py-name">new_parent</tt> <tt class="py-op">=</tt> <tt class="py-name">parent</tt> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> </tt>
<a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> <tt class="py-comment"># Finally, handle the original root according to number of descendents</tt> </tt>
<a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"> <tt class="py-name">old_root</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-268" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-268', 'root', 'link-4');">root</a></tt> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">outgroup</tt> <tt class="py-keyword">in</tt> <tt class="py-name">old_root</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">:</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">outgroup_path</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"> <tt class="py-name">old_root</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-269" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-269', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">old_root</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-270', 'index', 'link-159');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">outgroup</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"> <tt class="py-name">old_root</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-271" class="py-name"><a title="Bio.Seq.MutableSeq.pop
Bio.SeqIO._index._IndexedSeqFileDict.pop" class="py-name" href="#" onclick="return doclink('link-271', 'pop', 'link-23');">pop</a></tt><tt class="py-op">(</tt><tt class="py-name">old_root</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-272" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-272', 'index', 'link-159');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">new_parent</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">old_root</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="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"> <tt class="py-comment"># Delete the old bifurcating root & add branch lengths</tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"> <tt class="py-name">ingroup</tt> <tt class="py-op">=</tt> <tt class="py-name">old_root</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ingroup</tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-273', 'branch_length', 'link-108');">branch_length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"> <tt class="py-name">ingroup</tt><tt class="py-op">.</tt><tt id="link-274" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-274', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">prev_blen</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"> <tt class="py-name">ingroup</tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-275', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">prev_blen</tt> </tt>
<a name="L811"></a><tt class="py-lineno">811</tt> <tt class="py-line"> <tt class="py-name">new_parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-276" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-276', 'insert', 'link-194');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ingroup</tt><tt class="py-op">)</tt> </tt>
<a name="L812"></a><tt class="py-lineno">812</tt> <tt class="py-line"> <tt class="py-comment"># ENH: If annotations are attached to old_root, do... something.</tt> </tt>
<a name="L813"></a><tt class="py-lineno">813</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L814"></a><tt class="py-lineno">814</tt> <tt class="py-line"> <tt class="py-comment"># Keep the old trifurcating/polytomous root as an internal node</tt> </tt>
<a name="L815"></a><tt class="py-lineno">815</tt> <tt class="py-line"> <tt class="py-name">old_root</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-277', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">prev_blen</tt> </tt>
<a name="L816"></a><tt class="py-lineno">816</tt> <tt class="py-line"> <tt class="py-name">new_parent</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">.</tt><tt id="link-278" class="py-name"><a title="Bio.Crystal.Chain.insert
Bio.Seq.MutableSeq.insert" class="py-name" href="#" onclick="return doclink('link-278', 'insert', 'link-194');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">old_root</tt><tt class="py-op">)</tt> </tt>
<a name="L817"></a><tt class="py-lineno">817</tt> <tt class="py-line"> </tt>
<a name="L818"></a><tt class="py-lineno">818</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-279" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-279', 'root', 'link-4');">root</a></tt> <tt class="py-op">=</tt> <tt class="py-name">new_root</tt> </tt>
<a name="L819"></a><tt class="py-lineno">819</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">True</tt> </tt>
<a name="L820"></a><tt class="py-lineno">820</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
</div><a name="L821"></a><tt class="py-lineno">821</tt> <tt class="py-line"> </tt>
<a name="L822"></a><tt class="py-lineno">822</tt> <tt class="py-line"> <tt class="py-comment"># Method assumed by TreeMixin</tt> </tt>
<a name="L823"></a><tt class="py-lineno">823</tt> <tt class="py-line"> </tt>
<a name="Tree.is_terminal"></a><div id="Tree.is_terminal-def"><a name="L824"></a><tt class="py-lineno">824</tt> <a class="py-toggle" href="#" id="Tree.is_terminal-toggle" onclick="return toggle('Tree.is_terminal');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#is_terminal">is_terminal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.is_terminal-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.is_terminal-expanded"><a name="L825"></a><tt class="py-lineno">825</tt> <tt class="py-line"> <tt class="py-docstring">"""True if the root of this tree is terminal."""</tt> </tt>
<a name="L826"></a><tt class="py-lineno">826</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-280" class="py-name"><a title="Bio.Phylo.BaseTree.Clade.root" class="py-name" href="#" onclick="return doclink('link-280', 'root', 'link-4');">root</a></tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">)</tt> </tt>
</div><a name="L827"></a><tt class="py-lineno">827</tt> <tt class="py-line"> </tt>
<a name="L828"></a><tt class="py-lineno">828</tt> <tt class="py-line"> <tt class="py-comment"># Convention from SeqRecord and Alignment classes </tt> </tt>
<a name="L829"></a><tt class="py-lineno">829</tt> <tt class="py-line"> </tt>
<a name="Tree.__format__"></a><div id="Tree.__format__-def"><a name="L830"></a><tt class="py-lineno">830</tt> <a class="py-toggle" href="#" id="Tree.__format__-toggle" onclick="return toggle('Tree.__format__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#__format__">__format__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format_spec</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.__format__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.__format__-expanded"><a name="L831"></a><tt class="py-lineno">831</tt> <tt class="py-line"> <tt class="py-docstring">"""Serialize the tree as a string in the specified file format.</tt> </tt>
<a name="L832"></a><tt class="py-lineno">832</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L833"></a><tt class="py-lineno">833</tt> <tt class="py-line"><tt class="py-docstring"> This method supports the ``format`` built-in function added in Python</tt> </tt>
<a name="L834"></a><tt class="py-lineno">834</tt> <tt class="py-line"><tt class="py-docstring"> 2.6/3.0.</tt> </tt>
<a name="L835"></a><tt class="py-lineno">835</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L836"></a><tt class="py-lineno">836</tt> <tt class="py-line"><tt class="py-docstring"> :param format_spec: a lower-case string supported by `Bio.Phylo.write`</tt> </tt>
<a name="L837"></a><tt class="py-lineno">837</tt> <tt class="py-line"><tt class="py-docstring"> as an output file format.</tt> </tt>
<a name="L838"></a><tt class="py-lineno">838</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L839"></a><tt class="py-lineno">839</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">format_spec</tt><tt class="py-op">:</tt> </tt>
<a name="L840"></a><tt class="py-lineno">840</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L841"></a><tt class="py-lineno">841</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-281" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-281', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-282" class="py-name"><a title="Bio.Phylo" class="py-name" href="#" onclick="return doclink('link-282', 'Phylo', 'link-2');">Phylo</a></tt> <tt class="py-keyword">import</tt> <tt id="link-283" class="py-name" targets="Module Bio.Phylo._io=Bio.Phylo._io-module.html"><a title="Bio.Phylo._io" class="py-name" href="#" onclick="return doclink('link-283', '_io', 'link-283');">_io</a></tt> </tt>
<a name="L842"></a><tt class="py-lineno">842</tt> <tt class="py-line"> <tt id="link-284" 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-284', 'handle', 'link-284');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L843"></a><tt class="py-lineno">843</tt> <tt class="py-line"> <tt id="link-285" class="py-name"><a title="Bio.Phylo._io" class="py-name" href="#" onclick="return doclink('link-285', '_io', 'link-283');">_io</a></tt><tt class="py-op">.</tt><tt id="link-286" 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-286', 'write', 'link-286');">write</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-287" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-287', 'handle', 'link-284');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">format_spec</tt><tt class="py-op">)</tt> </tt>
<a name="L844"></a><tt class="py-lineno">844</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-288" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-288', 'handle', 'link-284');">handle</a></tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L845"></a><tt class="py-lineno">845</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L846"></a><tt class="py-lineno">846</tt> <tt class="py-line"> <tt class="py-comment"># Follow python convention and default to using __str__</tt> </tt>
<a name="L847"></a><tt class="py-lineno">847</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L848"></a><tt class="py-lineno">848</tt> <tt class="py-line"> </tt>
<a name="Tree.format"></a><div id="Tree.format-def"><a name="L849"></a><tt class="py-lineno">849</tt> <a class="py-toggle" href="#" id="Tree.format-toggle" onclick="return toggle('Tree.format');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#format">format</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.format-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.format-expanded"><a name="L850"></a><tt class="py-lineno">850</tt> <tt class="py-line"> <tt class="py-docstring">"""Serialize the tree as a string in the specified file format.</tt> </tt>
<a name="L851"></a><tt class="py-lineno">851</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L852"></a><tt class="py-lineno">852</tt> <tt class="py-line"><tt class="py-docstring"> This duplicates the __format__ magic method for pre-2.6 Pythons.</tt> </tt>
<a name="L853"></a><tt class="py-lineno">853</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L854"></a><tt class="py-lineno">854</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-289" class="py-name" targets="Method Bio.Align.Generic.Alignment.__format__()=Bio.Align.Generic.Alignment-class.html#__format__,Method Bio.Phylo.BaseTree.Tree.__format__()=Bio.Phylo.BaseTree.Tree-class.html#__format__,Method Bio.SeqRecord.SeqRecord.__format__()=Bio.SeqRecord.SeqRecord-class.html#__format__"><a title="Bio.Align.Generic.Alignment.__format__
Bio.Phylo.BaseTree.Tree.__format__
Bio.SeqRecord.SeqRecord.__format__" class="py-name" href="#" onclick="return doclink('link-289', '__format__', 'link-289');">__format__</a></tt><tt class="py-op">(</tt><tt id="link-290" class="py-name" targets="Method Bio.Align.Generic.Alignment.format()=Bio.Align.Generic.Alignment-class.html#format,Method Bio.Motif._Motif.Motif.format()=Bio.Motif._Motif.Motif-class.html#format,Method Bio.Phylo.BaseTree.Tree.format()=Bio.Phylo.BaseTree.Tree-class.html#format,Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Method Bio.SeqRecord.SeqRecord.format()=Bio.SeqRecord.SeqRecord-class.html#format"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-290', 'format', 'link-290');">format</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L855"></a><tt class="py-lineno">855</tt> <tt class="py-line"> </tt>
<a name="L856"></a><tt class="py-lineno">856</tt> <tt class="py-line"> <tt class="py-comment"># Pretty-printer for the entire tree hierarchy</tt> </tt>
<a name="L857"></a><tt class="py-lineno">857</tt> <tt class="py-line"> </tt>
<a name="Tree.__str__"></a><div id="Tree.__str__-def"><a name="L858"></a><tt class="py-lineno">858</tt> <a class="py-toggle" href="#" id="Tree.__str__-toggle" onclick="return toggle('Tree.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Tree-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tree.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tree.__str__-expanded"><a name="L859"></a><tt class="py-lineno">859</tt> <tt class="py-line"> <tt class="py-docstring">"""String representation of the entire tree.</tt> </tt>
<a name="L860"></a><tt class="py-lineno">860</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L861"></a><tt class="py-lineno">861</tt> <tt class="py-line"><tt class="py-docstring"> Serializes each sub-clade recursively using ``repr`` to create a summary</tt> </tt>
<a name="L862"></a><tt class="py-lineno">862</tt> <tt class="py-line"><tt class="py-docstring"> of the object structure.</tt> </tt>
<a name="L863"></a><tt class="py-lineno">863</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L864"></a><tt class="py-lineno">864</tt> <tt class="py-line"> <tt class="py-name">TAB</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt> </tt>
<a name="L865"></a><tt class="py-lineno">865</tt> <tt class="py-line"> <tt class="py-name">textlines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L866"></a><tt class="py-lineno">866</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">print_tree</tt><tt class="py-op">(</tt><tt class="py-param">obj</tt><tt class="py-op">,</tt> <tt class="py-param">indent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L867"></a><tt class="py-lineno">867</tt> <tt class="py-line"> <tt class="py-docstring">"""Recursively serialize sub-elements.</tt> </tt>
<a name="L868"></a><tt class="py-lineno">868</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L869"></a><tt class="py-lineno">869</tt> <tt class="py-line"><tt class="py-docstring"> This closes over textlines and modifies it in-place.</tt> </tt>
<a name="L870"></a><tt class="py-lineno">870</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L871"></a><tt class="py-lineno">871</tt> <tt class="py-line"> <tt class="py-name">textlines</tt><tt class="py-op">.</tt><tt id="link-291" 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-291', 'append', 'link-11');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">TAB</tt><tt class="py-op">*</tt><tt class="py-name">indent</tt> <tt class="py-op">+</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L872"></a><tt class="py-lineno">872</tt> <tt class="py-line"> <tt class="py-name">indent</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L873"></a><tt class="py-lineno">873</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">attr</tt> <tt class="py-keyword">in</tt> <tt class="py-name">obj</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">:</tt> </tt>
<a name="L874"></a><tt class="py-lineno">874</tt> <tt class="py-line"> <tt class="py-name">child</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-name">attr</tt><tt class="py-op">)</tt> </tt>
<a name="L875"></a><tt class="py-lineno">875</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">,</tt> <tt id="link-292" class="py-name"><a title="Bio.Phylo.BaseTree.TreeElement" class="py-name" href="#" onclick="return doclink('link-292', 'TreeElement', 'link-15');">TreeElement</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L876"></a><tt class="py-lineno">876</tt> <tt class="py-line"> <tt class="py-name">print_tree</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">,</tt> <tt class="py-name">indent</tt><tt class="py-op">)</tt> </tt>
<a name="L877"></a><tt class="py-lineno">877</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">,</tt> <tt id="link-293" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-293', 'list', 'link-9');">list</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L878"></a><tt class="py-lineno">878</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">elem</tt> <tt class="py-keyword">in</tt> <tt class="py-name">child</tt><tt class="py-op">:</tt> </tt>
<a name="L879"></a><tt class="py-lineno">879</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">elem</tt><tt class="py-op">,</tt> <tt id="link-294" class="py-name"><a title="Bio.Phylo.BaseTree.TreeElement" class="py-name" href="#" onclick="return doclink('link-294', 'TreeElement', 'link-15');">TreeElement</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L880"></a><tt class="py-lineno">880</tt> <tt class="py-line"> <tt class="py-name">print_tree</tt><tt class="py-op">(</tt><tt class="py-name">elem</tt><tt class="py-op">,</tt> <tt class="py-name">indent</tt><tt class="py-op">)</tt> </tt>
</div><a name="L881"></a><tt class="py-lineno">881</tt> <tt class="py-line"> <tt class="py-name">print_tree</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L882"></a><tt class="py-lineno">882</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'\n'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">textlines</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L883"></a><tt class="py-lineno">883</tt> <tt class="py-line"> </tt>
<a name="Clade"></a><div id="Clade-def"><a name="L884"></a><tt class="py-lineno">884</tt> <tt class="py-line"> </tt>
<a name="L885"></a><tt class="py-lineno">885</tt> <a class="py-toggle" href="#" id="Clade-toggle" onclick="return toggle('Clade');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html">Clade</a><tt class="py-op">(</tt><tt class="py-base-class">TreeElement</tt><tt class="py-op">,</tt> <tt class="py-base-class">TreeMixin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Clade-expanded"><a name="L886"></a><tt class="py-lineno">886</tt> <tt class="py-line"> <tt class="py-docstring">"""A recursively defined sub-tree.</tt> </tt>
<a name="L887"></a><tt class="py-lineno">887</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L888"></a><tt class="py-lineno">888</tt> <tt class="py-line"><tt class="py-docstring"> :Parameters:</tt> </tt>
<a name="L889"></a><tt class="py-lineno">889</tt> <tt class="py-line"><tt class="py-docstring"> branch_length : str</tt> </tt>
<a name="L890"></a><tt class="py-lineno">890</tt> <tt class="py-line"><tt class="py-docstring"> The length of the branch leading to the root node of this clade.</tt> </tt>
<a name="L891"></a><tt class="py-lineno">891</tt> <tt class="py-line"><tt class="py-docstring"> name : str</tt> </tt>
<a name="L892"></a><tt class="py-lineno">892</tt> <tt class="py-line"><tt class="py-docstring"> The clade's name (a label).</tt> </tt>
<a name="L893"></a><tt class="py-lineno">893</tt> <tt class="py-line"><tt class="py-docstring"> clades : list</tt> </tt>
<a name="L894"></a><tt class="py-lineno">894</tt> <tt class="py-line"><tt class="py-docstring"> Sub-trees rooted directly under this tree's root.</tt> </tt>
<a name="L895"></a><tt class="py-lineno">895</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Clade.__init__"></a><div id="Clade.__init__-def"><a name="L896"></a><tt class="py-lineno">896</tt> <a class="py-toggle" href="#" id="Clade.__init__-toggle" onclick="return toggle('Clade.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-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">branch_length</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">clades</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L897"></a><tt class="py-lineno">897</tt> <tt class="py-line"> <tt class="py-param">confidence</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="Clade.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.__init__-expanded"><a name="L898"></a><tt class="py-lineno">898</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-295" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-295', 'branch_length', 'link-108');">branch_length</a></tt> <tt class="py-op">=</tt> <tt id="link-296" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.branch_length" class="py-name" href="#" onclick="return doclink('link-296', 'branch_length', 'link-108');">branch_length</a></tt> </tt>
<a name="L899"></a><tt class="py-lineno">899</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-297', 'name', 'link-199');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-298" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-298', 'name', 'link-199');">name</a></tt> </tt>
<a name="L900"></a><tt class="py-lineno">900</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt> <tt class="py-op">=</tt> <tt class="py-name">clades</tt> <tt class="py-keyword">or</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L901"></a><tt class="py-lineno">901</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-299" 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-299', 'confidence', 'link-299');">confidence</a></tt> <tt class="py-op">=</tt> <tt id="link-300" 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-300', 'confidence', 'link-299');">confidence</a></tt> </tt>
</div><a name="L902"></a><tt class="py-lineno">902</tt> <tt class="py-line"> </tt>
<a name="L903"></a><tt class="py-lineno">903</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Clade.root"></a><div id="Clade.root-def"><a name="L904"></a><tt class="py-lineno">904</tt> <a class="py-toggle" href="#" id="Clade.root-toggle" onclick="return toggle('Clade.root');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html#root">root</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade.root-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.root-expanded"><a name="L905"></a><tt class="py-lineno">905</tt> <tt class="py-line"> <tt class="py-docstring">"""Allow TreeMixin methods to traverse clades properly."""</tt> </tt>
<a name="L906"></a><tt class="py-lineno">906</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
</div><a name="L907"></a><tt class="py-lineno">907</tt> <tt class="py-line"> </tt>
<a name="Clade.is_terminal"></a><div id="Clade.is_terminal-def"><a name="L908"></a><tt class="py-lineno">908</tt> <a class="py-toggle" href="#" id="Clade.is_terminal-toggle" onclick="return toggle('Clade.is_terminal');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html#is_terminal">is_terminal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade.is_terminal-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.is_terminal-expanded"><a name="L909"></a><tt class="py-lineno">909</tt> <tt class="py-line"> <tt class="py-docstring">"""True if this is a terminal (leaf) node."""</tt> </tt>
<a name="L910"></a><tt class="py-lineno">910</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">)</tt> </tt>
</div><a name="L911"></a><tt class="py-lineno">911</tt> <tt class="py-line"> </tt>
<a name="L912"></a><tt class="py-lineno">912</tt> <tt class="py-line"> <tt class="py-comment"># Sequence-type behavior methods</tt> </tt>
<a name="L913"></a><tt class="py-lineno">913</tt> <tt class="py-line"> </tt>
<a name="Clade.__getitem__"></a><div id="Clade.__getitem__-def"><a name="L914"></a><tt class="py-lineno">914</tt> <a class="py-toggle" href="#" id="Clade.__getitem__-toggle" onclick="return toggle('Clade.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.__getitem__-expanded"><a name="L915"></a><tt class="py-lineno">915</tt> <tt class="py-line"> <tt class="py-docstring">"""Get clades by index (integer or slice)."""</tt> </tt>
<a name="L916"></a><tt class="py-lineno">916</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-301" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-301', 'index', 'link-159');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-302" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-302', 'index', 'link-159');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">slice</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L917"></a><tt class="py-lineno">917</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">[</tt><tt id="link-303" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-303', 'index', 'link-159');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L918"></a><tt class="py-lineno">918</tt> <tt class="py-line"> <tt class="py-name">ref</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> </tt>
<a name="L919"></a><tt class="py-lineno">919</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">idx</tt> <tt class="py-keyword">in</tt> <tt id="link-304" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-304', 'index', 'link-159');">index</a></tt><tt class="py-op">:</tt> </tt>
<a name="L920"></a><tt class="py-lineno">920</tt> <tt class="py-line"> <tt class="py-name">ref</tt> <tt class="py-op">=</tt> <tt class="py-name">ref</tt><tt class="py-op">[</tt><tt class="py-name">idx</tt><tt class="py-op">]</tt> </tt>
<a name="L921"></a><tt class="py-lineno">921</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ref</tt> </tt>
</div><a name="L922"></a><tt class="py-lineno">922</tt> <tt class="py-line"> </tt>
<a name="Clade.__iter__"></a><div id="Clade.__iter__-def"><a name="L923"></a><tt class="py-lineno">923</tt> <a class="py-toggle" href="#" id="Clade.__iter__-toggle" onclick="return toggle('Clade.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html#__iter__">__iter__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.__iter__-expanded"><a name="L924"></a><tt class="py-lineno">924</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate through this tree's direct descendent clades (sub-trees)."""</tt> </tt>
<a name="L925"></a><tt class="py-lineno">925</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">)</tt> </tt>
</div><a name="L926"></a><tt class="py-lineno">926</tt> <tt class="py-line"> </tt>
<a name="Clade.__len__"></a><div id="Clade.__len__-def"><a name="L927"></a><tt class="py-lineno">927</tt> <a class="py-toggle" href="#" id="Clade.__len__-toggle" onclick="return toggle('Clade.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.__len__-expanded"><a name="L928"></a><tt class="py-lineno">928</tt> <tt class="py-line"> <tt class="py-docstring">"""Number of clades directy under the root."""</tt> </tt>
<a name="L929"></a><tt class="py-lineno">929</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">clades</tt><tt class="py-op">)</tt> </tt>
</div><a name="L930"></a><tt class="py-lineno">930</tt> <tt class="py-line"> </tt>
<a name="Clade.__nonzero__"></a><div id="Clade.__nonzero__-def"><a name="L931"></a><tt class="py-lineno">931</tt> <a class="py-toggle" href="#" id="Clade.__nonzero__-toggle" onclick="return toggle('Clade.__nonzero__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html#__nonzero__">__nonzero__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade.__nonzero__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.__nonzero__-expanded"><a name="L932"></a><tt class="py-lineno">932</tt> <tt class="py-line"> <tt class="py-docstring">"""Boolean value of an instance of this class.</tt> </tt>
<a name="L933"></a><tt class="py-lineno">933</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L934"></a><tt class="py-lineno">934</tt> <tt class="py-line"><tt class="py-docstring"> NB: If this method is not defined, but ``__len__`` is, then the object</tt> </tt>
<a name="L935"></a><tt class="py-lineno">935</tt> <tt class="py-line"><tt class="py-docstring"> is considered true if the result of ``__len__()`` is nonzero. We want</tt> </tt>
<a name="L936"></a><tt class="py-lineno">936</tt> <tt class="py-line"><tt class="py-docstring"> Clade instances to always be considered True.</tt> </tt>
<a name="L937"></a><tt class="py-lineno">937</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L938"></a><tt class="py-lineno">938</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L939"></a><tt class="py-lineno">939</tt> <tt class="py-line"> </tt>
<a name="Clade.__str__"></a><div id="Clade.__str__-def"><a name="L940"></a><tt class="py-lineno">940</tt> <a class="py-toggle" href="#" id="Clade.__str__-toggle" onclick="return toggle('Clade.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.BaseTree.Clade-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Clade.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Clade.__str__-expanded"><a name="L941"></a><tt class="py-lineno">941</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-305" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-305', 'name', 'link-199');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L942"></a><tt class="py-lineno">942</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-306" class="py-name"><a title="Bio.Phylo._sugar" class="py-name" href="#" onclick="return doclink('link-306', '_sugar', 'link-3');">_sugar</a></tt><tt class="py-op">.</tt><tt id="link-307" class="py-name"><a title="Bio.Phylo._sugar.trim_str" class="py-name" href="#" onclick="return doclink('link-307', 'trim_str', 'link-55');">trim_str</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-308" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-308', 'name', 'link-199');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">maxlen</tt><tt class="py-op">=</tt><tt class="py-number">40</tt><tt class="py-op">)</tt> </tt>
<a name="L943"></a><tt class="py-lineno">943</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> </tt>
</div></div><a name="L944"></a><tt class="py-lineno">944</tt> <tt class="py-line"> </tt><script type="text/javascript">
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