<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Nexus.Trees.Tree</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Nexus-module.html">Package Nexus</a> :: <a href="Bio.Nexus.Trees-module.html">Module Trees</a> :: Class Tree </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Nexus.Trees.Tree-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Tree</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree">source code</a></span></p> <pre class="base-tree"> <a href="Bio.Nexus.Nodes.Chain-class.html">Nodes.Chain</a> --+ | <strong class="uidshort">Tree</strong> </pre> <hr /> <p>Represents a tree using a chain of nodes with on predecessor (=ancestor) and multiple successors (=subclades).</p> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">tree</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">weight</span>=<span class="summary-sig-default">1.0</span>, <span class="summary-sig-arg">rooted</span>=<span class="summary-sig-default">False</span>, <span class="summary-sig-arg">name</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">data</span>=<span class="summary-sig-default"><class Bio.Nexus.Trees.NodeData at 0x2f8cbf0></span>, <span class="summary-sig-arg">values_are_support</span>=<span class="summary-sig-default">False</span>, <span class="summary-sig-arg">max_support</span>=<span class="summary-sig-default">1.0</span>)</span><br /> Ntree(self,tree).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_parse"></a><span class="summary-sig-name">_parse</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">tree</span>)</span><br /> Parses (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._parse">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#_add_subtree" class="summary-sig-name" onclick="show_private();">_add_subtree</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">parent_id</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">tree</span>=<span class="summary-sig-default">None</span>)</span><br /> Adds leaf or tree (in newick format) to a parent_id.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._add_subtree">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_get_values"></a><span class="summary-sig-name">_get_values</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">text</span>)</span><br /> Extracts values (support/branchlength) from xx[:yyy], xx.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._get_values">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_walk"></a><span class="summary-sig-name">_walk</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br /> Return all node_ids downwards from a node.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._walk">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#node" class="summary-sig-name">node</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node_id</span>)</span><br /> Return the instance of node_id.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.node">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#split" class="summary-sig-name">split</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">parent_id</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">n</span>=<span class="summary-sig-default">2</span>, <span class="summary-sig-arg">branchlength</span>=<span class="summary-sig-default">1.0</span>)</span><br /> Speciation: generates n (default two) descendants of a node.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.split">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#search_taxon" class="summary-sig-name">search_taxon</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">taxon</span>)</span><br /> Returns the first matching taxon in self.data.taxon.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.search_taxon">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#prune" class="summary-sig-name">prune</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">taxon</span>)</span><br /> Prunes a terminal taxon from the tree.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.prune">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#get_taxa" class="summary-sig-name">get_taxa</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node_id</span>=<span class="summary-sig-default">None</span>)</span><br /> Return a list of all otus downwards from a node (self, node_id).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.get_taxa">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="get_terminals"></a><span class="summary-sig-name">get_terminals</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return a list of all terminal nodes.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.get_terminals">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#sum_branchlength" class="summary-sig-name">sum_branchlength</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">root</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br /> Adds up the branchlengths from root (default self.root) to node.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#set_subtree" class="summary-sig-name">set_subtree</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node</span>)</span><br /> Return subtree as a set of nested sets.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.set_subtree">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#is_identical" class="summary-sig-name">is_identical</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">tree2</span>)</span><br /> Compare tree and tree2 for identity.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_identical">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#is_compatible" class="summary-sig-name">is_compatible</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">tree2</span>, <span class="summary-sig-arg">threshold</span>, <span class="summary-sig-arg">strict</span>=<span class="summary-sig-default">True</span>)</span><br /> Compares branches with support>threshold for compatibility.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_compatible">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#common_ancestor" class="summary-sig-name">common_ancestor</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node1</span>, <span class="summary-sig-arg">node2</span>)</span><br /> Return the common ancestor that connects to nodes.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.common_ancestor">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#distance" class="summary-sig-name">distance</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node1</span>, <span class="summary-sig-arg">node2</span>)</span><br /> Add and return the sum of the branchlengths between two nodes.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.distance">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#is_monophyletic" class="summary-sig-name">is_monophyletic</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">taxon_list</span>)</span><br /> Return node_id of common ancestor if taxon_list is monophyletic, -1 otherwise.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_monophyletic">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="is_bifurcating"></a><span class="summary-sig-name">is_bifurcating</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node</span>=<span class="summary-sig-default">None</span>)</span><br /> Return True if tree downstream of node is strictly bifurcating.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_bifurcating">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#branchlength2support" class="summary-sig-name">branchlength2support</a>(<span class="summary-sig-arg">self</span>)</span><br /> Move values stored in data.branchlength to data.support, and set branchlength to 0.0</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.branchlength2support">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#convert_absolute_support" class="summary-sig-name">convert_absolute_support</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">nrep</span>)</span><br /> Convert absolute support (clade-count) to rel.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.convert_absolute_support">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#randomize" class="summary-sig-name">randomize</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">ntax</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">taxon_list</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">branchlength</span>=<span class="summary-sig-default">1.0</span>, <span class="summary-sig-arg">branchlength_sd</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">bifurcate</span>=<span class="summary-sig-default">True</span>)</span><br /> Generates a random tree with ntax taxa and/or taxa from taxlabels.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.randomize">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="display"></a><span class="summary-sig-name">display</span>(<span class="summary-sig-arg">self</span>)</span><br /> Quick and dirty lists of all nodes.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.display">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Trees.Tree-class.html#to_string" class="summary-sig-name">to_string</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">support_as_branchlengths</span>=<span class="summary-sig-default">False</span>, <span class="summary-sig-arg">branchlengths_only</span>=<span class="summary-sig-default">False</span>, <span class="summary-sig-arg">plain</span>=<span class="summary-sig-default">True</span>, <span class="summary-sig-arg">plain_newick</span>=<span class="summary-sig-default">False</span>)</span><br /> Return a paup compatible tree line.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.to_string">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Short version of to_string(), gives plain tree</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.__str__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="unroot"></a><span class="summary-sig-name">unroot</span>(<span class="summary-sig-arg">self</span>)</span><br /> Defines a unrooted Tree structure, using data of a rooted Tree.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.unroot">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="root_with_outgroup"></a><span class="summary-sig-name">root_with_outgroup</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">outgroup</span>=<span class="summary-sig-default">None</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.root_with_outgroup">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Nexus.Nodes.Chain-class.html">Nodes.Chain</a></code></b>: <code><a href="Bio.Nexus.Nodes.Chain-class.html#add">add</a></code>, <code><a href="Bio.Nexus.Nodes.Chain-class.html#all_ids">all_ids</a></code>, <code><a href="Bio.Nexus.Nodes.Chain-class.html#collapse">collapse</a></code>, <code><a href="Bio.Nexus.Nodes.Chain-class.html#is_parent_of">is_parent_of</a></code>, <code><a href="Bio.Nexus.Nodes.Chain-class.html#kill">kill</a></code>, <code><a href="Bio.Nexus.Nodes.Chain-class.html#link">link</a></code>, <code><a href="Bio.Nexus.Nodes.Chain-class.html#trace">trace</a></code>, <code><a href="Bio.Nexus.Nodes.Chain-class.html#unlink">unlink</a></code> </p> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Nexus.Nodes.Chain-class.html">Nodes.Chain</a></code></b> (private): <code><a href="Bio.Nexus.Nodes.Chain-class.html#_get_id" onclick="show_private();">_get_id</a></code> </p></div> </td> </tr> </table> <!-- ==================== METHOD DETAILS ==================== --> <a name="section-MethodDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="__init__"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>, <span class="sig-arg">tree</span>=<span class="sig-default">None</span>, <span class="sig-arg">weight</span>=<span class="sig-default">1.0</span>, <span class="sig-arg">rooted</span>=<span class="sig-default">False</span>, <span class="sig-arg">name</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">data</span>=<span class="sig-default"><class Bio.Nexus.Trees.NodeData at 0x2f8cbf0></span>, <span class="sig-arg">values_are_support</span>=<span class="sig-default">False</span>, <span class="sig-arg">max_support</span>=<span class="sig-default">1.0</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.__init__">source code</a></span> </td> </tr></table> <p>Ntree(self,tree).</p> <dl class="fields"> <dt>Overrides: <a href="Bio.Nexus.Nodes.Chain-class.html#__init__">Nodes.Chain.__init__</a> </dt> </dl> </td></tr></table> </div> <a name="_add_subtree"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_add_subtree</span>(<span class="sig-arg">self</span>, <span class="sig-arg">parent_id</span>=<span class="sig-default">None</span>, <span class="sig-arg">tree</span>=<span class="sig-default">None</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree._add_subtree">source code</a></span> </td> </tr></table> <p>Adds leaf or tree (in newick format) to a parent_id. (self,parent_id,tree).</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="node"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">node</span>(<span class="sig-arg">self</span>, <span class="sig-arg">node_id</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.node">source code</a></span> </td> </tr></table> <p>Return the instance of node_id.</p> <p>node = node(self,node_id)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="split"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">split</span>(<span class="sig-arg">self</span>, <span class="sig-arg">parent_id</span>=<span class="sig-default">None</span>, <span class="sig-arg">n</span>=<span class="sig-default">2</span>, <span class="sig-arg">branchlength</span>=<span class="sig-default">1.0</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.split">source code</a></span> </td> </tr></table> <p>Speciation: generates n (default two) descendants of a node.</p> <p>[new ids] = split(self,parent_id=None,n=2,branchlength=1.0):</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="search_taxon"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">search_taxon</span>(<span class="sig-arg">self</span>, <span class="sig-arg">taxon</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.search_taxon">source code</a></span> </td> </tr></table> <p>Returns the first matching taxon in self.data.taxon. Not restricted to terminal nodes.</p> <p>node_id = search_taxon(self,taxon)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="prune"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">prune</span>(<span class="sig-arg">self</span>, <span class="sig-arg">taxon</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.prune">source code</a></span> </td> </tr></table> <p>Prunes a terminal taxon from the tree.</p> <p>id_of_previous_node = prune(self,taxon) If taxon is from a bifurcation, the connectiong node will be collapsed and its branchlength added to remaining terminal node. This might be no longer a meaningful value'</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="get_taxa"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">get_taxa</span>(<span class="sig-arg">self</span>, <span class="sig-arg">node_id</span>=<span class="sig-default">None</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.get_taxa">source code</a></span> </td> </tr></table> <p>Return a list of all otus downwards from a node (self, node_id).</p> <p>nodes = get_taxa(self,node_id=None)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="sum_branchlength"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">sum_branchlength</span>(<span class="sig-arg">self</span>, <span class="sig-arg">root</span>=<span class="sig-default">None</span>, <span class="sig-arg">node</span>=<span class="sig-default">None</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength">source code</a></span> </td> </tr></table> <p>Adds up the branchlengths from root (default self.root) to node.</p> <p>sum = sum_branchlength(self,root=None,node=None)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="set_subtree"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">set_subtree</span>(<span class="sig-arg">self</span>, <span class="sig-arg">node</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.set_subtree">source code</a></span> </td> </tr></table> <p>Return subtree as a set of nested sets.</p> <p>sets = set_subtree(self,node)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="is_identical"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">is_identical</span>(<span class="sig-arg">self</span>, <span class="sig-arg">tree2</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_identical">source code</a></span> </td> </tr></table> <p>Compare tree and tree2 for identity.</p> <p>result = is_identical(self,tree2)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="is_compatible"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">is_compatible</span>(<span class="sig-arg">self</span>, <span class="sig-arg">tree2</span>, <span class="sig-arg">threshold</span>, <span class="sig-arg">strict</span>=<span class="sig-default">True</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_compatible">source code</a></span> </td> </tr></table> <p>Compares branches with support>threshold for compatibility.</p> <p>result = is_compatible(self,tree2,threshold)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="common_ancestor"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">common_ancestor</span>(<span class="sig-arg">self</span>, <span class="sig-arg">node1</span>, <span class="sig-arg">node2</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.common_ancestor">source code</a></span> </td> </tr></table> <p>Return the common ancestor that connects to nodes.</p> <p>node_id = common_ancestor(self,node1,node2)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="distance"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">distance</span>(<span class="sig-arg">self</span>, <span class="sig-arg">node1</span>, <span class="sig-arg">node2</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.distance">source code</a></span> </td> </tr></table> <p>Add and return the sum of the branchlengths between two nodes. dist = distance(self,node1,node2)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="is_monophyletic"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">is_monophyletic</span>(<span class="sig-arg">self</span>, <span class="sig-arg">taxon_list</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.is_monophyletic">source code</a></span> </td> </tr></table> <p>Return node_id of common ancestor if taxon_list is monophyletic, -1 otherwise.</p> <p>result = is_monophyletic(self,taxon_list)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="branchlength2support"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">branchlength2support</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.branchlength2support">source code</a></span> </td> </tr></table> <p>Move values stored in data.branchlength to data.support, and set branchlength to 0.0</p> <p>This is necessary when support has been stored as branchlength (e.g. paup), and has thus been read in as branchlength.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="convert_absolute_support"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">convert_absolute_support</span>(<span class="sig-arg">self</span>, <span class="sig-arg">nrep</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.convert_absolute_support">source code</a></span> </td> </tr></table> <p>Convert absolute support (clade-count) to rel. frequencies.</p> <p>Some software (e.g. PHYLIP consense) just calculate how often clades appear, instead of calculating relative frequencies.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="randomize"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">randomize</span>(<span class="sig-arg">self</span>, <span class="sig-arg">ntax</span>=<span class="sig-default">None</span>, <span class="sig-arg">taxon_list</span>=<span class="sig-default">None</span>, <span class="sig-arg">branchlength</span>=<span class="sig-default">1.0</span>, <span class="sig-arg">branchlength_sd</span>=<span class="sig-default">None</span>, <span class="sig-arg">bifurcate</span>=<span class="sig-default">True</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.randomize">source code</a></span> </td> </tr></table> <p>Generates a random tree with ntax taxa and/or taxa from taxlabels.</p> <p>new_tree = randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True) Trees are bifurcating by default. (Polytomies not yet supported).</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="to_string"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">to_string</span>(<span class="sig-arg">self</span>, <span class="sig-arg">support_as_branchlengths</span>=<span class="sig-default">False</span>, <span class="sig-arg">branchlengths_only</span>=<span class="sig-default">False</span>, <span class="sig-arg">plain</span>=<span class="sig-default">True</span>, <span class="sig-arg">plain_newick</span>=<span class="sig-default">False</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Trees-pysrc.html#Tree.to_string">source code</a></span> </td> </tr></table> <p>Return a paup compatible tree line.</p> <p>to_string(self,support_as_branchlengths=False,branchlengths_only=False,plain=True)</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:36 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. So hide // them unless we have a cookie that says to show them. checkCookie(); // --> </script> </body> </html>