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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Phylo-module.html">Package Phylo</a> ::
<a href="Bio.Phylo.PhyloXML-module.html">Module PhyloXML</a> ::
Class Clade
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Clade</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a> --+
|
<a href="Bio.Phylo.PhyloXML.PhyloElement-class.html">PhyloElement</a> --+
|
object --+ |
| |
<a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a> --+ |
| |
object --+ | |
| | |
<a href="Bio.Phylo.BaseTree.TreeMixin-class.html">BaseTree.TreeMixin</a> --+ |
| |
<a href="Bio.Phylo.BaseTree.Clade-class.html">BaseTree.Clade</a> --+
|
<strong class="uidshort">Clade</strong>
</pre>
<hr />
<p>Describes a branch of the current phylogenetic tree.</p>
<p>Used recursively, describes the topology of a phylogenetic tree.</p>
<p>Both <tt class="rst-docutils literal">color</tt> and <tt class="rst-docutils literal">width</tt> elements should be interpreted by client code
as applying to the whole clade, including all descendents, unless
overwritten in-sub clades. This module doesn't automatically assign these
attributes to sub-clades to achieve this cascade -- and neither should you.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
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<td align="left"><span class="table-header">Instance Methods</span></td>
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><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">branch_length</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id_source</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">color</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">node_id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">events</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">binary_characters</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">date</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">confidences</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">taxonomies</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">sequences</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">distributions</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">references</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">properties</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">clades</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">other</span>=<span class="summary-sig-default">None</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade.__init__">source code</a></span>
</td>
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</td>
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<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="to_phylogeny"></a><span class="summary-sig-name">to_phylogeny</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">**kwargs</span>)</span><br />
Create a new phylogeny containing just this clade.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade.to_phylogeny">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_confidence"></a><span class="summary-sig-name">_get_confidence</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade._get_confidence">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="_set_confidence"></a><span class="summary-sig-name">_set_confidence</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade._set_confidence">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="_del_confidence"></a><span class="summary-sig-name">_del_confidence</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade._del_confidence">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_taxonomy"></a><span class="summary-sig-name">_get_taxonomy</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade._get_taxonomy">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="_set_taxonomy"></a><span class="summary-sig-name">_set_taxonomy</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade._set_taxonomy">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_color"></a><span class="summary-sig-name">_get_color</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade._get_color">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="_set_color"></a><span class="summary-sig-name">_set_color</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">arg</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade._set_color">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.Phylo.BaseTree.Clade-class.html">BaseTree.Clade</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.Clade-class.html#__getitem__">__getitem__</a></code>,
<code><a href="Bio.Phylo.BaseTree.Clade-class.html#__iter__">__iter__</a></code>,
<code><a href="Bio.Phylo.BaseTree.Clade-class.html#__len__">__len__</a></code>,
<code><a href="Bio.Phylo.BaseTree.Clade-class.html#__nonzero__">__nonzero__</a></code>,
<code><a href="Bio.Phylo.BaseTree.Clade-class.html#__str__">__str__</a></code>,
<code><a href="Bio.Phylo.BaseTree.Clade-class.html#is_terminal">is_terminal</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.TreeElement-class.html">BaseTree.TreeElement</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.TreeElement-class.html#__repr__">__repr__</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html">BaseTree.TreeMixin</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#collapse">collapse</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#collapse_all">collapse_all</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#common_ancestor">common_ancestor</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#count_terminals">count_terminals</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#depths">depths</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#distance">distance</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_any">find_any</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_clades">find_clades</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#find_elements">find_elements</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_nonterminals">get_nonterminals</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_path">get_path</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#get_terminals">get_terminals</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_bifurcating">is_bifurcating</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_monophyletic">is_monophyletic</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_parent_of">is_parent_of</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#is_preterminal">is_preterminal</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#ladderize">ladderize</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#prune">prune</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#split">split</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#total_branch_length">total_branch_length</a></code>,
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#trace">trace</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html">BaseTree.TreeMixin</a></code></b> (private):
<code><a href="Bio.Phylo.BaseTree.TreeMixin-class.html#_filter_search" onclick="show_private();">_filter_search</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== CLASS METHODS ==================== -->
<a name="section-ClassMethods"></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">Class Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassMethods"
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.Phylo.PhyloXML.Clade-class.html#from_clade" class="summary-sig-name">from_clade</a>(<span class="summary-sig-arg">cls</span>,
<span class="summary-sig-arg">clade</span>,
<span class="summary-sig-arg">**kwargs</span>)</span><br />
Create a new PhyloXML Clade from a Newick or BaseTree Clade object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade.from_clade">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></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">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
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">
<a href="Bio.Phylo.PhyloXML.Clade-class.html#confidence" class="summary-name">confidence</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Phylo.PhyloXML.Clade-class.html#taxonomy" class="summary-name">taxonomy</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Phylo.PhyloXML.Clade-class.html#color" class="summary-name">color</a><br />
Branch color.
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.BaseTree.Clade-class.html">BaseTree.Clade</a></code></b>:
<code><a href="Bio.Phylo.BaseTree.Clade-class.html#root">root</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</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">branch_length</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id_source</span>=<span class="sig-default">None</span>,
<span class="sig-arg">name</span>=<span class="sig-default">None</span>,
<span class="sig-arg">width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">color</span>=<span class="sig-default">None</span>,
<span class="sig-arg">node_id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">events</span>=<span class="sig-default">None</span>,
<span class="sig-arg">binary_characters</span>=<span class="sig-default">None</span>,
<span class="sig-arg">date</span>=<span class="sig-default">None</span>,
<span class="sig-arg">confidences</span>=<span class="sig-default">None</span>,
<span class="sig-arg">taxonomies</span>=<span class="sig-default">None</span>,
<span class="sig-arg">sequences</span>=<span class="sig-default">None</span>,
<span class="sig-arg">distributions</span>=<span class="sig-default">None</span>,
<span class="sig-arg">references</span>=<span class="sig-default">None</span>,
<span class="sig-arg">properties</span>=<span class="sig-default">None</span>,
<span class="sig-arg">clades</span>=<span class="sig-default">None</span>,
<span class="sig-arg">other</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade.__init__">source code</a></span>
</td>
</tr></table>
<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>branch_length</code></strong> - parent branch length of this clade</li>
<li><strong class="pname"><code>id_source</code></strong> - link other elements to a clade (on the xml-level)</li>
<li><strong class="pname"><code>name</code></strong> (string) - short label for this clade</li>
<li><strong class="pname"><code>confidences</code></strong> (list of Confidence objects) - used to indicate the support for a clade/parent branch.</li>
<li><strong class="pname"><code>width</code></strong> (float) - branch width for this clade (including branch from parent)</li>
<li><strong class="pname"><code>color</code></strong> (BranchColor) - color used for graphical display of this clade</li>
<li><strong class="pname"><code>node_id</code></strong> - unique identifier for the root node of this clade</li>
<li><strong class="pname"><code>taxonomies</code></strong> (list) - Taxonomy objects</li>
<li><strong class="pname"><code>sequences</code></strong> (list) - Sequence objects</li>
<li><strong class="pname"><code>events</code></strong> (Events) - describe such events as gene-duplications at the root node/parent
branch of this clade</li>
<li><strong class="pname"><code>binary_characters</code></strong> (BinaryCharacters) - binary characters</li>
<li><strong class="pname"><code>distributions</code></strong> (list of Distribution objects) - distribution(s) of this clade</li>
<li><strong class="pname"><code>date</code></strong> (Date) - a date for the root node of this clade</li>
<li><strong class="pname"><code>references</code></strong> (list) - Reference objects</li>
<li><strong class="pname"><code>properties</code></strong> (list) - Property objects</li>
<li><strong class="pname"><code>clades</code></strong> (list Clade objects) - Sub-clades</li>
<li><strong class="pname"><code>other</code></strong> (list of Other objects) - non-phyloXML objects</li>
</ul></dd>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
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<a name="from_clade"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">from_clade</span>(<span class="sig-arg">cls</span>,
<span class="sig-arg">clade</span>,
<span class="sig-arg">**kwargs</span>)</span>
<br /><em class="fname">Class Method</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PhyloXML-pysrc.html#Clade.from_clade">source code</a></span>
</td>
</tr></table>
<p>Create a new PhyloXML Clade from a Newick or BaseTree Clade object.</p>
<p>Keyword arguments are the usual PhyloXML Clade constructor parameters.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc">confidence</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#_get_confidence" class="summary-sig-name" onclick="show_private();">_get_confidence</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#_set_confidence" class="summary-sig-name" onclick="show_private();">_set_confidence</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
<dt>Delete Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#_del_confidence" class="summary-sig-name" onclick="show_private();">_del_confidence</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
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<h3 class="epydoc">taxonomy</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#_get_taxonomy" class="summary-sig-name" onclick="show_private();">_get_taxonomy</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#_set_taxonomy" class="summary-sig-name" onclick="show_private();">_set_taxonomy</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
</dl>
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<h3 class="epydoc">color</h3>
Branch color.
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#_get_color" class="summary-sig-name" onclick="show_private();">_get_color</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Phylo.PhyloXML.Clade-class.html#_set_color" class="summary-sig-name" onclick="show_private();">_set_color</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">arg</span>)</span>
</dd>
</dl>
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