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jordibc committed Jan 19, 2024
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10 changes: 7 additions & 3 deletions genindex.html
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Expand Up @@ -1513,18 +1513,22 @@ <h2 id="R">R</h2>
</li>
<li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.remove_selection">remove_selection() (in module ete4.smartview.gui.server)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="reference/reference_tree.html#ete4.Tree.remove_sister">remove_sister() (Tree method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="reference/reference_tree.html#ete4.Tree.render">render() (Tree method)</a>
</li>
<li><a href="reference/reference_parsers.html#ete4.parser.newick.repr_short">repr_short() (in module ete4.parser.newick)</a>
</li>
<li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.req_json">req_json() (in module ete4.smartview.gui.server)</a>
</li>
<li><a href="reference/reference_tree.html#ete4.Tree.resolve_polytomy">resolve_polytomy() (Tree method)</a>
<li><a href="reference/reference_operations.html#ete4.core.operations.resolve_polytomy">resolve_polytomy() (in module ete4.core.operations)</a>

<ul>
<li><a href="reference/reference_tree.html#ete4.Tree.resolve_polytomy">(Tree method)</a>
</li>
</ul></li>
<li><a href="reference/reference_smartview.html#ete4.smartview.renderer.drawer.Active.results">results (Active attribute)</a>
</li>
<li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.retrieve_layouts">retrieve_layouts() (in module ete4.smartview.gui.server)</a>
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1 change: 1 addition & 0 deletions reference/index.html
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Expand Up @@ -60,6 +60,7 @@ <h1>Reference Guide<a class="headerlink" href="#reference-guide" title="Link to
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.populate_yule"><code class="docutils literal notranslate"><span class="pre">populate_yule()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.rehang"><code class="docutils literal notranslate"><span class="pre">rehang()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.remove"><code class="docutils literal notranslate"><span class="pre">remove()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.resolve_polytomy"><code class="docutils literal notranslate"><span class="pre">resolve_polytomy()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.root_at"><code class="docutils literal notranslate"><span class="pre">root_at()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.set_outgroup"><code class="docutils literal notranslate"><span class="pre">set_outgroup()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.sort"><code class="docutils literal notranslate"><span class="pre">sort()</span></code></a></li>
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Expand Up @@ -228,6 +228,22 @@
<dd><p>Remove the given node from its tree.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="ete4.core.operations.resolve_polytomy">
<span class="sig-name descname"><span class="pre">resolve_polytomy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">descendants</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.resolve_polytomy" title="Link to this definition"></a></dt>
<dd><p>Convert tree to a series of dicotomies if it is a polytomy.</p>
<p>A polytomy is a node that has more than 2 children. This
function changes them to a ladderized series of dicotomic
branches. The tree topology modification is arbitrary (no
important results should depend on it!).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>descendants</strong> – If True, resolve all polytomies in the tree,
including all root descendants. Otherwise, do it only for the root.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="ete4.core.operations.root_at">
<span class="sig-name descname"><span class="pre">root_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bprops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.root_at" title="Link to this definition"></a></dt>
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2 changes: 1 addition & 1 deletion reference/reference_smartview.html
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Expand Up @@ -92,7 +92,7 @@ <h1><a class="toc-backref" href="#id1" role="doc-backlink">Smartview (web graphi

<dl class="py class">
<dt class="sig sig-object py" id="ete4.smartview.gui.server.TreeData">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TreeData</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree:</span> <span class="pre">ete4.core.tree.Tree</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name:</span> <span class="pre">str</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style:</span> <span class="pre">ete4.smartview.renderer.treestyle.TreeStyle</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer:</span> <span class="pre">float</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ultrametric:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active:</span> <span class="pre">&lt;function</span> <span class="pre">namedtuple</span> <span class="pre">at</span> <span class="pre">0x7f10dc542a20&gt;</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ete4/smartview/gui/server.html#TreeData"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.TreeData" title="Link to this definition"></a></dt>
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TreeData</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree:</span> <span class="pre">ete4.core.tree.Tree</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name:</span> <span class="pre">str</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style:</span> <span class="pre">ete4.smartview.renderer.treestyle.TreeStyle</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts:</span> <span class="pre">list</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer:</span> <span class="pre">float</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ultrametric:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active:</span> <span class="pre">&lt;function</span> <span class="pre">namedtuple</span> <span class="pre">at</span> <span class="pre">0x7f4b6df42a20&gt;</span> <span class="pre">=</span> <span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches:</span> <span class="pre">dict</span> <span class="pre">=</span> <span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ete4/smartview/gui/server.html#TreeData"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.gui.server.TreeData" title="Link to this definition"></a></dt>
<dd><dl class="py method">
<dt class="sig sig-object py" id="ete4.smartview.gui.server.TreeData.__init__">
<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="reference_tree.html#ete4.Tree" title="ete4.core.tree.Tree"><span class="pre">Tree</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">style</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#ete4.smartview.renderer.treestyle.TreeStyle" title="ete4.smartview.renderer.treestyle.TreeStyle"><span class="pre">TreeStyle</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nodestyles</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_props</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_props</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layouts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ultrametric</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initialized</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selected</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">active</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">namedtuple</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searches</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#ete4.smartview.gui.server.TreeData.__init__" title="Link to this definition"></a></dt>
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10 changes: 3 additions & 7 deletions reference/reference_tree.html
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Expand Up @@ -863,17 +863,13 @@ <h1>Tree (main class)<a class="headerlink" href="#tree-main-class" title="Link t
<dl class="py method">
<dt class="sig sig-object py" id="ete4.Tree.remove_sister">
<span class="sig-name descname"><span class="pre">remove_sister</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sister</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.Tree.remove_sister" title="Link to this definition"></a></dt>
<dd><p>Remove a sister node.</p>
<p>It has the same effect as self.up.remove_child(sister).</p>
<p>If a sister node is not supplied, the first sister will be deleted
and returned.</p>
<dd><p>Remove a sister node and return it.</p>
<p>It has the same effect as self.up.remove_child(sister). If a sister
node is not supplied, the first sister will be deleted.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>sister</strong> – A node instance to be removed as a sister.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The node removed.</p>
</dd>
</dl>
</dd></dl>

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2 changes: 1 addition & 1 deletion searchindex.js
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