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@jordibc
jordibc committed Nov 28, 2023
1 parent 2078c58 commit 008fb1f
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6 changes: 5 additions & 1 deletion genindex.html
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Expand Up @@ -1779,8 +1779,12 @@ <h2 id="U">U</h2>
</li>
<li><a href="reference/reference_parsers.html#ete4.parser.newick.unquote">unquote() (in module ete4.parser.newick)</a>
</li>
<li><a href="reference/reference_tree.html#ete4.Tree.unroot">unroot() (Tree method)</a>
<li><a href="reference/reference_operations.html#ete4.core.operations.unroot">unroot() (in module ete4.core.operations)</a>

<ul>
<li><a href="reference/reference_tree.html#ete4.Tree.unroot">(Tree method)</a>
</li>
</ul></li>
<li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.unselect_node">unselect_node() (in module ete4.smartview.gui.server)</a>
</li>
<li><a href="reference/reference_tree.html#ete4.Tree.up">up (Tree attribute)</a>
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1 change: 1 addition & 0 deletions reference/index.html
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Expand Up @@ -64,6 +64,7 @@ <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.sort"><code class="docutils literal notranslate"><span class="pre">sort()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.swap_props"><code class="docutils literal notranslate"><span class="pre">swap_props()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.to_ultrametric"><code class="docutils literal notranslate"><span class="pre">to_ultrametric()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.unroot"><code class="docutils literal notranslate"><span class="pre">unroot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.update_size"><code class="docutils literal notranslate"><span class="pre">update_size()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.update_sizes_all"><code class="docutils literal notranslate"><span class="pre">update_sizes_all()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.update_sizes_from"><code class="docutils literal notranslate"><span class="pre">update_sizes_from()</span></code></a></li>
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11 changes: 11 additions & 0 deletions reference/reference_operations.html
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Expand Up @@ -119,6 +119,7 @@
<dt class="sig sig-object py" id="ete4.core.operations.interchange_references">
<span class="sig-name descname"><span class="pre">interchange_references</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">node2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.interchange_references" title="Link to this definition"></a></dt>
<dd><p>Interchange the references of the given nodes.</p>
<p>node1 will point where node2 was, and viceversa.</p>
</dd></dl>

<dl class="py function">
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<dd><p>Convert tree to ultrametric (all leaves equidistant from root).</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="ete4.core.operations.unroot">
<span class="sig-name descname"><span class="pre">unroot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.unroot" title="Link to this definition"></a></dt>
<dd><p>Unroot the tree (make the root not have 2 children).</p>
<p>The convention in phylogenetic trees is that if the root has 2
children, it is a “rooted” tree (the root is a real ancestor).
Otherwise (typically a root with 3 children), the root is just
an arbitrary place to hang the tree.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="ete4.core.operations.update_size">
<span class="sig-name descname"><span class="pre">update_size</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.update_size" 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 @@ -91,7 +91,7 @@ <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">0x7efd8eb47e20&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">0x7fce37347e20&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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4 changes: 1 addition & 3 deletions reference/reference_tree.html
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Expand Up @@ -1033,9 +1033,7 @@ <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.sort_descendants">
<span class="sig-name descname"><span class="pre">sort_descendants</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">prop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'name'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.Tree.sort_descendants" title="Link to this definition"></a></dt>
<dd><p>Sort branches by node names.</p>
<p>After the tree is sorted, if duplicated names are present,
extra criteria should be added to sort nodes.</p>
<dd><p>Sort branches by leaf node values (names or any other given prop).</p>
</dd></dl>

<dl class="py method">
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2 changes: 1 addition & 1 deletion searchindex.js
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