deploy: b0c39a1

genindex.html

@@ -1095,10 +1095,12 @@ <h2 id="I">I</h2>
 </li>
       <li><a href="reference/reference_operations.html#ete4.core.operations.insert_intermediate">insert_intermediate() (in module ete4.core.operations)</a>
 </li>
-      <li><a href="reference/reference_clustering.html#ete4.clustering.clustertree.ClusterTree.intercluster_dist">intercluster_dist (ClusterTree property)</a>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.interchange_references">interchange_references() (in module ete4.core.operations)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="reference/reference_clustering.html#ete4.clustering.clustertree.ClusterTree.intercluster_dist">intercluster_dist (ClusterTree property)</a>
+</li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.renderer.draw_helpers.intersects_angles">intersects_angles() (in module ete4.smartview.renderer.draw_helpers)</a>
 </li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.renderer.draw_helpers.intersects_box">intersects_box() (in module ete4.smartview.renderer.draw_helpers)</a>
@@ -1533,6 +1535,8 @@ <h2 id="R">R</h2>
       <li><a href="reference/reference_tree.html#ete4.Tree.robinson_foulds">robinson_foulds() (Tree method)</a>
 </li>
       <li><a href="reference/reference_tree.html#ete4.Tree.root">root (Tree attribute)</a>
+</li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.root_at">root_at() (in module ete4.core.operations)</a>
 </li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.run_smartview">run_smartview() (in module ete4.smartview.gui.server)</a>
 </li>

reference/index.html

@@ -49,6 +49,7 @@ <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.common_ancestor"><code class="docutils literal notranslate"><span class="pre">common_ancestor()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.create_dichotomic_sister"><code class="docutils literal notranslate"><span class="pre">create_dichotomic_sister()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.insert_intermediate"><code class="docutils literal notranslate"><span class="pre">insert_intermediate()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.interchange_references"><code class="docutils literal notranslate"><span class="pre">interchange_references()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.join_branch"><code class="docutils literal notranslate"><span class="pre">join_branch()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.ladderize"><code class="docutils literal notranslate"><span class="pre">ladderize()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.make_name"><code class="docutils literal notranslate"><span class="pre">make_name()</span></code></a></li>
@@ -58,6 +59,7 @@ <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.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>
 <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>

reference/reference_operations.html

@@ -115,6 +115,12 @@
 <dd><p>Insert, between node and its parent, an intermediate node.</p>
 </dd></dl>
 
+<dl class="py function">
+<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>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.join_branch">
 <span class="sig-name descname"><span class="pre">join_branch</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.join_branch" title="Link to this definition">¶</a></dt>
@@ -211,7 +217,7 @@
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.rehang">
 <span class="sig-name descname"><span class="pre">rehang</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">child_pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bprops</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.rehang" title="Link to this definition">¶</a></dt>
-<dd><p>Rehang node on its child at position child_pos and return it.</p>
+<dd><p>Rehang root on its child at position child_pos and return it.</p>
 </dd></dl>
 
 <dl class="py function">
@@ -220,16 +226,32 @@
 <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.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>
+<dd><p>Set the given node as the root of the tree.</p>
+<p>The original root node will be used as the new root node, so any
+reference to it in the code will still be valid.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>node</strong> – Node to set as root. Its reference will be lost.</p></li>
+<li><p><strong>bprops</strong> – List of branch properties (other than “dist” and “support”).</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.set_outgroup">
 <span class="sig-name descname"><span class="pre">set_outgroup</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.set_outgroup" title="Link to this definition">¶</a></dt>
-<dd><p>Reroot the tree at the given outgroup node.</p>
+<dd><p>Change tree so the given node is set as outgroup.</p>
 <p>The original root node will be used as the new root node, so any
 reference to it in the code will still be valid.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>node</strong> – Node where to set root (future first child of the root).</p></li>
+<li><p><strong>node</strong> – Node to set as outgroup (future first child of the root).</p></li>
 <li><p><strong>bprops</strong> – List of branch properties (other than “dist” and “support”).</p></li>
 </ul>
 </dd>