deploy: 0411587

genindex.html

@@ -775,6 +775,10 @@ <h2 id="F">F</h2>
       <li><a href="reference/reference_smartview.html#ete4.smartview.renderer.faces.Face">Face (class in ete4.smartview.renderer.faces)</a>
 </li>
       <li><a href="reference/reference_tree.html#ete4.Tree.faces">faces (Tree attribute)</a>
+</li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.farthest">farthest() (in module ete4.core.operations)</a>
+</li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.farthest_descendant">farthest_descendant() (in module ete4.core.operations)</a>
 </li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.find_node">find_node() (in module ete4.smartview.gui.server)</a>
 </li>
@@ -1302,6 +1306,8 @@ <h2 id="M">M</h2>
         <li><a href="reference/reference_treematcher.html#ete4.treematcher.treematcher.TreePattern.match">(TreePattern method)</a>
 </li>
       </ul></li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.midpoint">midpoint() (in module ete4.core.operations)</a>
+</li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.renderer.drawer.Drawer.MIN_SIZE">MIN_SIZE (Drawer attribute)</a>
 </li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.modify_tree_fields">modify_tree_fields() (in module ete4.smartview.gui.server)</a>
@@ -1598,6 +1604,8 @@ <h2 id="S">S</h2>
       <li><a href="reference/reference_smartview.html#ete4.smartview.renderer.faces.SeqMotifFace">SeqMotifFace (class in ete4.smartview.renderer.faces)</a>
 </li>
       <li><a href="reference/reference_clustering.html#ete4.clustering.clustertree.ClusterTree.set_distance_function">set_distance_function() (ClusterTree method)</a>
+</li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.set_midpoint_outgroup">set_midpoint_outgroup() (in module ete4.core.operations)</a>
 </li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style">set_node_style() (LayoutAlignment method)</a>
 

reference/index.html

@@ -49,11 +49,14 @@ <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.assert_root_consistency"><code class="docutils literal notranslate"><span class="pre">assert_root_consistency()</span></code></a></li>
 <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.farthest"><code class="docutils literal notranslate"><span class="pre">farthest()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.farthest_descendant"><code class="docutils literal notranslate"><span class="pre">farthest_descendant()</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>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.midpoint"><code class="docutils literal notranslate"><span class="pre">midpoint()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.move"><code class="docutils literal notranslate"><span class="pre">move()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.populate"><code class="docutils literal notranslate"><span class="pre">populate()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.populate_uniform"><code class="docutils literal notranslate"><span class="pre">populate_uniform()</span></code></a></li>
@@ -62,6 +65,7 @@ <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.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_midpoint_outgroup"><code class="docutils literal notranslate"><span class="pre">set_midpoint_outgroup()</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

@@ -110,9 +110,21 @@
 <dd><p>Make tree start with a dichotomy, with the old tree and a new sister.</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.farthest">
+<span class="sig-name descname"><span class="pre">farthest</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">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.farthest" title="Link to this definition">¶</a></dt>
+<dd><p>Return the farthest nodes and the diameter of the tree.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.farthest_descendant">
+<span class="sig-name descname"><span class="pre">farthest_descendant</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">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.farthest_descendant" title="Link to this definition">¶</a></dt>
+<dd><p>Return the farthest descendant and its distance.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.insert_intermediate">
-<span class="sig-name descname"><span class="pre">insert_intermediate</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">intermediate</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.insert_intermediate" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">insert_intermediate</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">intermediate</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>, <em class="sig-param"><span class="n"><span class="pre">dist</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.insert_intermediate" title="Link to this definition">¶</a></dt>
 <dd><p>Insert, between node and its parent, an intermediate node.</p>
 </dd></dl>
 
@@ -170,6 +182,12 @@
 <dd><p>Return a short name corresponding to the index i.</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.midpoint">
+<span class="sig-name descname"><span class="pre">midpoint</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">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.midpoint" title="Link to this definition">¶</a></dt>
+<dd><p>Return the node in the middle and its distance from the exact center.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.move">
 <span class="sig-name descname"><span class="pre">move</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">shift</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.move" title="Link to this definition">¶</a></dt>
@@ -260,9 +278,14 @@
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.set_midpoint_outgroup">
+<span class="sig-name descname"><span class="pre">set_midpoint_outgroup</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">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.set_midpoint_outgroup" title="Link to this definition">¶</a></dt>
+<dd></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>
+<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>, <em class="sig-param"><span class="n"><span class="pre">dist</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>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>
@@ -271,6 +294,7 @@
 <dd class="field-odd"><ul class="simple">
 <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>
+<li><p><strong>dist</strong> – Distance from the node, where we put the new root of the tree.</p></li>
 </ul>
 </dd>
 </dl>