deploy: 3d00a20

_modules/ete4/smartview/gui/server.html

@@ -848,7 +848,7 @@ <h1>Source code for ete4.smartview.gui.server</h1><div class="highlight"><pre>
             <span class="p">(</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;rmin&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="mi">0</span><span class="p">,</span>
              <span class="n">get</span><span class="p">(</span><span class="s1">&#39;amin&#39;</span><span class="p">,</span> <span class="o">-</span><span class="mi">180</span><span class="p">)</span> <span class="o">*</span> <span class="n">pi</span><span class="o">/</span><span class="mi">180</span><span class="p">,</span> <span class="n">get</span><span class="p">(</span><span class="s1">&#39;amax&#39;</span><span class="p">,</span> <span class="mi">180</span><span class="p">)</span> <span class="o">*</span> <span class="n">pi</span><span class="o">/</span><span class="mi">180</span><span class="p">))</span>
 
-        <span class="n">collapsed_ids</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">node_id</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">))</span>
+        <span class="n">collapsed_ids</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">node_id</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">i</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
             <span class="k">for</span> <span class="n">node_id</span> <span class="ow">in</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;collapsed_ids&#39;</span><span class="p">,</span> <span class="s1">&#39;[]&#39;</span><span class="p">)))</span>
 
         <span class="n">ultrametric</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;ultrametric&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="s1">&#39;1&#39;</span>  <span class="c1"># asked for ultrametric?</span>

genindex.html

@@ -1724,6 +1724,8 @@ <h2 id="T">T</h2>
       <li><a href="reference/reference_smartview.html#ete4.smartview.renderer.faces.TextFace">TextFace (class in ete4.smartview.renderer.faces)</a>
 </li>
       <li><a href="reference/reference_smartview.html#ete4.smartview.gui.server.TreeData.timer">timer (TreeData attribute)</a>
+</li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.to_dendrogram">to_dendrogram() (in module ete4.core.operations)</a>
 </li>
       <li><a href="reference/reference_tree.html#ete4.Tree.to_str">to_str() (Tree method)</a>
 </li>

reference/index.html

@@ -65,6 +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.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>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.to_dendrogram"><code class="docutils literal notranslate"><span class="pre">to_dendrogram()</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.traverse"><code class="docutils literal notranslate"><span class="pre">traverse()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.traverse_bfs"><code class="docutils literal notranslate"><span class="pre">traverse_bfs()</span></code></a></li>

reference/reference_operations.html

@@ -288,6 +288,12 @@
 <dd><p>Swap properties between nodes n1 and n2.</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.to_dendrogram">
+<span class="sig-name descname"><span class="pre">to_dendrogram</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.to_dendrogram" title="Link to this definition">¶</a></dt>
+<dd><p>Convert tree to dendrogram (remove all distance values).</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.to_ultrametric">
 <span class="sig-name descname"><span class="pre">to_ultrametric</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.to_ultrametric" title="Link to this definition">¶</a></dt>

reference/reference_smartview.html

@@ -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">0x7f3166942a20&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">0x7f4a9fb46a20&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>