deploy: bee42aa

reference/reference_parsers.html

@@ -114,13 +114,13 @@ <h1>Parsers<a class="headerlink" href="#parsers" title="Link to this heading">¶
 
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.parser.newick.read_content">
-<span class="sig-name descname"><span class="pre">read_content</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unicode</span> <span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">int</span> <span class="pre">pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">endings=u'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">);'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.read_content" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">read_content</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unicode</span> <span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long</span> <span class="pre">pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">endings=u'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">);'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.read_content" title="Link to this definition">¶</a></dt>
 <dd><p>Return content starting at position pos in text, and where it ends.</p>
 </dd></dl>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.parser.newick.read_nodes">
-<span class="sig-name descname"><span class="pre">read_nodes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nodes_text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">int</span> <span class="pre">pos=0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tree_class=Tree</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.read_nodes" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">read_nodes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nodes_text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long</span> <span class="pre">pos=0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tree_class=Tree</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.read_nodes" title="Link to this definition">¶</a></dt>
 <dd><p>Return a list of nodes and the position in the text where they end.</p>
 </dd></dl>
 
@@ -132,13 +132,13 @@ <h1>Parsers<a class="headerlink" href="#parsers" title="Link to this heading">¶
 
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.parser.newick.skip_quoted_name">
-<span class="sig-name descname"><span class="pre">skip_quoted_name</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unicode</span> <span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">int</span> <span class="pre">pos</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.skip_quoted_name" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">skip_quoted_name</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unicode</span> <span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long</span> <span class="pre">pos</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.skip_quoted_name" title="Link to this definition">¶</a></dt>
 <dd><p>Return the position where a quoted name ends.</p>
 </dd></dl>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.parser.newick.skip_spaces_and_comments">
-<span class="sig-name descname"><span class="pre">skip_spaces_and_comments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">int</span> <span class="pre">pos</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.skip_spaces_and_comments" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">skip_spaces_and_comments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">text</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long</span> <span class="pre">pos</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.parser.newick.skip_spaces_and_comments" title="Link to this definition">¶</a></dt>
 <dd><p>Return position in text after pos and all whitespaces and comments.</p>
 </dd></dl>
 

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">0x7f98a5d42a20&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">0x7fae67142a20&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>