Skip to content

Commit c0fb7a9

Browse files
qiyunzhuqiyunzhu
committed
1 parent 29d98f6 commit c0fb7a9

File tree

66 files changed

+86
-75
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

66 files changed

+86
-75
lines changed

‎docs/dev/generated/skbio.tree.TreeNode.accumulate_to_ancestor.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -771,7 +771,7 @@
771771
<h1>skbio.tree.TreeNode.accumulate_to_ancestor<a class="headerlink" href="#skbio-tree-treenode-accumulate-to-ancestor" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.accumulate_to_ancestor">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">accumulate_to_ancestor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ancestor</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3283"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.accumulate_to_ancestor" title="Link to this definition">#</a></dt>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">accumulate_to_ancestor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ancestor</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3294"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.accumulate_to_ancestor" title="Link to this definition">#</a></dt>
775775
<dd><p>Calculate the distance between self and an ancestor.</p>
776776
<p>The distance is the sum of branch lengths connecting the current node and the
777777
given ancestral node.</p>

‎docs/dev/generated/skbio.tree.TreeNode.ancestors.html‎

Lines changed: 20 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66

77
<head>
88
<meta charset="utf-8" />
9-
<meta name="description" content="Return all ancestors from self back to the root." />
9+
<meta name="description" content="Return all ancestral nodes from self back to the root." />
1010
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
1111

1212
<title>skbio.tree.TreeNode.ancestors &#8212; scikit-bio 0.6.3-dev documentation</title>
@@ -771,23 +771,34 @@
771771
<h1>skbio.tree.TreeNode.ancestors<a class="headerlink" href="#skbio-tree-treenode-ancestors" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.ancestors">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ancestors</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L463"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ancestors" title="Link to this definition">#</a></dt>
775-
<dd><p>Return all ancestors from self back to the root.</p>
776-
<p>This call will return all nodes in the path back to root, but does not
777-
include the node instance that the call was made from.</p>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ancestors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">include_self</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="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L463"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ancestors" title="Link to this definition">#</a></dt>
775+
<dd><p>Return all ancestral nodes from self back to the root.</p>
778776
<dl class="field-list simple">
779777
<dt class="field-odd">Returns<span class="colon">:</span></dt>
780778
<dd class="field-odd"><dl class="simple">
781-
<dt>list of TreeNode</dt><dd><p>The path, toward the root, from self</p>
779+
<dt>list of TreeNode</dt><dd><p>The path, toward the root, from self.</p>
780+
</dd>
781+
<dt><strong>include_self</strong><span class="classifier">bool, optional</span></dt><dd><p>Whether to include the initial node in the path (default: False).</p>
782782
</dd>
783783
</dl>
784784
</dd>
785785
</dl>
786786
<p class="rubric">Examples</p>
787787
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">skbio</span> <span class="kn">import</span> <span class="n">TreeNode</span>
788-
<span class="gp">&gt;&gt;&gt; </span><span class="n">tree</span> <span class="o">=</span> <span class="n">TreeNode</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;((a,b)c,(d,e)f)root;&quot;</span><span class="p">])</span>
789-
<span class="gp">&gt;&gt;&gt; </span><span class="p">[</span><span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">tree</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">ancestors</span><span class="p">()]</span>
790-
<span class="go">[&#39;c&#39;, &#39;root&#39;]</span>
788+
<span class="gp">&gt;&gt;&gt; </span><span class="n">tree</span> <span class="o">=</span> <span class="n">TreeNode</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;((a,b)c,(d,e)f)g;&quot;</span><span class="p">])</span>
789+
<span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="n">tree</span><span class="o">.</span><span class="n">ascii_art</span><span class="p">())</span>
790+
<span class="go"> /-a</span>
791+
<span class="go"> /c-------|</span>
792+
<span class="go"> | \-b</span>
793+
<span class="go">-g-------|</span>
794+
<span class="go"> | /-d</span>
795+
<span class="go"> \f-------|</span>
796+
<span class="go"> \-e</span>
797+
<span class="gp">&gt;&gt;&gt; </span><span class="n">tip</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">)</span>
798+
<span class="gp">&gt;&gt;&gt; </span><span class="p">[</span><span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">tip</span><span class="o">.</span><span class="n">ancestors</span><span class="p">()]</span>
799+
<span class="go">[&#39;c&#39;, &#39;g&#39;]</span>
800+
<span class="gp">&gt;&gt;&gt; </span><span class="p">[</span><span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">tip</span><span class="o">.</span><span class="n">ancestors</span><span class="p">(</span><span class="n">include_self</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>
801+
<span class="go">[&#39;a&#39;, &#39;c&#39;, &#39;g&#39;]</span>
791802
</pre></div>
792803
</div>
793804
</dd></dl>

‎docs/dev/generated/skbio.tree.TreeNode.append.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -771,7 +771,7 @@
771771
<h1>skbio.tree.TreeNode.append<a class="headerlink" href="#skbio-tree-treenode-append" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.append">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">append</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">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1166"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.append" title="Link to this definition">#</a></dt>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">append</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">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1177"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.append" title="Link to this definition">#</a></dt>
775775
<dd><p>Add a node to self’s children.</p>
776776
<dl class="field-list">
777777
<dt class="field-odd">Parameters<span class="colon">:</span></dt>

‎docs/dev/generated/skbio.tree.TreeNode.ascii_art.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -771,7 +771,7 @@
771771
<h1>skbio.tree.TreeNode.ascii_art<a class="headerlink" href="#skbio-tree-treenode-ascii-art" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.ascii_art">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ascii_art</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">show_internal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compact</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="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4533"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ascii_art" title="Link to this definition">#</a></dt>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ascii_art</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">show_internal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compact</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="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4544"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ascii_art" title="Link to this definition">#</a></dt>
775775
<dd><p>Return a string containing an ascii drawing of the tree.</p>
776776
<p>Note, this method calls a private recursive function and is not safe
777777
for large trees.</p>

‎docs/dev/generated/skbio.tree.TreeNode.assign_ids.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -771,7 +771,7 @@
771771
<h1>skbio.tree.TreeNode.assign_ids<a class="headerlink" href="#skbio-tree-treenode-assign-ids" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.assign_ids">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_ids</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4149"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_ids" title="Link to this definition">#</a></dt>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_ids</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4160"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_ids" title="Link to this definition">#</a></dt>
775775
<dd><p>Assign topologically stable unique IDs to all nodes of the tree.</p>
776776
<div class="admonition seealso">
777777
<p class="admonition-title">See also</p>

‎docs/dev/generated/skbio.tree.TreeNode.assign_supports.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -771,7 +771,7 @@
771771
<h1>skbio.tree.TreeNode.assign_supports<a class="headerlink" href="#skbio-tree-treenode-assign-supports" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.assign_supports">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_supports</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3146"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_supports" title="Link to this definition">#</a></dt>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_supports</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3157"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_supports" title="Link to this definition">#</a></dt>
775775
<dd><p>Extract support values from internal node labels of a tree.</p>
776776
<p class="rubric">Notes</p>
777777
<p>A “support value” measures the confidence or frequency of the incoming

‎docs/dev/generated/skbio.tree.TreeNode.bifurcate.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -771,7 +771,7 @@
771771
<h1>skbio.tree.TreeNode.bifurcate<a class="headerlink" href="#skbio-tree-treenode-bifurcate" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.bifurcate">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">bifurcate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">insert_length</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">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1856"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.bifurcate" title="Link to this definition">#</a></dt>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">bifurcate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">insert_length</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">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L1867"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.bifurcate" title="Link to this definition">#</a></dt>
775775
<dd><p>Convert the tree into a bifurcating tree.</p>
776776
<p>All nodes that have more than two children will have additional intermediate
777777
nodes inserted to ensure that every node has only two children.</p>

‎docs/dev/generated/skbio.tree.TreeNode.cache_attr.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -771,7 +771,7 @@
771771
<h1>skbio.tree.TreeNode.cache_attr<a class="headerlink" href="#skbio-tree-treenode-cache-attr" title="Link to this heading">#</a></h1>
772772
<dl class="py method">
773773
<dt class="sig sig-object py" id="skbio.tree.TreeNode.cache_attr">
774-
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">cache_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_attrname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_type=&lt;class</span> <span class="pre">'list'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">register=True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3998"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.cache_attr" title="Link to this definition">#</a></dt>
774+
<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">cache_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_attrname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_type=&lt;class</span> <span class="pre">'list'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">register=True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L4009"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.cache_attr" title="Link to this definition">#</a></dt>
775775
<dd><p>Cache attributes on nodes of the tree through a postorder traversal.</p>
776776
<dl class="field-list">
777777
<dt class="field-odd">Parameters<span class="colon">:</span></dt>

0 commit comments

Comments
 (0)