deploy: 3026c8a

Author: jordibc

_modules/ete4/smartview/explorer.html

@@ -208,8 +208,9 @@ <h1>Source code for ete4.smartview.explorer</h1><div class="highlight"><pre>
         <span class="k">for</span> <span class="n">layout</span> <span class="ow">in</span> <span class="n">g_layouts</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="p">[]):</span>
             <span class="k">if</span> <span class="n">layout</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">active</span><span class="p">:</span>
                 <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">layout</span><span class="o">.</span><span class="n">draw_tree</span><span class="p">(</span><span class="n">t</span><span class="p">):</span>
-                    <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">dict</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">element</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">dict</span><span class="p">:</span>  <span class="c1"># a style element</span>
                         <span class="n">update_style</span><span class="p">(</span><span class="n">style</span><span class="p">,</span> <span class="n">element</span><span class="p">)</span>
+        <span class="c1"># Here we care only for the styles. For tree decorations see draw.py</span>
 
         <span class="c1"># Susbstitute aliases for their corresponding styles.</span>
         <span class="n">aliasable_keys</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;box&#39;</span><span class="p">,</span> <span class="s1">&#39;dot&#39;</span><span class="p">,</span> <span class="s1">&#39;hz-line&#39;</span><span class="p">,</span> <span class="s1">&#39;vt-line&#39;</span><span class="p">,</span> <span class="s1">&#39;collapsed&#39;</span><span class="p">}</span>

_modules/ete4/smartview/faces.html

@@ -40,6 +40,14 @@ <h1>Source code for ete4.smartview.faces</h1><div class="highlight"><pre>
 <span class="sd">different forms. Faces have a drawing function that returns the</span>
 <span class="sd">graphic elements that will show the information, and the size they</span>
 <span class="sd">occupy (in tree coordinates).</span>
+
+<span class="sd">They know how to represent node(s) information, confined to an area of</span>
+<span class="sd">a given size. They do it with a method face.draw(nodes, size, ...)</span>
+<span class="sd">which returns the graphic elements and the actual size they use</span>
+<span class="sd">(which may be smaller than the allocated size).</span>
+
+<span class="sd">The sizes are always given in &quot;tree units&quot;. The size in pixels is</span>
+<span class="sd">always that size multiplied by the zoom.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="c1"># Other names that may be better than &quot;face&quot;: glyph, chip, infobox,</span>

_modules/ete4/smartview/layout.html

@@ -68,23 +68,23 @@ <h1>Source code for ete4.smartview.layout</h1><div class="highlight"><pre>
 <span class="sd">Example of a tree style in use::</span>
 
 <span class="sd">  my_tree_style = {</span>
-<span class="sd">     &#39;shape&#39;: &#39;circular&#39;,  # or &#39;rectangular&#39;</span>
-<span class="sd">     &#39;radius&#39;: 5,</span>
-<span class="sd">     &#39;angle-start&#39;: -pi/2,</span>
-<span class="sd">     &#39;angle-end&#39;: pi/2,  # alternatively we can give &#39;angle-span&#39;</span>
-<span class="sd">     &#39;node-height-min&#39;: 10,</span>
-<span class="sd">     &#39;content-height-min&#39;: 5,</span>
-<span class="sd">     &#39;collapsed&#39;: {&#39;shape&#39;: &#39;outline&#39;, &#39;fill-opacity&#39;: 0.8},</span>
-<span class="sd">     &#39;show-popup-props&#39;: None,  # all defined properties</span>
-<span class="sd">     &#39;hide-popup-props&#39;: [&#39;support&#39;],  # except support</span>
-<span class="sd">     &#39;is-leaf-fn&#39;: lambda node: node.level &gt; 4,</span>
-<span class="sd">     &#39;box&#39;: {&#39;fill&#39;: &#39;green&#39;, &#39;opacity&#39;: 0.1, &#39;stroke&#39;: &#39;blue&#39;},</span>
-<span class="sd">     &#39;dot&#39;: {&#39;shape&#39;: &#39;hexagon&#39;, &#39;fill&#39;: &#39;red&#39;},</span>
-<span class="sd">     &#39;hz-line&#39;: {&#39;stroke-width&#39;: 2},</span>
-<span class="sd">     &#39;vt-line&#39;: {&#39;stroke&#39;: &#39;#ffff00&#39;},</span>
-<span class="sd">     &#39;aliases&#39;: {</span>
-<span class="sd">         &#39;support&#39;: {&#39;fill&#39;: &#39;green&#39;},  # changes the default one</span>
-<span class="sd">         &#39;my-leaf&#39;: {&#39;fill&#39;: &#39;blue&#39;, &#39;font-weight&#39;: &#39;bold&#39;},</span>
+<span class="sd">      &#39;shape&#39;: &#39;circular&#39;,  # or &#39;rectangular&#39;</span>
+<span class="sd">      &#39;radius&#39;: 5,</span>
+<span class="sd">      &#39;angle-start&#39;: -180,</span>
+<span class="sd">      &#39;angle-end&#39;: 180,  # alternatively we can give &#39;angle-span&#39;</span>
+<span class="sd">      &#39;node-height-min&#39;: 10,</span>
+<span class="sd">      &#39;content-height-min&#39;: 5,</span>
+<span class="sd">      &#39;collapsed&#39;: {&#39;shape&#39;: &#39;outline&#39;, &#39;fill-opacity&#39;: 0.8},</span>
+<span class="sd">      &#39;show-popup-props&#39;: None,  # all defined properties</span>
+<span class="sd">      &#39;hide-popup-props&#39;: [&#39;support&#39;],  # except support</span>
+<span class="sd">      &#39;is-leaf-fn&#39;: lambda node: node.level &gt; 4,</span>
+<span class="sd">      &#39;box&#39;: {&#39;fill&#39;: &#39;green&#39;, &#39;opacity&#39;: 0.1, &#39;stroke&#39;: &#39;blue&#39;},</span>
+<span class="sd">      &#39;dot&#39;: {&#39;shape&#39;: &#39;hexagon&#39;, &#39;fill&#39;: &#39;red&#39;},</span>
+<span class="sd">      &#39;hz-line&#39;: {&#39;stroke-width&#39;: 2},</span>
+<span class="sd">      &#39;vt-line&#39;: {&#39;stroke&#39;: &#39;#ffff00&#39;},</span>
+<span class="sd">      &#39;aliases&#39;: {</span>
+<span class="sd">          &#39;support&#39;: {&#39;fill&#39;: &#39;green&#39;},  # changes the default one</span>
+<span class="sd">          &#39;my-leaf&#39;: {&#39;fill&#39;: &#39;blue&#39;, &#39;font-weight&#39;: &#39;bold&#39;},</span>
 <span class="sd">      },</span>
 <span class="sd">  }</span>
 

reference/reference_smartview.html

@@ -256,23 +256,23 @@ <h1><a class="toc-backref" href="#id1" role="doc-backlink">Smartview (web graphi
 <p>And the “aliases” part will tell the frontend which styles are referenced.</p>
 <p>Example of a tree style in use:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">my_tree_style</span> <span class="o">=</span> <span class="p">{</span>
-   <span class="s1">&#39;shape&#39;</span><span class="p">:</span> <span class="s1">&#39;circular&#39;</span><span class="p">,</span>  <span class="c1"># or &#39;rectangular&#39;</span>
-   <span class="s1">&#39;radius&#39;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
-   <span class="s1">&#39;angle-start&#39;</span><span class="p">:</span> <span class="o">-</span><span class="n">pi</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span>
-   <span class="s1">&#39;angle-end&#39;</span><span class="p">:</span> <span class="n">pi</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span>  <span class="c1"># alternatively we can give &#39;angle-span&#39;</span>
-   <span class="s1">&#39;node-height-min&#39;</span><span class="p">:</span> <span class="mi">10</span><span class="p">,</span>
-   <span class="s1">&#39;content-height-min&#39;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
-   <span class="s1">&#39;collapsed&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;shape&#39;</span><span class="p">:</span> <span class="s1">&#39;outline&#39;</span><span class="p">,</span> <span class="s1">&#39;fill-opacity&#39;</span><span class="p">:</span> <span class="mf">0.8</span><span class="p">},</span>
-   <span class="s1">&#39;show-popup-props&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>  <span class="c1"># all defined properties</span>
-   <span class="s1">&#39;hide-popup-props&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;support&#39;</span><span class="p">],</span>  <span class="c1"># except support</span>
-   <span class="s1">&#39;is-leaf-fn&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">node</span><span class="p">:</span> <span class="n">node</span><span class="o">.</span><span class="n">level</span> <span class="o">&gt;</span> <span class="mi">4</span><span class="p">,</span>
-   <span class="s1">&#39;box&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;green&#39;</span><span class="p">,</span> <span class="s1">&#39;opacity&#39;</span><span class="p">:</span> <span class="mf">0.1</span><span class="p">,</span> <span class="s1">&#39;stroke&#39;</span><span class="p">:</span> <span class="s1">&#39;blue&#39;</span><span class="p">},</span>
-   <span class="s1">&#39;dot&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;shape&#39;</span><span class="p">:</span> <span class="s1">&#39;hexagon&#39;</span><span class="p">,</span> <span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;red&#39;</span><span class="p">},</span>
-   <span class="s1">&#39;hz-line&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;stroke-width&#39;</span><span class="p">:</span> <span class="mi">2</span><span class="p">},</span>
-   <span class="s1">&#39;vt-line&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;stroke&#39;</span><span class="p">:</span> <span class="s1">&#39;#ffff00&#39;</span><span class="p">},</span>
-   <span class="s1">&#39;aliases&#39;</span><span class="p">:</span> <span class="p">{</span>
-       <span class="s1">&#39;support&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;green&#39;</span><span class="p">},</span>  <span class="c1"># changes the default one</span>
-       <span class="s1">&#39;my-leaf&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;blue&#39;</span><span class="p">,</span> <span class="s1">&#39;font-weight&#39;</span><span class="p">:</span> <span class="s1">&#39;bold&#39;</span><span class="p">},</span>
+    <span class="s1">&#39;shape&#39;</span><span class="p">:</span> <span class="s1">&#39;circular&#39;</span><span class="p">,</span>  <span class="c1"># or &#39;rectangular&#39;</span>
+    <span class="s1">&#39;radius&#39;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
+    <span class="s1">&#39;angle-start&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">180</span><span class="p">,</span>
+    <span class="s1">&#39;angle-end&#39;</span><span class="p">:</span> <span class="mi">180</span><span class="p">,</span>  <span class="c1"># alternatively we can give &#39;angle-span&#39;</span>
+    <span class="s1">&#39;node-height-min&#39;</span><span class="p">:</span> <span class="mi">10</span><span class="p">,</span>
+    <span class="s1">&#39;content-height-min&#39;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
+    <span class="s1">&#39;collapsed&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;shape&#39;</span><span class="p">:</span> <span class="s1">&#39;outline&#39;</span><span class="p">,</span> <span class="s1">&#39;fill-opacity&#39;</span><span class="p">:</span> <span class="mf">0.8</span><span class="p">},</span>
+    <span class="s1">&#39;show-popup-props&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>  <span class="c1"># all defined properties</span>
+    <span class="s1">&#39;hide-popup-props&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;support&#39;</span><span class="p">],</span>  <span class="c1"># except support</span>
+    <span class="s1">&#39;is-leaf-fn&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">node</span><span class="p">:</span> <span class="n">node</span><span class="o">.</span><span class="n">level</span> <span class="o">&gt;</span> <span class="mi">4</span><span class="p">,</span>
+    <span class="s1">&#39;box&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;green&#39;</span><span class="p">,</span> <span class="s1">&#39;opacity&#39;</span><span class="p">:</span> <span class="mf">0.1</span><span class="p">,</span> <span class="s1">&#39;stroke&#39;</span><span class="p">:</span> <span class="s1">&#39;blue&#39;</span><span class="p">},</span>
+    <span class="s1">&#39;dot&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;shape&#39;</span><span class="p">:</span> <span class="s1">&#39;hexagon&#39;</span><span class="p">,</span> <span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;red&#39;</span><span class="p">},</span>
+    <span class="s1">&#39;hz-line&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;stroke-width&#39;</span><span class="p">:</span> <span class="mi">2</span><span class="p">},</span>
+    <span class="s1">&#39;vt-line&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;stroke&#39;</span><span class="p">:</span> <span class="s1">&#39;#ffff00&#39;</span><span class="p">},</span>
+    <span class="s1">&#39;aliases&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;support&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;green&#39;</span><span class="p">},</span>  <span class="c1"># changes the default one</span>
+        <span class="s1">&#39;my-leaf&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;fill&#39;</span><span class="p">:</span> <span class="s1">&#39;blue&#39;</span><span class="p">,</span> <span class="s1">&#39;font-weight&#39;</span><span class="p">:</span> <span class="s1">&#39;bold&#39;</span><span class="p">},</span>
     <span class="p">},</span>
 <span class="p">}</span>
 
@@ -423,6 +423,12 @@ <h1><a class="toc-backref" href="#id1" role="doc-backlink">Smartview (web graphi
 different forms. Faces have a drawing function that returns the
 graphic elements that will show the information, and the size they
 occupy (in tree coordinates).</p>
+<p>They know how to represent node(s) information, confined to an area of
+a given size. They do it with a method face.draw(nodes, size, …)
+which returns the graphic elements and the actual size they use
+(which may be smaller than the allocated size).</p>
+<p>The sizes are always given in “tree units”. The size in pixels is
+always that size multiplied by the zoom.</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="ete4.smartview.faces.BoxFace">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BoxFace</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wmax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hmax</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">style</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">text</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="reference internal" href="../_modules/ete4/smartview/faces.html#BoxFace"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ete4.smartview.faces.BoxFace" title="Link to this definition">¶</a></dt>