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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Graphics-module.html">Package Graphics</a> ::
<a href="Bio.Graphics.BasicChromosome-module.html">Module BasicChromosome</a> ::
Class Organism
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Organism</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism">source code</a></span></p>
<pre class="base-tree">
reportlab.graphics.widgetbase.PropHolder --+
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reportlab.graphics.shapes._DrawTimeResizeable --+ |
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reportlab.graphics.shapes.UserNode --+
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reportlab.graphics.widgetbase.Widget --+
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<a href="Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html" onclick="show_private();">_ChromosomeComponent</a> --+
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<strong class="uidshort">Organism</strong>
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<hr />
<p>Top level class for drawing chromosomes.</p>
<p>This class holds information about an organism and all of it's
chromosomes, and provides the top level object which could be used for
drawing a chromosome representation of an organism.</p>
<p>Chromosomes should be added and removed from the Organism via the add
and remove functions.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Graphics.BasicChromosome.Organism-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">output_format</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">pdf</code><code class="variable-quote">'</code></span>)</span><br />
Initialize a chromosome component.</td>
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<span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Graphics.BasicChromosome.Organism-class.html#draw" class="summary-sig-name">draw</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">output_file</span>,
<span class="summary-sig-arg">title</span>)</span><br />
Draw out the information for the Organism.</td>
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<span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism.draw">source code</a></span>
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<td><span class="summary-sig"><a name="_draw_title"></a><span class="summary-sig-name">_draw_title</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">cur_drawing</span>,
<span class="summary-sig-arg">title</span>,
<span class="summary-sig-arg">width</span>,
<span class="summary-sig-arg">height</span>)</span><br />
Write out the title of the organism figure.</td>
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<span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism._draw_title">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Graphics.BasicChromosome.Organism-class.html#_draw_legend" class="summary-sig-name" onclick="show_private();">_draw_legend</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">cur_drawing</span>,
<span class="summary-sig-arg">start_y</span>,
<span class="summary-sig-arg">width</span>)</span><br />
Draw a legend for the figure.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism._draw_legend">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html" onclick="show_private();">_ChromosomeComponent</a></code></b>:
<code><a href="Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add">add</a></code>,
<code><a href="Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove">remove</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>reportlab.graphics.widgetbase.Widget</code></b>:
<code>demo</code>,
<code>getBounds</code>,
<code>provideNode</code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>reportlab.graphics.widgetbase.Widget</code></b> (private):
<code>_setKeywords</code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>reportlab.graphics.widgetbase.PropHolder</code></b>:
<code>__setattr__</code>,
<code>dumpProperties</code>,
<code>getProperties</code>,
<code>setProperties</code>,
<code>verify</code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>reportlab.graphics.shapes._DrawTimeResizeable</code></b> (private):
<code>_drawTimeResize</code>
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<a name="VALID_FORMATS"></a><span class="summary-name">VALID_FORMATS</span> = <code title="['pdf', 'eps']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">pdf</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">eps</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>reportlab.graphics.widgetbase.PropHolder</code></b> (private):
<code>_attrMap</code>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">output_format</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">pdf</code><code class="variable-quote">'</code></span>)</span>
<br /><em class="fname">(Constructor)</em>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism.__init__">source code</a></span>
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<p>Initialize a chromosome component.</p>
<p>Attributes:</p>
<p>o _sub_components -- Any components which are contained under this
parent component. This attribute should be accessed through the add() and
remove() functions.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#__init__">_ChromosomeComponent.__init__</a>
<dd><em class="note">(inherited documentation)</em></dd>
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<a name="draw"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">draw</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">output_file</span>,
<span class="sig-arg">title</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism.draw">source code</a></span>
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<p>Draw out the information for the Organism.</p>
<p>Arguments:</p>
<p>o output_file -- The name of a file specifying where the pdf document
drawn should be saved.</p>
<p>o title -- The output title of the produced document.</p>
<dl class="fields">
<dt>Overrides:
reportlab.graphics.widgetbase.Widget.draw
</dt>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_draw_legend</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">cur_drawing</span>,
<span class="sig-arg">start_y</span>,
<span class="sig-arg">width</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.BasicChromosome-pysrc.html#Organism._draw_legend">source code</a></span>
</td>
</tr></table>
<p>Draw a legend for the figure.</p>
<p>Subclasses should implement this to provide specialized legends.</p>
<dl class="fields">
</dl>
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