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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GA-module.html">Package GA</a> ::
<a href="Bio.GA.Organism-module.html">Module Organism</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.GA.Organism-pysrc.html#Organism">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Organism</strong>
</pre>
<hr />
<p>Represent a single individual in a population.</p>
<p>Attributes:</p>
<p>o genome -- The genome of the organism. This is a Bio.MutableSeq
object that has the sequence of the genome, and the alphabet describing
all elements that can be a part of the genome.</p>
<p>o fitness -- The calculate fitness of the organism. This fitness is
based on the last time it was calculated using the fitness_calculator.
So... the fitness could potentially be out of date with the real genome
if you are not careful to recalculate it after changes with
recalculate_fitness()</p>
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<td><span class="summary-sig"><a href="Bio.GA.Organism.Organism-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">genome</span>,
<span class="summary-sig-arg">fitness_calculator</span>,
<span class="summary-sig-arg">start_fitness</span>=<span class="summary-sig-default">None</span>)</span><br />
Initialize an organism</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.GA.Organism.Organism-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Provide a string output for debugging.</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__str__">source code</a></span>
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<td><span class="summary-sig"><a name="__eq__"></a><span class="summary-sig-name">__eq__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Compare organisms by their genomes (as strings of letters).</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__eq__">source code</a></span>
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<td><span class="summary-sig"><a name="__ne__"></a><span class="summary-sig-name">__ne__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Compare organisms by their genomes (as strings of letters).</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__ne__">source code</a></span>
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<td><span class="summary-sig"><a name="__lt__"></a><span class="summary-sig-name">__lt__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Compare organisms by their genomes (as strings of letters).</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__lt__">source code</a></span>
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<td><span class="summary-sig"><a name="__le__"></a><span class="summary-sig-name">__le__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Compare organisms by their genomes (as strings of letters).</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__le__">source code</a></span>
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<td><span class="summary-sig"><a name="__gt__"></a><span class="summary-sig-name">__gt__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Compare organisms by their genomes (as strings of letters).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__gt__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__ge__"></a><span class="summary-sig-name">__ge__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Compare organisms by their genomes (as strings of letters).</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__ge__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.GA.Organism.Organism-class.html#copy" class="summary-sig-name">copy</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return a copy of the organism.</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.copy">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GA.Organism.Organism-class.html#recalculate_fitness" class="summary-sig-name">recalculate_fitness</a>(<span class="summary-sig-arg">self</span>)</span><br />
Calculate and reset the fitness of the current genome</td>
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<span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.recalculate_fitness">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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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">genome</span>,
<span class="sig-arg">fitness_calculator</span>,
<span class="sig-arg">start_fitness</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
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<p>Initialize an organism</p>
<p>Arguments:</p>
<p>o genome -- A MutableSeq object representing the sequence of the
genome.</p>
<p>o fitness_calculator -- A funtion that will calculate the fitness of
the organism when given the organisms genome.</p>
<p>o start_fitness - the starting fitness corresponding with the given
genome. If not supplied, the fitness will be calculated using
fitness_calculator.</p>
<dl class="fields">
<dt>Overrides:
object.__init__
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.__str__">source code</a></span>
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<p>Provide a string output for debugging.</p>
<dl class="fields">
<dt>Overrides:
object.__str__
</dt>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">copy</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.copy">source code</a></span>
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<p>Return a copy of the organism.</p>
<p>This makes it easy to duplicate an organism before changing it.</p>
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</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">recalculate_fitness</span>(<span class="sig-arg">self</span>)</span>
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><span class="codelink"><a href="Bio.GA.Organism-pysrc.html#Organism.recalculate_fitness">source code</a></span>
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<p>Calculate and reset the fitness of the current genome</p>
<p>This should be called after the genome is updated to ensure that
fitness always stays in sync with the current genome.</p>
<dl class="fields">
</dl>
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