<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.NeuralNetwork-module.html">Package NeuralNetwork</a> ::
<a href="Bio.NeuralNetwork.Gene-module.html">Package Gene</a> ::
<a href="Bio.NeuralNetwork.Gene.Schema-module.html">Module Schema</a> ::
Class DifferentialSchemaFitness
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class DifferentialSchemaFitness</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#DifferentialSchemaFitness">source code</a></span></p>
<p>Calculate fitness for schemas that differentiate between
sequences.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">positive_seqs</span>,
<span class="summary-sig-arg">negative_seqs</span>,
<span class="summary-sig-arg">schema_evaluator</span>)</span><br />
Initialize with different sequences to evaluate</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#DifferentialSchemaFitness.__init__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html#calculate_fitness" class="summary-sig-name">calculate_fitness</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">genome</span>)</span><br />
Calculate the fitness for a given schema.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#DifferentialSchemaFitness.calculate_fitness">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">positive_seqs</span>,
<span class="sig-arg">negative_seqs</span>,
<span class="sig-arg">schema_evaluator</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#DifferentialSchemaFitness.__init__">source code</a></span>
</td>
</tr></table>
<p>Initialize with different sequences to evaluate</p>
<p>Arguments:</p>
<p>o positive_seq - A list of SeqRecord objects which are the 'positive'
sequences -- the ones we want to select for.</p>
<p>o negative_seq - A list of SeqRecord objects which are the 'negative'
sequences that we want to avoid selecting.</p>
<p>o schema_evaluator - An Schema class which can be used to evaluate
find motif matches in sequences.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="calculate_fitness"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">calculate_fitness</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">genome</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#DifferentialSchemaFitness.calculate_fitness">source code</a></span>
</td>
</tr></table>
<p>Calculate the fitness for a given schema.</p>
<p>Fitness is specified by the number of occurances of the schema in the
positive sequences minus the number of occurances in the negative
examples.</p>
<p>This fitness is then modified by multiplying by the length of the
schema and then dividing by the number of ambiguous characters in the
schema. This helps select for schema which are longer and have less
redundancy.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:36 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
