<?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.SchemaCoder</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 SchemaCoder </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.SchemaCoder-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class SchemaCoder</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#SchemaCoder">source code</a></span></p> <p>Convert a sequence into a representation of ambiguous motifs (schemas).</p> <p>This takes a sequence, and returns the number of times specified motifs are found in the sequence. This lets you represent a sequence as just a count of (possibly ambiguous) motifs.</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.SchemaCoder-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">schemas</span>, <span class="summary-sig-arg">ambiguous_converter</span>)</span><br /> Initialize the coder to convert sequences</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#SchemaCoder.__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.SchemaCoder-class.html#representation" class="summary-sig-name">representation</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">sequence</span>)</span><br /> Represent the given input sequence as a bunch of motif counts.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#SchemaCoder.representation">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">schemas</span>, <span class="sig-arg">ambiguous_converter</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#SchemaCoder.__init__">source code</a></span> </td> </tr></table> <p>Initialize the coder to convert sequences</p> <p>Arguments:</p> <p>o schema - A list of all of the schemas we want to search for in input sequences.</p> <p>o ambiguous_converter - An Schema class which can be used to convert motifs into regular expressions for searching.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="representation"></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">representation</span>(<span class="sig-arg">self</span>, <span class="sig-arg">sequence</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#SchemaCoder.representation">source code</a></span> </td> </tr></table> <p>Represent the given input sequence as a bunch of motif counts.</p> <p>Arguments:</p> <p>o sequence - A Bio.Seq object we are going to represent as schemas.</p> <p>This takes the sequence, searches for the motifs within it, and then returns counts specifying the relative number of times each motifs was found. The frequencies are in the order the original motifs were passed into the initializer.</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. 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