<?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.HMM.DynamicProgramming.ScaledDPAlgorithms</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.HMM-module.html">Package HMM</a> :: <a href="Bio.HMM.DynamicProgramming-module.html">Module DynamicProgramming</a> :: Class ScaledDPAlgorithms </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.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class ScaledDPAlgorithms</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms">source code</a></span></p> <pre class="base-tree"> <a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html">AbstractDPAlgorithms</a> --+ | <strong class="uidshort">ScaledDPAlgorithms</strong> </pre> <hr /> <p>Implement forward and backward algorithms using a rescaling approach.</p> <p>This scales the f and b variables, so that they remain within a manageable numerical interval during calculations. This approach is described in Durbin et al. on p 78.</p> <p>This approach is a little more straightfoward then log transformation but may still give underflow errors for some types of models. In these cases, the LogDPAlgorithms class should be used.</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.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">markov_model</span>, <span class="summary-sig-arg">sequence</span>)</span><br /> Initialize the scaled approach to calculating probabilities.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_calculate_s_value" class="summary-sig-name" onclick="show_private();">_calculate_s_value</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">seq_pos</span>, <span class="summary-sig-arg">previous_vars</span>)</span><br /> Calculate the next scaling variable for a sequence position.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms._calculate_s_value">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_forward_recursion" class="summary-sig-name" onclick="show_private();">_forward_recursion</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">cur_state</span>, <span class="summary-sig-arg">sequence_pos</span>, <span class="summary-sig-arg">forward_vars</span>)</span><br /> Calculate the value of the forward recursion.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms._forward_recursion">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#_backward_recursion" class="summary-sig-name" onclick="show_private();">_backward_recursion</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">cur_state</span>, <span class="summary-sig-arg">sequence_pos</span>, <span class="summary-sig-arg">backward_vars</span>)</span><br /> Calculate the value of the backward recursion</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms._backward_recursion">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html">AbstractDPAlgorithms</a></code></b>: <code><a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#backward_algorithm">backward_algorithm</a></code>, <code><a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#forward_algorithm">forward_algorithm</a></code> </p> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html">AbstractDPAlgorithms</a></code></b> (private): <code><a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#_foward_recursion" onclick="show_private();">_foward_recursion</a></code> </p></div> </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">markov_model</span>, <span class="sig-arg">sequence</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms.__init__">source code</a></span> </td> </tr></table> <p>Initialize the scaled approach to calculating probabilities. Arguments:</p> <p>o markov_model -- The current Markov model we are working with.</p> <p>o sequence -- A TrainingSequence object that must have a set of emissions to work with.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#__init__">AbstractDPAlgorithms.__init__</a> </dt> </dl> </td></tr></table> </div> <a name="_calculate_s_value"></a> <div class="private"> <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_s_value</span>(<span class="sig-arg">self</span>, <span class="sig-arg">seq_pos</span>, <span class="sig-arg">previous_vars</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms._calculate_s_value">source code</a></span> </td> </tr></table> <p>Calculate the next scaling variable for a sequence position.</p> <p>This utilizes the approach of choosing s values such that the sum of all of the scaled f values is equal to 1.</p> <p>Arguments:</p> <p>o seq_pos -- The current position we are at in the sequence.</p> <p>o previous_vars -- All of the forward or backward variables calculated so far.</p> <p>Returns:</p> <p>o The calculated scaling variable for the sequence item.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_forward_recursion"></a> <div class="private"> <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">_forward_recursion</span>(<span class="sig-arg">self</span>, <span class="sig-arg">cur_state</span>, <span class="sig-arg">sequence_pos</span>, <span class="sig-arg">forward_vars</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms._forward_recursion">source code</a></span> </td> </tr></table> <p>Calculate the value of the forward recursion.</p> <p>Arguments:</p> <p>o cur_state -- The letter of the state we are calculating the forward variable for.</p> <p>o sequence_pos -- The position we are at in the training seq.</p> <p>o forward_vars -- The current set of forward variables</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_backward_recursion"></a> <div class="private"> <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">_backward_recursion</span>(<span class="sig-arg">self</span>, <span class="sig-arg">cur_state</span>, <span class="sig-arg">sequence_pos</span>, <span class="sig-arg">backward_vars</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.HMM.DynamicProgramming-pysrc.html#ScaledDPAlgorithms._backward_recursion">source code</a></span> </td> </tr></table> <p>Calculate the value of the backward recursion</p> <p>Arguments:</p> <p>o cur_state -- The letter of the state we are calculating the forward variable for.</p> <p>o sequence_pos -- The position we are at in the training seq.</p> <p>o backward_vars -- The current set of backward variables</p> <dl class="fields"> <dt>Overrides: <a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#_backward_recursion" onclick="show_private();">AbstractDPAlgorithms._backward_recursion</a> </dt> </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 09:26:35 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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