<?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.Utilities</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> :: Module Utilities </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.Utilities-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module Utilities</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.HMM.Utilities-pysrc.html">source code</a></span></p> <p>Generic functions which are useful for working with HMMs.</p> <p>This just collects general functions which you might like to use in dealing with HMMs.</p> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></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">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" 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.Utilities-module.html#pretty_print_prediction" class="summary-sig-name">pretty_print_prediction</a>(<span class="summary-sig-arg">emissions</span>, <span class="summary-sig-arg">real_state</span>, <span class="summary-sig-arg">predicted_state</span>, <span class="summary-sig-arg">emission_title</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">Emissions</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">real_title</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">Real State</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">predicted_title</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">Predicted State</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">line_width</span>=<span class="summary-sig-default">75</span>)</span><br /> Print out a state sequence prediction in a nice manner.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.HMM.Utilities-pysrc.html#pretty_print_prediction">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></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">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="pretty_print_prediction"></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">pretty_print_prediction</span>(<span class="sig-arg">emissions</span>, <span class="sig-arg">real_state</span>, <span class="sig-arg">predicted_state</span>, <span class="sig-arg">emission_title</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">Emissions</code><code class="variable-quote">'</code></span>, <span class="sig-arg">real_title</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">Real State</code><code class="variable-quote">'</code></span>, <span class="sig-arg">predicted_title</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">Predicted State</code><code class="variable-quote">'</code></span>, <span class="sig-arg">line_width</span>=<span class="sig-default">75</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.HMM.Utilities-pysrc.html#pretty_print_prediction">source code</a></span> </td> </tr></table> <p>Print out a state sequence prediction in a nice manner.</p> <p>Arguments:</p> <p>o emissions -- The sequence of emissions of the sequence you are dealing with.</p> <p>o real_state -- The actual state path that generated the emissions.</p> <p>o predicted_state -- A state path predicted by some kind of HMM model.</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 09:26:24 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>