<?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.SubsMat.SubstitutionMatrix</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.SubsMat-module.html">Package SubsMat</a> ::
Class SubstitutionMatrix
</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.SubsMat.SubstitutionMatrix-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SubstitutionMatrix</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SubstitutionMatrix">source code</a></span></p>
<pre class="base-tree">
object --+
|
dict --+
|
<a href="Bio.SubsMat.SeqMat-class.html">SeqMat</a> --+
|
<strong class="uidshort">SubstitutionMatrix</strong>
</pre>
<hr />
<p>Substitution matrix</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 name="calculate_relative_entropy"></a><span class="summary-sig-name">calculate_relative_entropy</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">obs_freq_mat</span>)</span><br />
Calculate and return the relative entropy with respect to an observed
frequency matrix</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SubstitutionMatrix.calculate_relative_entropy">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.SubsMat.SeqMat-class.html">SeqMat</a></code></b>:
<code><a href="Bio.SubsMat.SeqMat-class.html#__add__">__add__</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#__init__">__init__</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#__mul__">__mul__</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#__str__">__str__</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#__sub__">__sub__</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#make_entropy">make_entropy</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#print_full_mat">print_full_mat</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#print_mat">print_mat</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#sum">sum</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SubsMat.SeqMat-class.html">SeqMat</a></code></b> (private):
<code><a href="Bio.SubsMat.SeqMat-class.html#_alphabet_from_matrix" onclick="show_private();">_alphabet_from_matrix</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#_correct_matrix" onclick="show_private();">_correct_matrix</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#_full_to_half" onclick="show_private();">_full_to_half</a></code>,
<code><a href="Bio.SubsMat.SeqMat-class.html#_init_zero" onclick="show_private();">_init_zero</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>dict</code></b>:
<code>__cmp__</code>,
<code>__contains__</code>,
<code>__delitem__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__getattribute__</code>,
<code>__getitem__</code>,
<code>__gt__</code>,
<code>__iter__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__ne__</code>,
<code>__new__</code>,
<code>__repr__</code>,
<code>__setitem__</code>,
<code>__sizeof__</code>,
<code>clear</code>,
<code>copy</code>,
<code>fromkeys</code>,
<code>get</code>,
<code>has_key</code>,
<code>items</code>,
<code>iteritems</code>,
<code>iterkeys</code>,
<code>itervalues</code>,
<code>keys</code>,
<code>pop</code>,
<code>popitem</code>,
<code>setdefault</code>,
<code>update</code>,
<code>values</code>,
<code>viewitems</code>,
<code>viewkeys</code>,
<code>viewvalues</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></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">Class Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassVariables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>dict</code></b>:
<code>__hash__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></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">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== 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 Thu Aug 18 18:22:17 2011
</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>
