<?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.SeqMat</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 SeqMat </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.SeqMat-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class SeqMat</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat">source code</a></span></p> <pre class="base-tree"> object --+ | dict --+ | <strong class="uidshort">SeqMat</strong> </pre> <hr /> <p>A Generic sequence matrix class The key is a 2-tuple containing the letter indices of the matrix. Those should be sorted in the tuple (low, high). Because each matrix is dealt with as a half-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 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 name="_alphabet_from_matrix"></a><span class="summary-sig-name">_alphabet_from_matrix</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._alphabet_from_matrix">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"><pre class="literalblock"> new empty dictionary </pre></span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.SubsMat.SeqMat-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">data</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">mat_type</span>=<span class="summary-sig-default">0</span>, <span class="summary-sig-arg">mat_name</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">build_later</span>=<span class="summary-sig-default">0</span>)</span><br /> x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__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 name="_correct_matrix"></a><span class="summary-sig-name">_correct_matrix</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._correct_matrix">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 name="_full_to_half"></a><span class="summary-sig-name">_full_to_half</span>(<span class="summary-sig-arg">self</span>)</span><br /> Convert a full-matrix to a half-matrix</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._full_to_half">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 name="_init_zero"></a><span class="summary-sig-name">_init_zero</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._init_zero">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 name="make_relative_entropy"></a><span class="summary-sig-name">make_relative_entropy</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">obs_freq_mat</span>)</span><br /> if this matrix is a log-odds matrix, return its entropy Needs the observed frequency matrix for that</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.make_relative_entropy">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 name="make_entropy"></a><span class="summary-sig-name">make_entropy</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.make_entropy">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 name="letter_sum"></a><span class="summary-sig-name">letter_sum</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">letter</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.letter_sum">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 name="all_letters_sum"></a><span class="summary-sig-name">all_letters_sum</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.all_letters_sum">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 name="print_full_mat"></a><span class="summary-sig-name">print_full_mat</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">f</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">format</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4d</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">topformat</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4s</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">factor</span>=<span class="summary-sig-default">1</span>, <span class="summary-sig-arg">non_sym</span>=<span class="summary-sig-default">None</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.print_full_mat">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.SubsMat.SeqMat-class.html#print_mat" class="summary-sig-name">print_mat</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">f</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">format</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4d</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">bottomformat</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4s</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">factor</span>=<span class="summary-sig-default">1</span>)</span><br /> Print a nice half-matrix.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.print_mat">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 name="__sub__"></a><span class="summary-sig-name">__sub__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span><br /> returns a number which is the subtraction product of the two matrices</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__sub__">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 name="__mul__"></a><span class="summary-sig-name">__mul__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span><br /> returns a matrix for which each entry is the multiplication product of the two matrices passed</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__mul__">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 name="__sum__"></a><span class="summary-sig-name">__sum__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__sum__">source code</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>__cmp__</code>, <code>__contains__</code>, <code>__delitem__</code>, <code>__eq__</code>, <code>__ge__</code>, <code>__getattribute__</code>, <code>__getitem__</code>, <code>__gt__</code>, <code>__hash__</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>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> </p> <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>: <code>__delattr__</code>, <code>__reduce__</code>, <code>__reduce_ex__</code>, <code>__setattr__</code>, <code>__str__</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> <!-- ==================== 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">data</span>=<span class="sig-default">None</span>, <span class="sig-arg">alphabet</span>=<span class="sig-default">None</span>, <span class="sig-arg">mat_type</span>=<span class="sig-default">0</span>, <span class="sig-arg">mat_name</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">build_later</span>=<span class="sig-default">0</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__init__">source code</a></span> </td> </tr></table> <p>x.__init__(...) initializes x; see x.__class__.__doc__ for signature</p> <dl class="fields"> <dt>Returns: <pre class="literalblock"> new empty dictionary </pre></dt> <dt>Overrides: object.__init__ <dd><em class="note">(inherited documentation)</em></dd> </dt> </dl> </td></tr></table> </div> <a name="print_mat"></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">print_mat</span>(<span class="sig-arg">self</span>, <span class="sig-arg">f</span>=<span class="sig-default">None</span>, <span class="sig-arg">format</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">%4d</code><code class="variable-quote">'</code></span>, <span class="sig-arg">bottomformat</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">%4s</code><code class="variable-quote">'</code></span>, <span class="sig-arg">alphabet</span>=<span class="sig-default">None</span>, <span class="sig-arg">factor</span>=<span class="sig-default">1</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.print_mat">source code</a></span> </td> </tr></table> <p>Print a nice half-matrix. f=sys.stdout to see on the screen User may pass own alphabet, which should contain all letters in the alphabet of the matrix, but may be in a different order. This order will be the order of the letters on the axes</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 09:26:39 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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