<?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.Ais.Immune</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.Ais-module.html">Package Ais</a> :: Class Immune </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.Ais.Immune-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Immune</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Ais-pysrc.html#Immune">source code</a></span></p> <p>friendly should be an instance of Align. It should contain the set of protected sequences.</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="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">friendly_seq</span>, <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">acgt</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">tuner_dict</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">hot_mode</span>=<span class="summary-sig-default">0</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.__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 name="set_defaults"></a><span class="summary-sig-name">set_defaults</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.set_defaults">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="tune"></a><span class="summary-sig-name">tune</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.tune">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="build_align"></a><span class="summary-sig-name">build_align</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">seq</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.build_align">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="select_at_random"></a><span class="summary-sig-name">select_at_random</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">items</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.select_at_random">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="guess_gaps"></a><span class="summary-sig-name">guess_gaps</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">seq</span>)</span><br /> Fill gaps with random selction from alphabet</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.guess_gaps">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="scramble"></a><span class="summary-sig-name">scramble</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">seq</span>)</span><br /> Substitute residues in sequence at random.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.scramble">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="found_antigen"></a><span class="summary-sig-name">found_antigen</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">detector</span>, <span class="summary-sig-arg">mystery_sequence</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.found_antigen">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="lazy_auto_immune_check"></a><span class="summary-sig-name">lazy_auto_immune_check</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">seq</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.lazy_auto_immune_check">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="compute_accum_weight"></a><span class="summary-sig-name">compute_accum_weight</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.compute_accum_weight">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="search_accum_weight"></a><span class="summary-sig-name">search_accum_weight</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">t</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.search_accum_weight">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="pick_a_lymphocyte"></a><span class="summary-sig-name">pick_a_lymphocyte</span>(<span class="summary-sig-arg">self</span>)</span><br /> Random selection biased by weight</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.pick_a_lymphocyte">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.Ais.Immune-class.html#random_test" class="summary-sig-name">random_test</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">mystery_sequence</span>)</span><br /> A single test probably won't catch a corrupted sequence.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.random_test">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="create_lymphocyte"></a><span class="summary-sig-name">create_lymphocyte</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.create_lymphocyte">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="lymphocyte_factory"></a><span class="summary-sig-name">lymphocyte_factory</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.lymphocyte_factory">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="random_test"></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">random_test</span>(<span class="sig-arg">self</span>, <span class="sig-arg">mystery_sequence</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Ais-pysrc.html#Immune.random_test">source code</a></span> </td> </tr></table> <p>A single test probably won't catch a corrupted sequence. Lots of tests are required</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 09:26:30 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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